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Candeias C, Almeida ST, Paulo AC, Simões AS, Ferreira B, Cruz AR, Queirós M, Touret T, Brito-Avô A, de Lencastre H, Sá-Leão R. Streptococcus pneumoniae carriage, serotypes, genotypes, and antimicrobial resistance trends among children in Portugal, after introduction of PCV13 in National Immunization Program: A cross-sectional study. Vaccine 2024; 42:126219. [PMID: 39146858 DOI: 10.1016/j.vaccine.2024.126219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Streptococcus pneumoniae carriage studies are crucial to monitor changes induced by use of pneumococcal conjugate vaccines and inform vaccination policies. In this cross-sectional study, we examined changes within the pneumococcal population following introduction of PCV13 in 2015 in the National Immunization Program (NIP), in Portugal. In 2018-2020 (NIP-PCV13), we obtained 1450 nasopharyngeal samples from children ≤6 years attending day-care. We assessed serotypes, antimicrobial resistance, and genotypes (MLST and GPSC) and compared findings with earlier periods: 2009-2010 (pre-PCV13), 2011-2012 (early-PCV13), and 2015-2016 (late-PCV13). Pneumococcal carriage prevalence remained stable at 60.2 %. Carriage of PCV13 serotypes was 10.7 %, markedly reduced compared to pre-PCV13 period (47.6 %). The most prevalent PCV13 serotypes were 19F, 3, and 19A all showing a significant decreasing trend compared to the pre-PCV13 period (from 7.1 % to 4.7 %, 10.1 % to 1.8 %, and 14.1 % to 1.8 %, respectively), a notable observation given the described limited effectiveness of PCV13 against serotype 3. Non-vaccinated children and children aged 4-6 years were more likely to carry PCV13 serotypes (2.5-fold, 95 %CI [1.1-5.6], and 2.9-fold, 95 %CI [1.3-6.8], respectively). The most prevalent non-PCV13 serotypes were 15B/C, 11A, 23B, 23A, and NT, collectively accounting for 51.9 % of all isolates. In total, 30.5 % of all pneumococci were potentially covered by PCV20. Resistance to penicillin (low-level) and macrolides increased significantly, from 9.3 % and 13.4 %, respectively, in the late-PCV13 period, to approximately 20 % each, mostly due to lineages expressing non-PCV13 serotypes, nearing pre-PCV13 levels. An expansion of lineages traditionally associated with PCV13 serotypes, like CC156-GPSC6 (serotype 14) and CC193-GPSC11 (serotype 19F), but now predominantly expressing non-PCV13 serotypes (11A, 15B/C, and 24F for GPSC6; and 15A and 21 for GPSC11) was noted. These findings indicate that the pneumococcal population is adapting to the pressures conferred by PCV13 and antimicrobial use and indicate the need to maintain close surveillance.
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Affiliation(s)
- Catarina Candeias
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sónia T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - A Cristina Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Bárbara Ferreira
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Ana R Cruz
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Miguel Queirós
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Tiago Touret
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.
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Kalizang'oma A, Richard D, Kwambana-Adams B, Coelho J, Broughton K, Pichon B, Hopkins KL, Chalker V, Beleza S, Bentley SD, Chaguza C, Heyderman RS. Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases. Nat Commun 2024; 15:7812. [PMID: 39242612 DOI: 10.1038/s41467-024-52120-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Streptococcus mitis is a leading cause of infective endocarditis (IE). However, our understanding of the genomic epidemiology and pathogenicity of IE-associated S. mitis is hampered by low IE incidence. Here we use whole genome sequencing of 129 S. mitis bloodstream infection (BSI) isolates collected between 2001-2016 from clinically diagnosed IE cases in the UK to investigate genetic diversity, antimicrobial resistance, and pathogenicity. We show high genetic diversity of IE-associated S. mitis with virtually all isolates belonging to distinct lineages indicating no predominance of specific lineages. Additionally, we find a highly variable distribution of known pneumococcal virulence genes among the isolates, some of which are overrepresented in disease when compared to carriage strains. Our findings suggest that S. mitis in patients with clinically diagnosed IE is not primarily caused by specific hypervirulent or antimicrobial resistant lineages, highlighting the accidental pathogenic nature of S. mitis in patients with clinically diagnosed IE.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK. akuzike.kalizang'
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi. akuzike.kalizang'
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi. akuzike.kalizang'
| | - Damien Richard
- UCL Genetics Institute, University College London, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Juliana Coelho
- Public Health Microbiology Division, UK Health Security Agency, Colindale, London, UK
| | - Karen Broughton
- Public Health Microbiology Division, UK Health Security Agency, Colindale, London, UK
| | - Bruno Pichon
- Public Health Microbiology Division, UK Health Security Agency, Colindale, London, UK
| | - Katie L Hopkins
- Public Health Microbiology Division, UK Health Security Agency, Colindale, London, UK
| | | | - Sandra Beleza
- University of Leicester, Department of Genetics and Genome Biology, Leicester, UK
| | | | - Chrispin Chaguza
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK.
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3
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Qiu X, McGee L, Hammitt LL, Grant LR, O'Brien KL, Hanage WP, Lipsitch M. Prediction of post-PCV13 pneumococcal evolution using invasive disease data enhanced by inverse-invasiveness weighting. mBio 2024:e0335523. [PMID: 39207103 DOI: 10.1128/mbio.03355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
After introducing pneumococcal conjugate vaccines (PCVs), serotype replacement occurred in Streptococcus pneumoniae. Predicting which pneumococcal strains will become common in carriage after vaccination can enhance vaccine design, public health interventions, and understanding of pneumococcal evolution. Invasive pneumococcal isolates were collected during 1998-2018 by the Active Bacterial Core surveillance (ABCs). Carriage data from Massachusetts (MA) and Southwest United States were used to calculate weights. Using pre-vaccine data, serotype-specific inverse-invasiveness weights were defined as the ratio of the proportion of the serotype in carriage to the proportion in invasive data. Genomic data were processed under bioinformatic pipelines to define genetically similar sequence clusters (i.e., strains), and accessory genes (COGs) present in 5-95% of isolates. Weights were applied to adjust observed strain proportions and COG frequencies. The negative frequency-dependent selection (NFDS) model predicted strain proportions by calculating the post-vaccine strain composition in the weighted invasive disease population that would best match pre-vaccine COG frequencies. Inverse-invasiveness weighting increased the correlation of COG frequencies between invasive and carriage data in linear or logit scale for pre-vaccine, post-PCV7, and post-PCV13; and between different epochs in the invasive data. Weighting the invasive data significantly improved the NFDS model's accuracy in predicting strain proportions in the carriage population in the post-PCV13 epoch, with the adjusted R2 increasing from 0.254 before weighting to 0.545 after weighting. The weighting system adjusted invasive disease data to better represent the pneumococcal carriage population, allowing the NFDS mechanism to predict strain proportions in carriage in the post-PCV13 epoch. Our methods enrich the value of genomic sequences from invasive disease surveillance.IMPORTANCEStreptococcus pneumoniae, a common colonizer in the human nasopharynx, can cause invasive diseases including pneumonia, bacteremia, and meningitis mostly in children under 5 years or older adults. The PCV7 was introduced in 2000 in the United States within the pediatric population to prevent disease and reduce deaths, followed by PCV13 in 2010, PCV15 in 2022, and PCV20 in 2023. After the removal of vaccine serotypes, the prevalence of carriage remained stable as the vacated pediatric ecological niche was filled with certain non-vaccine serotypes. Predicting which pneumococcal clones, and which serotypes, will be most successful in colonization after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. While carriage data, which are collected from the pneumococcal population that is competing to colonize and transmit, are most directly relevant to evolutionary studies, invasive disease data are often more plentiful. Previously, evolutionary models based on negative frequency-dependent selection (NFDS) on the accessory genome were shown to predict which non-vaccine strains and serotypes were most successful in colonization following the introduction of PCV7. Here, we show that an inverse-invasiveness weighting system applied to invasive disease surveillance data allows the NFDS model to predict strain proportions in the projected carriage population in the post-PCV13/pre-PCV15 and pre-PCV20 epoch. The significance of our research lies in using a sample of invasive disease surveillance data to extend the use of NFDS as an evolutionary mechanism to predict post-PCV13 population dynamics. This has shown that we can correct for biased sampling that arises from differences in virulence and can enrich the value of genomic data from disease surveillance and advance our understanding of how NFDS impacts carriage population dynamics after both PCV7 and PCV13 vaccination.
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Affiliation(s)
- Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Lesley McGee
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Laura L Hammitt
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lindsay R Grant
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Katherine L O'Brien
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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4
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Peñil-Celis A, Tagg KA, Webb HE, Redondo-Salvo S, Francois Watkins L, Vielva L, Griffin C, Kim JY, Folster JP, Garcillan-Barcia MP, de la Cruz F. Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome. mSystems 2024; 9:e0036524. [PMID: 39058093 PMCID: PMC11334464 DOI: 10.1128/msystems.00365-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.
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Affiliation(s)
- Arancha Peñil-Celis
- Instituto de Biomedicina y Biotecnología de Cantabria, (CSIC, Universidad de Cantabria), Santander, Spain
| | - Kaitlin A. Tagg
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hattie E. Webb
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Santiago Redondo-Salvo
- Instituto de Biomedicina y Biotecnología de Cantabria, (CSIC, Universidad de Cantabria), Santander, Spain
- Biomar Microbial Technologies, León, Spain
| | - Louise Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luis Vielva
- Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain
| | - Chelsey Griffin
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Justin Y. Kim
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- ASRT, Inc., Suwanee, Georgia, USA
| | - Jason P. Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - M. Pilar Garcillan-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria, (CSIC, Universidad de Cantabria), Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, (CSIC, Universidad de Cantabria), Santander, Spain
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5
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Kuronen J, Horsfield ST, Pöntinen AK, Mallawaarachchi S, Arredondo-Alonso S, Thorpe H, Gladstone RA, Willems RJL, Bentley SD, Croucher NJ, Pensar J, Lees JA, Tonkin-Hill G, Corander J. Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome Res 2024; 34:1081-1088. [PMID: 39134411 PMCID: PMC11368177 DOI: 10.1101/gr.278485.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 07/25/2024] [Indexed: 08/22/2024]
Abstract
Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance, and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable high-accuracy long-read sequencing technologies. To exploit this opportunity, we introduce a phenotype- and alignment-free method for discovering coselected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact colored de Bruijn graph to approximate the intragenome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens Streptococcus pneumoniae and Enterococcus faecalis.
