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Larsen TG, Samaniego Castruita JA, Worning P, Westh H, Bartels MD. Within-host genomic evolution of methicillin-resistant Staphylococcus aureus in long-term carriers. Appl Microbiol Biotechnol 2024; 108:95. [PMID: 38212970 PMCID: PMC10784349 DOI: 10.1007/s00253-023-12932-3] [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: 08/01/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Assessing the genomic evolution of Staphylococcus aureus can help us understand how the bacteria adapt to its environment. In this study, we aimed to assess the mutation rate within 144 methicillin-resistant Staphylococcus aureus (MRSA) carriers with a carriage time from 4 to 11 years, including some carriers who belonged to the same households. We found that 23 of the 144 individuals had completely different MRSA types over time and were therefore not long-term carriers of the same MRSA. From the remaining 121 individuals, we performed whole-genome sequencing (WGS) on 424 isolates and then compared these pairwise using core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses. We found a median within-host mutation rate in long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year and 2.7 (1.8-4.2) allelic differences/genome/year, when excluding presumed recombination. Furthermore, we stratified the cohort into subgroups and found no significant difference between the median mutation rate of members of households, individuals with presumed continued exposure, e.g., from travel and persons without known continued exposure. Finally, we found that SNPs occurred at random within the genes in our cohort. KEY POINTS: • Median mutation rate within long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year • Similar median mutation rates in subgroups (households, travelers) • No hotspots for SNPs within the genome.
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Affiliation(s)
- Tine Graakjær Larsen
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Damkjær Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