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Affiliation(s)
- Juri Kuronen
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
| | - Samuel T Horsfield
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9019 Tromsø, Norway
| | - Sudaraka Mallawaarachchi
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3052, Australia
| | | | - Harry Thorpe
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
| | | | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12 0BZ, United Kingdom
| | - Johan Pensar
- Department of Mathematics, University of Oslo, 0372 Blindern, Norway
| | - John A Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom;
| | - Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3052, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3052, Australia
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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Thorpe HA, Pesonen M, Corbella M, Pesonen H, Gaiarsa S, Boinett CJ, Tonkin-Hill G, Mäklin T, Pöntinen AK, MacAlasdair N, Gladstone RA, Arredondo-Alonso S, Kallonen T, Jamrozy D, Lo SW, Chaguza C, Blackwell GA, Honkela A, Schürch AC, Willems RJL, Merla C, Petazzoni G, Feil EJ, Cambieri P, Thomson NR, Bentley SD, Sassera D, Corander J. Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. THE LANCET. MICROBE 2024:100890. [PMID: 39178869 DOI: 10.1016/s2666-5247(24)00113-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 08/26/2024]
Abstract
BACKGROUND Nosocomial infections pose a considerable risk to patients who are susceptible, and this is particularly acute in intensive care units when hospital-associated bacteria are endemic. During the first wave of the COVID-19 pandemic, the surge of patients presented a significant obstacle to the effectiveness of infection control measures. We aimed to assess the risks and extent of nosocomial pathogen transmission under a high patient burden by designing a novel bacterial pan-pathogen deep-sequencing approach that could be integrated with standard clinical surveillance and diagnostics workflows. METHODS We did a prospective cohort study in a region of northern Italy that was severely affected by the first wave of the COVID-19 pandemic. Inpatients on both ordinary and intensive care unit (ICU) wards at the San Matteo hospital, Pavia were sampled on multiple occasions to identify bacterial pathogens from respiratory, nasal, and rectal samples. Diagnostic samples collected between April 7 and May 10, 2020 were cultured on six different selective media designed to enrich for Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae, and DNA from each plate with positive growth was deep sequenced en masse. We used mSWEEP and mGEMS to bin sequencing reads by sequence cluster for each species, followed by mapping with snippy to generate high quality alignments. Antimicrobial resistance genes were detected by use of ARIBA and CARD. Estimates of hospital transmission were obtained from pairwise bacterial single nucleotide polymorphism distances, partitioned by within-patient and between-patient samples. Finally, we compared the accuracy of our binned Acinetobacter baumannii genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital. FINDINGS We recruited patients from March 1 to May 7, 2020. The pathogen population among the patients was large and diverse, with 2148 species detections overall among the 2418 sequenced samples from the 256 patients. In total, 55 sequence clusters from key pathogen species were detected at least five times. The antimicrobial resistance gene prevalence was correspondingly high, with key carbapenemase and extended spectrum ß-lactamase genes detected in at least 50 (40%) of 125 patients in ICUs. Using high-resolution mapping to infer transmission, we established that hospital transmission was likely to be a significant mode of acquisition for each of the pathogen species. Finally, comparison with single colony Acinetobacter baumannii genomes showed that the resolution offered by deep sequencing was equivalent to single-colony sequencing, with the additional benefit of detection of co-colonisation of highly similar strains. INTERPRETATION Our study shows that a culture-based deep-sequencing approach is a possible route towards improving future pathogen surveillance and infection control at hospitals. Future studies should be designed to directly compare the accuracy, cost, and feasibility of culture-based deep sequencing with single colony whole-genome sequencing on a range of bacterial species. FUNDING Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.
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Affiliation(s)
- Harry A Thorpe
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Maiju Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Stefano Gaiarsa
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Gerry Tonkin-Hill
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Tommi Mäklin
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Neil MacAlasdair
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Teemu Kallonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Antti Honkela
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Anita C Schürch
- Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, Universitair Medisch Centrum Utrecht, Utrecht, Netherlands
| | - Cristina Merla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Greta Petazzoni
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Medical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Patrizia Cambieri
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | | | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy; Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK; Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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7
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Pham NP, Gingras H, Godin C, Feng J, Groppi A, Nikolski M, Leprohon P, Ouellette M. Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning. mBio 2024:e0136024. [PMID: 39120145 DOI: 10.1128/mbio.01360-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae. We explored a collection of 662 S. pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic. IMPORTANCE In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.
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Affiliation(s)
- Nguyen-Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alexis Groppi
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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8
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Krishnakant Kushwaha S, Wu Y, Leonardo Avila H, Anand A, Sicheritz-Pontén T, Millard A, Amol Marathe S, Nobrega FL. Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes. PLoS Biol 2024; 22:e3002746. [PMID: 39110680 PMCID: PMC11305592 DOI: 10.1371/journal.pbio.3002746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores the role of the flexible genome, organised in regions of genomic plasticity (RGP), in shaping the pathogenicity of Salmonella lineages. Through comprehensive genomic analysis of 12,244 Salmonella spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns of pathogenicity-related gene clusters into RGP, challenging traditional views of gene distribution. These RGP exhibit distinct preferences for specific genomic spots, and the presence or absence of such spots across Salmonella lineages profoundly shapes strain pathogenicity. RGP preferences are guided by conserved flanking genes surrounding integration spots, implicating their involvement in regulatory networks and functional synergies with integrated gene clusters. Additionally, we emphasise the multifaceted contributions of plasmids and prophages to the pathogenicity of diverse Salmonella lineages. Overall, this study provides a comprehensive blueprint of the pathogenicity potential of Salmonella. This unique insight identifies genomic spots in nonpathogenic lineages that hold the potential for harbouring pathogenicity genes, providing a foundation for predicting future adaptations and developing targeted strategies against emerging human pathogenic strains.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Yi Wu
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Hugo Leonardo Avila
- Laboratory for Applied Science and Technology in Health, Instituto Carlos Chagas, FIOCRUZ Paraná, Brazil
| | - Abhirath Anand
- Department of Computer Sciences and Information Systems, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
| | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Kedah, Malaysia
| | - Andrew Millard
- Centre for Phage Research, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, India
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
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9
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King AC, Kumar N, Mellor KC, Hawkins PA, McGee L, Croucher NJ, Bentley SD, Lees JA, Lo SW. Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae. Microb Genom 2024; 10. [PMID: 39196267 DOI: 10.1099/mgen.0.001278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26 306 Streptococcus pneumoniae genomes to compare four clustering methods: gene-by-gene seven-locus MLST, core genome MLST (cgMLST)-based hierarchical clustering (HierCC) assignments, life identification number (LIN) barcoding and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (adjusted mutual information score=0.950), which was expected given that both methods utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI=0.946), showing that k-mer-based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae, standardized and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven-locus MLST, whilst cgMLST, GPSC and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardized within the research.
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Affiliation(s)
- Alannah C King
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Narender Kumar
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kate C Mellor
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Lesley McGee
- Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John A Lees
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
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10
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Jansen van Rensburg MJ, Berger DJ, Yassine I, Shaw D, Fohrmann A, Bray JE, Jolley KA, Maiden MCJ, Brueggemann AB. Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure. Microb Genom 2024; 10:001280. [PMID: 39137139 PMCID: PMC11321556 DOI: 10.1099/mgen.0.001280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/17/2024] [Indexed: 08/15/2024] Open
Abstract
Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.
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Affiliation(s)
| | - Duncan J. Berger
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iman Yassine
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David Shaw
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Andy Fohrmann
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James E. Bray
- Department of Biology, University of Oxford, Oxford, UK
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11
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House LC, Hasan A, Asnayanti A, Alrubaye AAK, Pummill J, Rhoads D. Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts. Microorganisms 2024; 12:1549. [PMID: 39203392 PMCID: PMC11356006 DOI: 10.3390/microorganisms12081549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50-440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.
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Affiliation(s)
- L. Caroline House
- John Brown University, Siloam Springs, AR 72761, USA;
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
| | - Amer Hasan
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
- Department of Veterinary Public Health, College of Veterinary Medicine, University of Baghdad, Baghdad P.O. Box 1417, Iraq
| | - Andi Asnayanti
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
| | - Adnan A. K. Alrubaye
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72703, USA
| | - Jeff Pummill
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR 72703, USA
| | - Douglas Rhoads
- Cell and Molecular Biology Pogram, University of Arkansas, Fayetteville, AR 72703, USA; (A.H.); (A.A.); (A.A.K.A.); (J.P.)
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12
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Kalizang'oma A, Swarthout TD, Mwalukomo TS, Kamng’ona A, Brown C, Msefula J, Demetriou H, Chan JM, Roalfe L, Obolski U, Lourenço J, Goldblatt D, Chaguza C, French N, Heyderman RS. Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction. J Infect Dis 2024; 230:e189-e198. [PMID: 39052729 PMCID: PMC11272040 DOI: 10.1093/infdis/jiae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/21/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 3 remains a problem globally. Malawi introduced 13-valent pneumococcal conjugate vaccine (PCV13) in 2011, but there has been no direct protection against serotype 3 carriage. We explored whether vaccine escape by serotype 3 is due to clonal expansion of a lineage with a competitive advantage. METHODS The distribution of serotype 3 Global Pneumococcal Sequence Clusters (GPSCs) and sequence types (STs) globally was assessed using sequences from the Global Pneumococcal Sequencing Project. Whole-genome sequences of 135 serotype 3 carriage isolates from Blantyre, Malawi (2015-2019) were analyzed. Comparative analysis of the capsule locus, entire genomes, antimicrobial resistance, and phylogenetic reconstructions were undertaken. Opsonophagocytosis was evaluated using serum samples from vaccinated adults and children. RESULTS Serotype 3 GPSC10-ST700 isolates were most prominent in Malawi. Compared with the prototypical serotype 3 capsular polysaccharide locus sequence, 6 genes are absent, with retention of capsule polysaccharide biosynthesis. This lineage is characterized by increased antimicrobial resistance and lower susceptibility to opsonophagocytic killing. CONCLUSIONS A serotype 3 variant in Malawi has genotypic and phenotypic characteristics that could enhance vaccine escape and clonal expansion after post-PCV13 introduction. Genomic surveillance among high-burden populations is essential to improve the effectiveness of next-generation pneumococcal vaccines.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Todd D Swarthout
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thandie S Mwalukomo
- School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox Kamng’ona
- School of Life Sciences and Allied Health Professionals, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Comfort Brown
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Jacquline Msefula
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Hayley Demetriou
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jia Mun Chan
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Lucy Roalfe
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Uri Obolski
- Porter School of the Environment and Earth Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Jose Lourenço
- Faculdade de Ciências, BioISI, Universidade de Lisboa, Lisbon, Portugal
| | - David Goldblatt
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chrispin Chaguza
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Robert S Heyderman
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
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13
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Sekulovic O, Gallagher C, Lee J, Hao L, Zinonos S, Tan CY, Anderson A, Kanevsky I. Evidence of Reduced Virulence and Increased Colonization Among Pneumococcal Isolates of Serotype 3 Clade II Lineage in Mice. J Infect Dis 2024; 230:e182-e188. [PMID: 39052735 PMCID: PMC11272092 DOI: 10.1093/infdis/jiae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 01/30/2024] Open
Abstract
Recent phylogenetic profiling of pneumococcal serotype 3 (Pn3) isolates revealed a dynamic interplay among major lineages with the emergence and global spread of a variant termed clade II. The cause of Pn3 clade II dissemination along with epidemiological and clinical ramifications are currently unknown. Here, we sought to explore biological characteristics of dominant Pn3 clades in a mouse model of pneumococcal invasive disease and carriage. Carriage and virulence potential were strain dependent with marked differences among clades. We found that clinical isolates from Pn3 clade II are less virulent and less invasive in mice compared to clade I isolates. We also observed that clade II isolates are carried for longer and at higher bacterial densities in mice compared to clade I isolates. Taken together, our data suggest that the epidemiological success of Pn3 clade II could be related to alterations in the pathogen's ability to cause invasive disease and to establish a robust carriage episode.
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Affiliation(s)
- Ognjen Sekulovic
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
| | - Caitlyn Gallagher
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
| | - Jonathan Lee
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
| | - Li Hao
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
| | - Stavros Zinonos
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
| | - Charles Y Tan
- Pfizer Inc, Early Clinical Development, Collegeville, Pennsylvania
| | | | - Isis Kanevsky
- Pfizer Inc, Bacterial Vaccines and Technology, Pearl River, New York
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14
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Gambino M, Kushwaha SK, Wu Y, van Haastrecht P, Klein-Sousa V, Lutz VT, Bejaoui S, Jensen CMC, Bojer MS, Song W, Xiao M, Taylor NMI, Nobrega FL, Brøndsted L. Diversity and phage sensitivity to phages of porcine enterotoxigenic Escherichia coli. Appl Environ Microbiol 2024; 90:e0080724. [PMID: 38940562 PMCID: PMC11267873 DOI: 10.1128/aem.00807-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species-E. coli.
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Affiliation(s)
- Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Institute of Conservation, The Royal Danish Academy, Copenhagen, Denmark
| | - Simran Krishnakant Kushwaha
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Yi Wu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Pauline van Haastrecht
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Victor Klein-Sousa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Veronika T. Lutz
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Semeh Bejaoui
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Martin S. Bojer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Nicholas M. I. Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Franklin L. Nobrega
- School of Biological Sciences, Faculty of Environmental & Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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15
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Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, West TE, Thomson NR, Parkhill J, Chewapreecha C, Chantratita N. Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand. Nat Commun 2024; 15:5699. [PMID: 38972886 PMCID: PMC11228029 DOI: 10.1038/s41467-024-50067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024] Open
Abstract
Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conduct a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identifies three dominant lineages, each with unique gene sets potentially enhancing bacterial fitness in the environment. We find that recombination drives lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage reveal increased expression of lineage-specific genes under environmental conditions in two out of three lineages. This underscores the potential importance of environmental persistence for these dominant lineages. The study also highlights the influence of environmental factors such as terrain slope, altitude, and river direction on the geographical dispersal of B. pseudomallei. Collectively, our findings suggest that environmental persistence may play a role in facilitating the spread of B. pseudomallei, and as a prerequisite for exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T Eoin West
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK.
- Previous Affiliations: Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut University of Technology Thonburi, Bangkok, Thailand.
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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16
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Payne M, Hu D, Wang Q, Sullivan G, Graham RM, Rathnayake IU, Jennison AV, Sintchenko V, Lan R. DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae427. [PMID: 38954842 PMCID: PMC11244691 DOI: 10.1093/bioinformatics/btae427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/03/2024] [Accepted: 07/01/2024] [Indexed: 07/04/2024]
Abstract
SUMMARY The reliable and timely recognition of outbreaks is a key component of public health surveillance for foodborne diseases. Whole genome sequencing (WGS) offers high resolution typing of foodborne bacterial pathogens and facilitates the accurate detection of outbreaks. This detection relies on grouping WGS data into clusters at an appropriate genetic threshold. However, methods and tools for selecting and adjusting such thresholds according to the required resolution of surveillance and epidemiological context are lacking. Here we present DODGE (Dynamic Outbreak Detection for Genomic Epidemiology), an algorithm to dynamically select and compare these genetic thresholds. DODGE can analyse expanding datasets over time and clusters that are predicted to correspond to outbreaks (or "investigation clusters") can be named with established genomic nomenclature systems to facilitate integrated analysis across jurisdictions. DODGE was tested in two real-world Salmonella genomic surveillance datasets of different duration, 2 months from Australia and 9 years from the United Kingdom. In both cases only a minority of isolates were identified as investigation clusters. Two known outbreaks in the United Kingdom dataset were detected by DODGE and were recognized at an earlier timepoint than the outbreaks were reported. These findings demonstrated the potential of the DODGE approach to improve the effectiveness and timeliness of genomic surveillance for foodborne diseases and the effectiveness of the algorithm developed. AVAILABILITY AND IMPLEMENTATION DODGE is freely available at https://github.com/LanLab/dodge and can easily be installed using Conda.
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Affiliation(s)
- Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-NSW Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Geraldine Sullivan
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-NSW Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Rikki M Graham
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD 4108, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD 4108, Australia
| | - Amy V Jennison
- Public Health Microbiology, Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, QLD 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research-NSW Health Pathology, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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17
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Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW, McGee L, Madhi SA, von Gottberg A, Bentley SD, Salje H. Geographical migration and fitness dynamics of Streptococcus pneumoniae. Nature 2024; 631:386-392. [PMID: 38961295 PMCID: PMC11236706 DOI: 10.1038/s41586-024-07626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59-1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.
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Affiliation(s)
- Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Nzenze
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sarah Downs
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Lesley McGee
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
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18
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Luo H, Yang Z, Lei T, Li C, Zhou Z, Wang M, Zhu D, Li P, Cheng A. RATA: A novel class A carbapenemase with broad geographic distribution and potential for global spread. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172873. [PMID: 38692330 DOI: 10.1016/j.scitotenv.2024.172873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/07/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Carbapenem resistance's global proliferation poses a significant public health challenge. The primary resistance mechanism is carbapenemase production. In this study, we discovered a novel carbapenemase, RATA, located on the chromosome of Riemerella anatipestifer isolates. This enzyme shares ≤52 % amino acid sequence identity with other known β-lactamases. Antimicrobial susceptibility tests and kinetic assays demonstrated that RATA could hydrolyze not only penicillins and extended-spectrum cephalosporins but also monobactams, cephamycins, and carbapenems. Furthermore, its activity was readily inhibited by β-lactamase inhibitors. Bioinformatic analysis revealed 46 blaRATA-like genes encoding 27 variants in the NCBI database, involving 21 different species, including pathogens, host-associated bacteria, and environmental isolates. Notably, blaRATA-positive strains were globally distributed and primarily collected from marine environments. Concurrently, taxonomic analysis and GC content analysis indicated that blaRATA orthologue genes were predominantly located on the chromosomes of Flavobacteriaceae and shared a similar GC content as Flavobacteriaceae. Although no explicit mobile genetic elements were identified by genetic environment analysis, blaRATA-2 possessed the ability of horizontal transfer in R. anatipestifer via natural transformation. This work's data suggest that RATA is a new chromosome-encoded class A carbapenemase, and Flavobacteriaceae from marine environments could be the primary reservoir of the blaRATA gene.
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Affiliation(s)
- Hongyan Luo
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Ting Lei
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Caixia Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Zuoyong Zhou
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Pei Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China; National Center of Technology Innovation for Pigs, Rongchang, Chongqing, China.
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
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19
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Khawaja T, Mäklin T, Kallonen T, Gladstone RA, Pöntinen AK, Mero S, Thorpe HA, Samuelsen Ø, Parkhill J, Izhar M, Akhtar MW, Corander J, Kantele A. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nat Commun 2024; 15:5196. [PMID: 38890378 PMCID: PMC11189469 DOI: 10.1038/s41467-024-49591-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.
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Affiliation(s)
- Tamim Khawaja
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Sointu Mero
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mateen Izhar
- Department of Microbiology, Shaikh Zayed Post-Graduate Medical Institute, Lahore, Pakistan
| | - M Waheed Akhtar
- School of Biological Science, University of the Punjab, Lahore, Pakistan
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
- Department of Biostatistics, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland.
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland.
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20
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Chan YX, Cao H, Jiang S, Li X, Fung KK, Lee CH, Sridhar S, Chen JHK, Ho PL. Genomic investigation of Lactococcus formosensis, Lactococcus garvieae, and Lactococcus petauri reveals differences in species distribution by human and animal sources. Microbiol Spectr 2024; 12:e0054124. [PMID: 38687062 PMCID: PMC11237765 DOI: 10.1128/spectrum.00541-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Lactococcus garvieae is a fish pathogen that can cause diseases in humans and cows. Two genetically related species, Lactococcus formosensis and Lactococcus petauri, may be misidentified as L. garvieae. It is unclear if these species differ in host specificity and virulence genes. This study analyzed the genomes of 120 L. petauri, 53 L. formosensis, and 39 L. garvieae isolates from various sources. The genetic diversity and virulence gene content of these isolates were compared. The results showed that 77 isolates previously reported as L. garvieae were actually L. formosensis or L. petauri. The distribution of the three species varied across different collection sources, with L. petauri being predominant in human infections, human fecal sources, and rainbow trout, while L. formosensis was more common in bovine isolates. The genetic diversity of isolates within each species was high and similar. Using a genomic clustering method, L. petauri, L. formosensis, and L. garvieae were divided into 45, 22, and 13 clusters, respectively. Most rainbow trout and human isolates of L. petauri belonged to different clusters, while L. formosensis isolates from bovine and human sources were also segregated into separate clusters. In L. garvieae, most human isolates were grouped into three clusters that also included isolates from food or other sources. Non-metric multidimensional scaling ordination revealed the differential association of 15 virulence genes, including 14 adherence genes and a bile salt hydrolase gene, with bacterial species and certain collection sources. In conclusion, this work provides evidence of host specificity among the three species. IMPORTANCE Lactococcus formosensis and Lactococcus petauri are two newly discovered bacteria, which are closely related to Lactococcus garvieae, a pathogen that affects farmed rainbow trout, as well as causes cow mastitis and human infections. It is unclear whether the three bacteria differ in their host preference and the presence of genes that contribute to the development of disease. This study shows that L. formosensis and L. petauri were commonly misidentified as L. garvieae. The three bacteria showed different distribution patterns across various sources. L. petauri was predominantly found in human infections and rainbow trout, while L. formosensis was more commonly detected in cow mastitis. Fifteen genes displayed a differential distribution among the three bacteria from certain sources, indicating a genetic basis for the observed host preference. This work indicates the importance of differentiating the three bacteria in diagnostic laboratories for surveillance and outbreak investigation purposes.
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Affiliation(s)
- You-Xiang Chan
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Huiluo Cao
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Shuo Jiang
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Xin Li
- Department of Microbiology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
| | - Ka-Kin Fung
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hospital Authority, Hong Kong, China
| | - Chung-Ho Lee
- Department of Clinical Pathology, Kwong Wah Hospital, Hospital Authority, Hong Kong, China
| | - Siddharth Sridhar
- Department of Microbiology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
| | | | - Pak-Leung Ho
- Department of Microbiology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
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21
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Cheng HCR, Belman S, Salje H, Dagan R, Bentley SD. Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data. Microb Genom 2024; 10:001262. [PMID: 38913413 PMCID: PMC11261897 DOI: 10.1099/mgen.0.001262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.
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Affiliation(s)
| | - Sophie Belman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ron Dagan
- Gunzburger Chair for Study of Infectious Diseases, The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stephen D. Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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22
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Cave R, Kalizang'oma A, Chaguza C, Mwalukomo TS, Kamng’ona A, Brown C, Msefula J, Bonomali F, Nyirenda R, Swarthout TD, Kwambana-Adams B, French N, Heyderman RS. Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi. Microb Genom 2024; 10:001264. [PMID: 38896467 PMCID: PMC11261835 DOI: 10.1099/mgen.0.001264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT) Streptococcus pneumoniae, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccine's introduction, we compared 1022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predicted in silico to alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbours a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post-PCV13 rollout.
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Affiliation(s)
- Rory Cave
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
| | - Akuzike Kalizang'oma
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | | | | | - Comfort Brown
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | | | | | | | - Todd D. Swarthout
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Brenda Kwambana-Adams
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, UK
| | - Robert S. Heyderman
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, UK
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
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23
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Lan Y, Liu L, Hu D, Ge L, Xiang X, Peng M, Fu Y, Wang Y, Li S, Chen Y, Jiang Y, Tu Y, Vidal JE, Yu Y, Chen Z, Wu X. Limited protection of pneumococcal vaccines against emergent Streptococcus pneumoniae serotype 14/ST876 strains. Infection 2024; 52:801-811. [PMID: 37919621 PMCID: PMC11143005 DOI: 10.1007/s15010-023-02110-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/08/2023] [Indexed: 11/04/2023]
Abstract
PURPOSE Streptococcus pneumoniae (Spn) is a major cause of child death. We investigated the epidemiology of S. pneumoniae in a pediatric fever clinic and explored the genomics basis of the limited vaccine response of serotype 14 strains worldwide. METHODS Febrile disease and pneumonia were diagnosed following criteria from the WHO at the end of 2019 at a tertiary children's hospital. Spn was isolated by culture from nasopharyngeal (NP) swabs. The density was determined by lytA-base qPCR. Isolates were serotyped by Quellung and underwent antimicrobial susceptibility testing. Whole-genome sequencing was employed for molecular serotyping, MLST, antibiotic gene determination, SNP calling, recombination prediction, and phylogenetic analysis. RESULTS The presence of pneumococcus in the nasopharynx (87.5%, 7/8, p = 0.0227) and a high carriage (100%, 7/7, p = 0.0123) were significantly associated with pneumonia development. Living with siblings (73.7%, 14/19, p = 0.0125) and non-vaccination (56.0%, 28/50, p = 0.0377) contributed significantly to the Spn carriage. Serotype 14 was the most prevalent strain (16.67%, 5/30). The genome analysis of 1497 serotype 14 strains indicated S14/ST876 strains were only prevalent in China, presented limited vaccine responses with higher recombination activities within its cps locus, and unique variation patterns in the genes wzg and lrp. CONCLUSION With the lifting of the one-child policy, it will be crucial for families with multiple children to get PCV vaccinations in China. Due to the highly variant cps locus and distinctive variation patterns in capsule shedding and binding proteins genes, the prevalent S14/ST876 strains have shown poor response to current vaccines. It is necessary to continue monitoring the molecular epidemiology of this vaccine escape clone.
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Affiliation(s)
- Yinle Lan
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Lin Liu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People;s Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Dongping Hu
- Department of Infectious Disease, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Lihong Ge
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Minfei Peng
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuxian Li
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuexing Tu
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jorge E Vidal
- Department of Cell and Molecular Biology, Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhimin Chen
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China.
| | - Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang, China.
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Amadesi S, Vocale C, Guariglia D, Cricca M, Lazzarotto T, Sambri V, Gaibani P. Complete genome sequence of invasive Streptococcus pneumoniae serotype 11A causing meningitis in an adult patient, Italy 2022. Microbiol Resour Announc 2024; 13:e0005424. [PMID: 38587417 PMCID: PMC11080556 DOI: 10.1128/mra.00054-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Streptococcus pneumoniae is a major global health concern, being a common cause of meningitis in both children and adults. Here, we report the complete genome sequence of P10_PNE_LCR, a S. pneumoniae 11A strain isolated in Northern Italy from an adult patient diagnosed with meningitis.
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Affiliation(s)
- Stefano Amadesi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Caterina Vocale
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Davide Guariglia
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Monica Cricca
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Tiziana Lazzarotto
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Vittorio Sambri
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Paolo Gaibani
- Department of Diagnostics and Public Health, Microbiology Section, Verona University, Verona, Italy
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25
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Bessen DE, Beall BW, Hayes A, Huang W, DiChiara JM, Velusamy S, Tettelin H, Jolley KA, Fallon JT, Chochua S, Alobaidallah MSA, Higgs C, Barnett TC, Steemson JT, Proft T, Davies MR. Recombinational exchange of M-fibril and T-pilus genes generates extensive cell surface diversity in the global group A Streptococcus population. mBio 2024; 15:e0069324. [PMID: 38587426 PMCID: PMC11078000 DOI: 10.1128/mbio.00693-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Among genes present in all group A streptococci (GAS), those encoding M-fibril and T-pilus proteins display the highest levels of sequence diversity, giving rise to the two primary serological typing schemes historically used to define strain. A new genotyping scheme for the pilin adhesin and backbone genes is developed and, when combined with emm typing, provides an account of the global GAS strain population. Cluster analysis based on nucleotide sequence similarity assigns most T-serotypes to discrete pilin backbone sequence clusters, yet the established T-types correspond to only half the clusters. The major pilin adhesin and backbone sequence clusters yield 98 unique combinations, defined as "pilin types." Numerous horizontal transfer events that involve pilin or emm genes generate extensive antigenic and functional diversity on the bacterial cell surface and lead to the emergence of new strains. Inferred pilin genotypes applied to a meta-analysis of global population-based collections of pharyngitis and impetigo isolates reveal highly significant associations between pilin genotypes and GAS infection at distinct ecological niches, consistent with a role for pilin gene products in adaptive evolution. Integration of emm and pilin typing into open-access online tools (pubmlst.org) ensures broad utility for end-users wanting to determine the architecture of M-fibril and T-pilus genes from genome assemblies.IMPORTANCEPrecision in defining the variant forms of infectious agents is critical to understanding their population biology and the epidemiology of associated diseases. Group A Streptococcus (GAS) is a global pathogen that causes a wide range of diseases and displays a highly diverse cell surface due to the antigenic heterogeneity of M-fibril and T-pilus proteins which also act as virulence factors of varied functions. emm genotyping is well-established and highly utilized, but there is no counterpart for pilin genes. A global GAS collection provides the basis for a comprehensive pilin typing scheme, and online tools for determining emm and pilin genotypes are developed. Application of these tools reveals the expansion of structural-functional diversity among GAS via horizontal gene transfer, as evidenced by unique combinations of surface protein genes. Pilin and emm genotype correlations with superficial throat vs skin infection provide new insights on the molecular determinants underlying key ecological and epidemiological trends.
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Affiliation(s)
- Debra E. Bessen
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Bernard W. Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
- Eagle Global Scientific, LLC, Atlanta, Georgia, USA
| | - Andrew Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Weihua Huang
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
- Department of Pathology, Brody School of Medicine, Eastern Carolina University, Greenville, North Carolina, USA
| | - Jeanne M. DiChiara
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Srinivasan Velusamy
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Keith A. Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - John T. Fallon
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
- Department of Pathology, Brody School of Medicine, Eastern Carolina University, Greenville, North Carolina, USA
| | - Sopio Chochua
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mosaed S. A. Alobaidallah
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, New York, USA
| | - Charlie Higgs
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy C. Barnett
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Australia
| | - John T. Steemson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas Proft
- School of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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26
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Da Silva Morais E, Grimaud GM, Warda A, Stanton C, Ross P. Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus. Sci Rep 2024; 14:10109. [PMID: 38698002 PMCID: PMC11066082 DOI: 10.1038/s41598-024-59148-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.
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Affiliation(s)
- Emilene Da Silva Morais
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Ghjuvan Micaelu Grimaud
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Alicja Warda
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- Microbiology Department, University College Cork, Co. Cork, Ireland.
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27
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Cheney L, Payne M, Kaur S, Lan R. SaLTy: a novel Staphylococcus aureus Lineage Typer. Microb Genom 2024; 10:001250. [PMID: 38739116 PMCID: PMC11165655 DOI: 10.1099/mgen.0.001250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024] Open
Abstract
Staphylococcus aureus asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 S. aureus was associated with 20 000 deaths in the USA alone. Dividing S. aureus isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus genome sequences when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (n=21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCCmec) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCCmec and the four largest lineages varied in SCCmec over time. Classifying isolates into SaLTy lineages, which were further SCCmec typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of S. aureus genome data. SaLTy will aid the characterisation of S. aureus populations and ongoing surveillance of sub-groups that threaten human health.
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Affiliation(s)
- Liam Cheney
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
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28
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Barnes AJ, Bennett EF, Vezina B, Hudson AW, Hernandez GE, Nutter NA, Bray AS, Nagpal R, Wyres KL, Zafar MA. Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut. PLoS Pathog 2024; 20:e1012189. [PMID: 38713723 PMCID: PMC11101070 DOI: 10.1371/journal.ppat.1012189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 05/17/2024] [Accepted: 04/10/2024] [Indexed: 05/09/2024] Open
Abstract
Successful microbial colonization of the gastrointestinal (GI) tract hinges on an organism's ability to overcome the intense competition for nutrients in the gut between the host and the resident gut microbiome. Enteric pathogens can exploit ethanolamine (EA) in the gut to bypass nutrient competition. However, Klebsiella pneumoniae (K. pneumoniae) is an asymptomatic gut colonizer and, unlike well-studied enteric pathogens, harbors two genetically distinct ethanolamine utilization (eut) loci. Our investigation uncovered unique roles for each eut locus depending on EA utilization as a carbon or nitrogen source. Murine gut colonization studies demonstrated the necessity of both eut loci in the presence of intact gut microbiota for robust GI colonization by K. pneumoniae. Additionally, while some Escherichia coli gut isolates could metabolize EA, other commensals were incapable, suggesting that EA metabolism likely provides K. pneumoniae a selective advantage in gut colonization. Molecular and bioinformatic analyses unveiled the conservation of two eut loci among K. pneumoniae and a subset of the related taxa in the K. pneumoniae species complex, with the NtrC-RpoN regulatory cascade playing a pivotal role in regulation. These findings identify EA metabolism as a critical driver of K. pneumoniae niche establishment in the gut and propose microbial metabolism as a potential therapeutic avenue to combat K. pneumoniae infections.
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Affiliation(s)
- Andrew J. Barnes
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Emma F. Bennett
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andrew W. Hudson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Noah A. Nutter
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Andrew S. Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ravinder Nagpal
- Department of Health, Nutrition, and Food Science, Florida State University, Tallahassee, Florida, United States of America
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - M. Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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29
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Bertran M, D'Aeth JC, Abdullahi F, Eletu S, Andrews NJ, Ramsay ME, Litt DJ, Ladhani SN. Invasive pneumococcal disease 3 years after introduction of a reduced 1 + 1 infant 13-valent pneumococcal conjugate vaccine immunisation schedule in England: a prospective national observational surveillance study. THE LANCET. INFECTIOUS DISEASES 2024; 24:546-556. [PMID: 38310905 DOI: 10.1016/s1473-3099(23)00706-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND The UK transition from a 2 + 1 to a 1 + 1 infant immunisation schedule with the 13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided with the start of the COVID-19 pandemic. We describe the epidemiology of invasive pneumococcal disease (IPD) in England over 6 financial years (April 1 to March 31) between 2017-18 and 2022-23. METHODS We used prospective national surveillance data, including serotyping and whole-genome sequencing of invasive isolates, to analyse IPD trends in England by age and financial year. We compared breakthrough infections and vaccine failure rates in 2022-23 among children eligible for the 1 + 1 schedule with rates in cohorts of children eligible for the 2 + 1 schedule between 2017-18 and 2019-20. We assessed genomic changes over time by comparing Global Pneumococcal Sequencing Clusters and multilocus sequence types among PCV13 serotypes causing IPD. FINDINGS There were 4598 laboratory-confirmed IPD cases in 2022-23, 3025 in 2021-22, 1240 in 2020-21, and 5316 in 2019-20. IPD incidence in 2022-23 was 14% lower than in 2019-20 (incidence rate ratio [IRR] 0·86, 95% CI 0·81-0·91; p<0·001). IPD incidence in 2022-23 compared with 2019-20 was 34% higher in children (aged <15 years) (378 cases vs 292 cases; IRR 1·34, 95% CI 1·08-1·68; p=0·009) and 17% lower in adults (aged 15 years and older; 4220 vs 5024; 0·83, 0·78-0·88; p<0·001). The proportion of PCV13-type IPD increased from 19·4% (95% CI 18·2-20·4; 957 of 4947) in 2019-20 to 29·7% (28·3-31·0; 1283 of 4326) in 2022-23, mainly due to serotype 3, but also serotypes 19F, 19A, and 4, alongside a decrease in non-PCV13 serotypes 8, 12F, and 9N. The increase in IPD incidence due to serotypes 3, 19A, and 19F was driven by clonal expansion of previously circulating strains, whereas serotype 4 expansion was driven by newer strains (ie, sequence types 801 and 15603). Breakthrough infections and vaccine failure rates were similar in children eligible for the 1 + 1 (1·08 per 100 000 person-years) and 2 + 1 (0·76 per 100 000 person-years; IRR 1·42, 95% CI 0·78-2·49; p=0·20) PCV13 schedules. INTERPRETATION Overall, IPD incidence in England was lower in 2022-23, 2 years after removal of pandemic restrictions, than in 2019-20. Breakthrough and vaccine failure rates were not significantly different between children who received the 1 + 1 compared with the 2 + 1 PCV13 immunisation schedule. The post-pandemic increase in childhood IPD incidence and especially PCV13-type IPD will require close monitoring. FUNDING None.
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Affiliation(s)
- Marta Bertran
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK
| | - Joshua C D'Aeth
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Fariyo Abdullahi
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Nick J Andrews
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK
| | - Mary E Ramsay
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - David J Litt
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK; Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Shamez N Ladhani
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, UK; Paediatric Infectious Diseases Research Group, St George's University of London, London, UK.
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30
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Rodriguez-Ruiz JP, Xavier BB, Stöhr W, van Heirstraeten L, Lammens C, Finn A, Goossens H, Bielicki JA, Sharland M, Malhotra-Kumar S. High-resolution genomics identifies pneumococcal diversity and persistence of vaccine types in children with community-acquired pneumonia in the UK and Ireland. BMC Microbiol 2024; 24:146. [PMID: 38678217 PMCID: PMC11055344 DOI: 10.1186/s12866-024-03300-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae is a global cause of community-acquired pneumonia (CAP) and invasive disease in children. The CAP-IT trial (grant No. 13/88/11; https://www.capitstudy.org.uk/ ) collected nasopharyngeal swabs from children discharged from hospitals with clinically diagnosed CAP, and found no differences in pneumococci susceptibility between higher and lower antibiotic doses and shorter and longer durations of oral amoxicillin treatment. Here, we studied in-depth the genomic epidemiology of pneumococcal (vaccine) serotypes and their antibiotic resistance profiles. METHODS Three-hundred and ninety pneumococci cultured from 1132 nasopharyngeal swabs from 718 children were whole-genome sequenced (Illumina) and tested for susceptibility to penicillin and amoxicillin. Genome heterogeneity analysis was performed using long-read sequenced isolates (PacBio, n = 10) and publicly available sequences. RESULTS Among 390 unique pneumococcal isolates, serotypes 15B/C, 11 A, 15 A and 23B1 were most prevalent (n = 145, 37.2%). PCV13 serotypes 3, 19A, and 19F were also identified (n = 25, 6.4%). STs associated with 19A and 19F demonstrated high genome variability, in contrast to serotype 3 (n = 13, 3.3%) that remained highly stable over a 20-year period. Non-susceptibility to penicillin (n = 61, 15.6%) and amoxicillin (n = 10, 2.6%) was low among the pneumococci analysed here and was independent of treatment dosage and duration. However, all 23B1 isolates (n = 27, 6.9%) were penicillin non-susceptible. This serotype was also identified in ST177, which is historically associated with the PCV13 serotype 19F and penicillin susceptibility, indicating a potential capsule-switch event. CONCLUSIONS Our data suggest that amoxicillin use does not drive pneumococcal serotype prevalence among children in the UK, and prompts consideration of PCVs with additional serotype coverage that are likely to further decrease CAP in this target population. Genotype 23B1 represents the convergence of a non-vaccine genotype with penicillin non-susceptibility and might provide a persistence strategy for ST types historically associated with vaccine serotypes. This highlights the need for continued genomic surveillance.
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Affiliation(s)
- Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Wolfgang Stöhr
- MRC Clinical Trials Unit, University College London, London, UK
| | - Liesbet van Heirstraeten
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | | | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Julia Anna Bielicki
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Michael Sharland
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium.
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Xie O, Zachreson C, Tonkin-Hill G, Price DJ, Lacey JA, Morris JM, McDonald MI, Bowen AC, Giffard PM, Currie BJ, Carapetis JR, Holt DC, Bentley SD, Davies MR, Tong SYC. Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange. Nat Commun 2024; 15:3477. [PMID: 38658529 PMCID: PMC11043366 DOI: 10.1038/s41467-024-47816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Cameron Zachreson
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | | | - David J Price
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Malcolm I McDonald
- Division of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Asha C Bowen
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Philip M Giffard
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Faculty of Health, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Jonathan R Carapetis
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Deborah C Holt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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32
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Leigh SA, Evans JD. Genetic comparison of the Mycoplasma gallisepticum 6/85 vaccine strain and 6/85-like field isolates. Vet Microbiol 2024; 291:110008. [PMID: 38364465 DOI: 10.1016/j.vetmic.2024.110008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/18/2024]
Abstract
Mycoplasma gallisepticum infection in poultry leads to disease and pathology that can reduce producer profits. Live attenuated vaccines are available that can limit or completely prevent the effects of infection. Field isolates that are genetically related to the attenuated vaccine strains have been isolated, raising the question of whether the attenuation of the vaccine strains is limited and can lead the strains to revert to more virulent forms. The 6/85 live attenuated vaccine is derived from a field isolate collected in the United States. Analysis of the genome of sequenced M. gallisepticum strains revealed a cluster of 10 6/85-like strains that group with the 6/85 vaccine strain. Four genomic regions were identified that allowed for strain differentiation. The genetic differences between strains points toward nine of the ten strains most likely being sister strains to the 6/85 vaccine strain. Insufficient differences are present in the tenth strain to make a definitive conclusion. These results suggest that most if not all strains similar to the live attenuated vaccine strain are field isolates of the parent strain used to derive the live attenuated vaccine.
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Affiliation(s)
- Spencer A Leigh
- USDA-ARS Poultry Research Unit, PO Box 5367, Mississippi State, MS 39762, USA.
| | - Jeff D Evans
- USDA-ARS Poultry Research Unit, PO Box 5367, Mississippi State, MS 39762, USA
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33
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Marais G, Moodley C, Claassen-Weitz S, Patel F, Prentice E, Tootla H, Nyakutira N, Lennard K, Reddy K, Bamford C, Niehaus A, Whitelaw A, Brink A. Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization. JAC Antimicrob Resist 2024; 6:dlae050. [PMID: 38529003 PMCID: PMC10963078 DOI: 10.1093/jacamr/dlae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Background The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. Objectives This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. Methods Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. Results MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. Conclusions CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.
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Affiliation(s)
- Gert Marais
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Fadheela Patel
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Hafsah Tootla
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Nyasha Nyakutira
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katie Lennard
- Division of Computational Biology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Pathcare, Cape Town, South Africa
| | - Abraham Niehaus
- Division of Medical Microbiology, Ampath, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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34
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Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP, Tonkin-Hill G, Schrieber L, McIntyre L, Lacey JA, James TB, Sriprakash KS, Beatson SA, Hasegawa T, Giffard P, Steer AC, Batzloff MR, Beall BW, Pinho MD, Ramirez M, Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nat Commun 2024; 15:2286. [PMID: 38480728 PMCID: PMC10937727 DOI: 10.1038/s41467-024-46530-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rebecca J Towers
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, Cambridgeshire, UK
| | - Nouri L Ben Zakour
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Olga Berking
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen P Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Layla Schrieber
- Faculty of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Taylah B James
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kadaba S Sriprakash
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Science & Technology, University of New England, Armidale, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Tadao Hasegawa
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Phil Giffard
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, Parkville, Australia
| | - Michael R Batzloff
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute for Glycomics, Griffith University, Southport, Australia
| | - Bernard W Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marcos D Pinho
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Debra E Bessen
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David J McMillan
- School of Science, Technology and Engineering, and Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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Hegstad K, Pöntinen AK, Bjørnholt JV, Quist-Paulsen E, Sundsfjord A. The first tigecycline resistant Enterococcus faecium in Norway was related to tigecycline exposure. J Glob Antimicrob Resist 2024; 36:112-115. [PMID: 38122982 DOI: 10.1016/j.jgar.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES We describe the first tigecycline resistant enterococcal isolate in Norway and the mechanisms involved. MATERIAL AND METHODS The Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res). received in 2022 an Enterococcus faecium blood culture isolate with decreased susceptibility to tigecycline from a hospitalized patient in the South-Eastern Norway Health region for confirmatory testing. K-res verified a tigecycline-resistant E. faecium (TigR) with broth microdilution MIC of 0.5 mg/L. The patient had received treatment with tigecycline because of an infection with a linezolid- and vancomycin-resistant but tigecycline susceptible E. faecium (TigS) 47 days prior to the detection of the corresponding tigecycline-resistant isolate. Whole-genome comparisons, cgMLST and SNP analyses revealed that the two ST117 strains were closely related. RESULTS The TigR isolate showed a novel deletion of 2 amino acids (K57Y58) in a polymorphic region of ribosomal protein S10 previously associated with tigecycline resistance and a deletion of the tet(M) leader peptide previously related to increased expression of tet(M) and tigecycline resistance in enterococci. CONCLUSIONS Genomic and epidemiological analyses confirm that the two E. faecium (TigR and TigS) are closely related isolates of the same strain and that the two deletions (in rpsJ and of tet(M) leader peptide) account for the tigecycline resistance in TigR.
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Affiliation(s)
- Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Anna K Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jørgen V Bjørnholt
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Else Quist-Paulsen
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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36
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Tanabe M, Denda T, Natori T, Horiuchi K, Sakaguchi K, Koide S, Nagano Y, Nagano N. Commonality of multispecies GES carbapenemase-producing organisms in hospital wastewater with those in previously investigated epidemiologically linked municipal wastewater influents. J Glob Antimicrob Resist 2024; 36:139-141. [PMID: 38154748 DOI: 10.1016/j.jgar.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023] Open
Affiliation(s)
- Mizuki Tanabe
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Nagano, Japan
| | - Tomohiro Denda
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Nagano, Japan
| | - Tatsuya Natori
- Department of Laboratory Medicine, Shinshu University Hospital, Nagano, Japan
| | - Kazuki Horiuchi
- Department of Laboratory Medicine, Shinshu University Hospital, Nagano, Japan
| | - Kanae Sakaguchi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Nagano, Japan
| | - Shota Koide
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Yukiko Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Nagano, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Nagano, Japan; Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan.
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37
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Batisti Biffignandi G, Chindelevitch L, Corbella M, Feil EJ, Sassera D, Lees JA. Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae. Microb Genom 2024; 10:001222. [PMID: 38529944 PMCID: PMC10995625 DOI: 10.1099/mgen.0.001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative approach which overcomes some of these difficulties, albeit the interpretation of MIC is still needed. Nevertheless, precisely how we should handle MIC data when dealing with predictive models remains unclear, since they are measured semi-quantitatively, with varying resolution, and are typically also left- and right-censored within varying ranges. We therefore investigated genome-based prediction of MICs in the pathogen Klebsiella pneumoniae using 4367 genomes with both simulated semi-quantitative traits and real MICs. As we were focused on clinical interpretation, we used interpretable rather than black-box machine learning models, namely, Elastic Net, Random Forests, and linear mixed models. Simulated traits were generated accounting for oligogenic, polygenic, and homoplastic genetic effects with different levels of heritability. Then we assessed how model prediction accuracy was affected when MICs were framed as regression and classification. Our results showed that treating the MICs differently depending on the number of concentration levels of antibiotic available was the most promising learning strategy. Specifically, to optimise both prediction accuracy and inference of the correct causal variants, we recommend considering the MICs as continuous and framing the learning problem as a regression when the number of observed antibiotic concentration levels is large, whereas with a smaller number of concentration levels they should be treated as a categorical variable and the learning problem should be framed as a classification. Our findings also underline how predictive models can be improved when prior biological knowledge is taken into account, due to the varying genetic architecture of each antibiotic resistance trait. Finally, we emphasise that incrementing the population database is pivotal for the future clinical implementation of these models to support routine machine-learning based diagnostics.
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Affiliation(s)
- Gherard Batisti Biffignandi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - John A. Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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38
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Nhu NTK, Rahman MA, Goh KGK, Kim SJ, Phan MD, Peters KM, Alvarez-Fraga L, Hancock SJ, Ravi C, Kidd TJ, Sullivan MJ, Irvine KM, Beatson SA, Sweet MJ, Irwin AD, Vukovic J, Ulett GC, Hasnain SZ, Schembri MA. A convergent evolutionary pathway attenuating cellulose production drives enhanced virulence of some bacteria. Nat Commun 2024; 15:1441. [PMID: 38383596 PMCID: PMC10881479 DOI: 10.1038/s41467-024-45176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria adapt to selective pressure in their immediate environment in multiple ways. One mechanism involves the acquisition of independent mutations that disable or modify a key pathway, providing a signature of adaptation via convergent evolution. Extra-intestinal pathogenic Escherichia coli (ExPEC) belonging to sequence type 95 (ST95) represent a global clone frequently associated with severe human infections including acute pyelonephritis, sepsis, and neonatal meningitis. Here, we analysed a publicly available dataset of 613 ST95 genomes and identified a series of loss-of-function mutations that disrupt cellulose production or its modification in 55.3% of strains. We show the inability to produce cellulose significantly enhances ST95 invasive infection in a rat model of neonatal meningitis, leading to the disruption of intestinal barrier integrity in newborn pups and enhanced dissemination to the liver, spleen and brain. Consistent with these observations, disruption of cellulose production in ST95 augmented innate immune signalling and tissue neutrophil infiltration in a mouse model of urinary tract infection. Mutations that disrupt cellulose production were also identified in other virulent ExPEC STs, Shigella and Salmonella, suggesting a correlative association with many Enterobacteriaceae that cause severe human infection. Together, our findings provide an explanation for the emergence of hypervirulent Enterobacteriaceae clones.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - M Arifur Rahman
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Kelvin G K Goh
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Seung Jae Kim
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- INRAE, Univ Montpellier, LBE, 102 Avenue des Etangs, Narbonne, 11100, France
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chitra Ravi
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Matthew J Sullivan
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Katharine M Irvine
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Centre for Clinical Research, Brisbane, Australia
- Queensland Children's Hospital, Brisbane, Australia
| | - Jana Vukovic
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Glen C Ulett
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia.
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.
| | - Sumaira Z Hasnain
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
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Yang Z, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, He Y, Wu Z, Zhu D, Cheng A. Genome-based assessment of antimicrobial resistance reveals the lineage specificity of resistance and resistance gene profiles in Riemerella anatipestifer from China. Microbiol Spectr 2024; 12:e0313223. [PMID: 38169285 PMCID: PMC10846147 DOI: 10.1128/spectrum.03132-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/12/2023] [Indexed: 01/05/2024] Open
Abstract
Riemerella anatipestifer (R. anatipestifer) is an important pathogen that causes severe systemic infections in domestic ducks, resulting in substantial economic losses for China's waterfowl industry. Controlling R. anatipestifer with antibiotics is extremely challenging due to its multidrug resistance. Notably, large-scale studies on antimicrobial resistance (AMR) and the corresponding genetic determinants in R. anatipestifer remain scarce. To solve this dilemma, more than 400 nonredundant R. anatipestifer isolates collected from 22 provinces in China between 1994 and 2021 were subjected to broth dilution antibiotic susceptibility assays, and their resistance-associated genetic determinants were characterized by whole-genome sequencing. While over 90% of the isolates was resistant to sulfamethoxazole, kanamycin, gentamicin, ofloxacin, norfloxacin, and trimethoprim, 88.48% of the isolates was resistant to the last-resort drug (tigecycline). Notably, R. anatipestifer resistance to oxacillin, norfloxacin, ofloxacin, and tetracycline was found to increase relatively over time. Genome-wide analysis revealed the alarmingly high prevalence of blaOXA-like (93.05%) and tet(X) (90.64%) genes and the uneven distribution of resistance genes among lineages. Overall, this study reveals a serious AMR situation regarding R. anatipestifer in China, with a high prevalence and high diversity of antimicrobial resistance genes, providing important data for the rational use of antibiotics in veterinary practice.IMPORTANCERiemerella anatipestifer (R. anatipestifer), an important waterfowl pathogen, has caused substantial economic losses worldwide, especially in China. Antimicrobial resistance (AMR) is a major challenge in controlling this pathogen. Although a few studies have reported antimicrobial resistance in R. anatipestifer, comprehensive data remain a gap. This study aims to address the lack of information on R. anatipestifer AMR and its genetic basis. By analyzing more than 400 isolates collected over two decades, this study reveals alarming levels of resistance to several antibiotics, including drugs of last resort. The study also revealed the lineage-specificity of resistance profiles and resistance gene profiles. Overall, this study provides new insights and updated data support for understanding AMR and its genetic determinants in R. anatipestifer.
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Affiliation(s)
- Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Yu He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhen Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
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Rafiqullah IM, Varghese R, Hellmann KT, Velmurugan A, Neeravi A, Kumar Daniel JL, Vidal JE, Kompithra RZ, Verghese VP, Veeraraghavan B, Robinson DA. Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India. Microb Genom 2024; 10:001191. [PMID: 38315173 PMCID: PMC10926699 DOI: 10.1099/mgen.0.001191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.
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Affiliation(s)
- Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Aravind Velmurugan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | | | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rajeev Z. Kompithra
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Valsan P. Verghese
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
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Selvaraj Anand S, Wu CT, Bremer J, Bhatti M, Treangen TJ, Kalia A, Shelburne SA, Shropshire WC. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microb Genom 2024; 10:001201. [PMID: 38407244 PMCID: PMC10926705 DOI: 10.1099/mgen.0.001201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/31/2024] [Indexed: 02/27/2024] Open
Abstract
Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.
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Affiliation(s)
- Selvalakshmi Selvaraj Anand
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Chin-Ting Wu
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Micah Bhatti
- Department of Laboratory Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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42
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Rhoads DD, Pummill J, Alrubaye AAK. Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers. Microorganisms 2024; 12:250. [PMID: 38399654 PMCID: PMC10892122 DOI: 10.3390/microorganisms12020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all the sepsis isolates. Core genome single nucleotide polymorphism analyses have identified a number of mutations, affecting the protein-coding sequences, that are enriched in sepsis isolates. The analysis of the protein substitutions supports the mutational origins of sepsis isolates.
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Affiliation(s)
- Douglas D. Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jeff Pummill
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adnan Ali Khalaf Alrubaye
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
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43
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Manna S, Werren JP, Ortika BD, Bellich B, Pell CL, Nikolaou E, Gjuroski I, Lo S, Hinds J, Tundev O, Dunne EM, Gessner BD, Bentley SD, Russell FM, Mulholland EK, Mungun T, von Mollendorf C, Licciardi PV, Cescutti P, Ravenscroft N, Hilty M, Satzke C. Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type. Microbiol Spectr 2024; 12:e0357923. [PMID: 38059623 PMCID: PMC10782959 DOI: 10.1128/spectrum.03579-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.
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Affiliation(s)
- Sam Manna
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Joel P. Werren
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Belinda D. Ortika
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Casey L. Pell
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Elissavet Nikolaou
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ilche Gjuroski
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jason Hinds
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
- BUGS Bioscience, London Bioscience Innovation Center, London, United Kingdom
| | - Odgerel Tundev
- National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia
| | | | | | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Fiona M. Russell
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - E. Kim Mulholland
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tuya Mungun
- National Center for Communicable Diseases, Ministry of Health, Ulaanbaatar, Mongolia
| | - Claire von Mollendorf
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - Paul V. Licciardi
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Neil Ravenscroft
- Department of Chemistry, University of Cape Town, Rondebosch, South Africa
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Catherine Satzke
- Infection, Immunity, and Global Health, Murdoch Children’s Research Institute, Melbourne, Australia
- Department of Pediatrics, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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44
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Ritchie G, Chorlton SD, Matic N, Bilawka J, Gowland L, Leung V, Stefanovic A, Romney MG, Lowe CF. WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing. J Antimicrob Chemother 2024; 79:55-60. [PMID: 37965757 DOI: 10.1093/jac/dkad346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVES To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR). METHODS WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder. RESULTS Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified. CONCLUSIONS WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
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Affiliation(s)
- Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer Bilawka
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
| | - Leah Gowland
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Javaid N, Lo SW, Nisar MI, Basharat A, Jaleel H, Rasool K, Sultana Q, Kabir F, Hotwani A, Breiman RF, Bentley SD, Shakoor S, Mirza S. Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan. Microb Genom 2024; 10:001163. [PMID: 38270581 PMCID: PMC10868622 DOI: 10.1099/mgen.0.001163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024] Open
Abstract
Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between 2002 and 2020, this study presents characteristics of pneumococcal strains in Pakistan in the pre- and post-vaccine era. The isolates were characterized on the basis of serotype distribution, genetic lineages (or Global Pneumococcal Sequence Cluster, GPSC) and antibiotic resistance. A high level of diversity in serotype and genetic lineages of pneumococci was observed in Pakistan. Among 190 isolates, we identified 54 serotypes, 67 GPSCs and 116 sequence types (STs) including 23 new STs. The most prevalent GPSCs and their associated serotypes in nasopharyngeal carriage were GPSC54 (expressing serotype 9V), GPSC5 (15A and 7B, and serogroup 24), GPSC25 (15B/15C), GPSC67 (18C) and GPSC376 (6A and 6D). Similarly, among 113 disease-causing isolates, the most prevalent GPSC/serotype combinations were GPSC2 (serotype 1), GPSC10 (serotypes 14, 10A, 19A and 19F), GPSC43 (serotypes 13, 11A, 23B, 35A and 9V), GPSC67 (serotypes 18A and 18C) and GPSC642 (serotype 11A). Of the 190 isolates, the highest levels of resistance were observed against penicillin (58.9 %, n=122), erythromycin (29.5 %, n=56), clindamycin (13.2 %, n=25), co-trimoxazole (94.2 %, n=179) and tetracycline/doxycycline (53.2 %, n=101). A higher proportion of disease-causing isolates were multidrug resistant as compared to carriage isolates (54 % vs 25 %). Our data suggest limited coverage of PCV10 in nasopharyngeal (21.6 %, 16/74) as well as disease-causing (38.1 %, 16/42) isolates among children ≤5 years old; however, higher valent vaccine PCV13 would increase the coverage rates to 33.8 % in nasopharyngeal and 54.8 % in disease-causing isolates, whereas PCV24/25 would offer the highest coverage rates. Owing to the diversity of serotypes observed during the post-vaccine period, the suggested inclusion of serotype in future vaccine formulations will require investigations with larger data sets with an extended temporal window. This article contains data hosted by Microreact.
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Affiliation(s)
- Nida Javaid
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie W. Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
- Milner Centre for Evolution, Department of Life Science, University of Bath, Bath, UK
| | - Muhammad Imran Nisar
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Asma Basharat
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Hadiqa Jaleel
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Karam Rasool
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Qamar Sultana
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Furqan Kabir
- Infectious Diseases Research Laboratory (IDRL), Dept. of Paediatrics & Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Robert F. Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Sadia Shakoor
- Departments of Pathology, Pediatrics, and Medicine, Aga Khan University, Karachi, Pakistan
| | - Shaper Mirza
- Department of Life Sciences, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
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Yang Z, Lan T, Luo H, Li P, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A, Zhu D. Emergence and mobilization of a novel lincosamide resistance gene lnu(I): From environmental reservoirs to pathogenic bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167400. [PMID: 37769725 DOI: 10.1016/j.scitotenv.2023.167400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Antimicrobial resistance remains an utmost concern in human and veterinary medicine, impacting humans, animals, and the environment while significantly influencing the principles of One Health. While Riemerella anatipestifer (R. anatipestifer) is recognized as a waterfowl pathogen with multidrug-resistant properties, the specifics of its lincosamide resistance mechanism are inadequately understood. In this study, we identified a novel lincosamide resistance gene, lnu(I), in R. anatipestifer RCAD0121, and investigated its potential origin, transfer mechanisms, and dissemination status through genomic epidemiology. This exhibited 74.80 % amino acid identity with a previously reported gene, lnu(H). PCR analysis revealed lnu(I) prevalence in at least 44 R. anatipestifer isolates collected from multiple provinces in China. Furthermore, genomic mining unveiled 56 lnu(I) sequences within publicly available databases, primarily originating from environmental sources. In addition, members of the family Flavobacteriaceae were the dominant (16/56, 28.57 %) bacteria carrying the lnu(I) gene, with Flavobacterium exhibiting a similar GC content as lnu(I). Notably, specific instances of the lnu(I) gene were linked to mobile genetic elements within human and animal pathogenic bacteria. These findings suggest that Flavobacterium species within the environment could serve as potential ancestral sources of the novel lnu(I) gene, which has undergone mobilization events toward pathogenic bacteria.
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Affiliation(s)
- Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Tianjing Lan
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Hongyan Luo
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Pei Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Sai Mao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Qun Gao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, China; International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, China.
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Chaguza C, Pöntinen AK, Top J, Arredondo-Alonso S, Freitas AR, Novais C, Torres C, Bentley SD, Peixe L, Coque TM, Willems RJL, Corander J. The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiol Spectr 2023; 11:e0020123. [PMID: 37811975 PMCID: PMC10714801 DOI: 10.1128/spectrum.00201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity-infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anna K. Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
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48
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Tanabe M, Sugawara Y, Denda T, Sakaguchi K, Takizawa S, Koide S, Hayashi W, Yu L, Kayama S, Sugai M, Nagano Y, Nagano N. Municipal wastewater monitoring revealed the predominance of bla GES genes with diverse variants among carbapenemase-producing organisms: high occurrence and persistence of Aeromonas caviae harboring the new bla GES variant bla GES-48. Microbiol Spectr 2023; 11:e0218823. [PMID: 37811969 PMCID: PMC10715227 DOI: 10.1128/spectrum.02188-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE The emergence and spread of carbapenemase-producing organisms (CPOs) represent a global health threat because they are associated with limited treatment options and poor clinical outcomes. Wastewater is considered a hotspot for the evolution and dissemination of antimicrobial resistance. Thus, analyses of municipal wastewater are critical for understanding the circulation of these CPOs and carbapenemase genes in local communities, which remains scarcely known in Japan. This study resulted in several key observations: (i) the vast majority of bla GES genes, including six new bla GES variants, and less frequent bla IMP genes were carbapenemase genes encountered exclusively in wastewater influent; (ii) the most dominant CPO species were Aeromonas spp., in which a remarkable diversity of new sequence types was observed; and (iii) CPOs were detected from combined sewer wastewater, but not from separate sewer wastewater, suggesting that the load of CPOs from unrecognized environmental sources could greatly contribute to their detection in influent wastewater.
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Affiliation(s)
- Mizuki Tanabe
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Tomohiro Denda
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
| | - Kanae Sakaguchi
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
| | - Shino Takizawa
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
| | - Shota Koide
- Department of Medical Sciences, Shinshu University, Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
| | - Wataru Hayashi
- Department of Medical Sciences, Shinshu University, Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yukiko Nagano
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
- Department of Medical Sciences, Shinshu University, Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Nagano, Japan
- Department of Medical Sciences, Shinshu University, Graduate School of Medicine, Science and Technology, Matsumoto, Nagano, Japan
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49
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Rosa MN, Vezina B, Marogna G, Canu A, Molotzu MR, Tola S. Streptococcus ruminantium-associated sheep mastitis outbreak detected in Italy is distinct from bovine isolates. Vet Res 2023; 54:118. [PMID: 38087338 PMCID: PMC10717183 DOI: 10.1186/s13567-023-01248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Streptococcus ruminantium is the causative agent of several bovine and ovine diseases, however reports are uncommon and application of whole genome sequencing to identify is rare. We report for the first time, a severe ovine mastitis outbreak caused by S. ruminantium in Italy, 2022. S. ruminantium was isolated from 12 adult lactating ewes with diffuse nodules in the mammary parenchyma and predominantly serous and clotted milk. All outbreak isolates, along with five additional historical Italian isolates (between 2011 and 2017), were genomically characterised and then analysed in the context of all publicly available S. ruminantium genomes. Antimicrobial susceptibility testing was performed to determine the MICs of 16 antibiotics. The results showed that all isolates were susceptible to all antimicrobials tested except kanamycin. Single Nucleotide Variant analysis confirmed this as a clonal outbreak across 10 sheep (≤ 15 SNVs), while the two others were colonised by more distantly related clones (≤ 53 pairwise SNVs), indicating the presence of multiple infecting lineages. The five historical S. ruminantium isolates were comprised of genetically-distant singletons (between 1259 and 5430 pairwise SNVs to 2022 outbreak isolates). Ovine isolates were found to be genetically distinct to bovine isolates, forming monophyletic groups. Bovine isolates were similarly made up of singleton clones in all but two isolates. Taken together, our genomic analysis using all globally available genomes is consistent with general opportunistic pathogenesis of S. ruminantium. We encourage future genomic surveillance efforts to facilitate outbreak detection, as well as improve our understanding of this poorly-understood, multi-host, zoonotic pathogen.
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Affiliation(s)
- Maria Nives Rosa
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University and the Alfred Hospital, Melbourne, VIC, Australia.
| | - Gavino Marogna
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Antonella Canu
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Monica Rosaria Molotzu
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Sebastiana Tola
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy.
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50
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Qiu X, McGee L, Hammitt LL, Grant LR, O’Brien KL, Hanage WP, Lipsitch M. Prediction of post-PCV13 pneumococcal evolution using invasive disease data enhanced by inverse-invasiveness weighting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.10.23299786. [PMID: 38168234 PMCID: PMC10760274 DOI: 10.1101/2023.12.10.23299786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background After introduction of pneumococcal conjugate vaccines (PCVs), serotype replacement occurred in the population of Streptococcus pneumoniae. Predicting which pneumococcal clones and serotypes will become more common in carriage after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. We sought to use invasive disease data to assess how well negative frequency-dependent selection (NFDS) models could explain pneumococcal carriage population evolution in the post-PCV13 epoch by weighting invasive data to approximate strain proportions in the carriage population. Methods Invasive pneumococcal isolates were collected and sequenced during 1998-2018 by the Active Bacterial Core surveillance (ABCs) from the Centers for Disease Control and Prevention (CDC). To predict the post-PCV13 population dynamics in the carriage population using a NFDS model, all genomic data were processed under a bioinformatic pipeline of assembly, annotation, and pangenome analysis to define genetically similar sequence clusters (i.e., strains) and a set of accessory genes present in 5% to 95% of the isolates. The NFDS model predicted the strain proportion by calculating the post-vaccine strain composition in the weighted invasive disease population that would best match pre-vaccine accessory gene frequencies. To overcome the biases of invasive disease data, serotype-specific inverse-invasiveness weights were defined as the ratio of the proportion of the serotype in the carriage data to the proportion in the invasive data, using data from 1998-2001 in the United States, before conjugate vaccine introduction. The weights were applied to adjust both the observed strain proportion and the accessory gene frequencies. Results Inverse-invasiveness weighting increased the correlation of accessory gene frequencies between invasive and carriage data with reduced residuals in linear or logit scale for pre-vaccine, post-PCV7, and post-PCV13. Similarly, weighting increased the correlation of accessory gene frequencies between different time periods in the invasive data. By weighting the invasive data, we were able to use the NFDS model to predict strain proportions in the carriage population in the post-PCV13 epoch, with the adjusted R-squared between predicted and observed strain proportions increasing from 0.176 to 0.544 after weighting. Conclusions The weighting system adjusted the invasive disease surveillance data to better represent the carriage population of S. pneumoniae. The NFDS mechanism predicted the strain proportions in the projected carriage population as estimated from the weighted invasive disease frequencies in the post-PCV13 epoch. Our methods enrich the value of genomic sequences from invasive disease surveillance, which is readily available, easy to collect, and of direct interest to public health.
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Affiliation(s)
- Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Lesley McGee
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Laura L Hammitt
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lindsay R Grant
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Katherine L O’Brien
- Center for Indigenous Health, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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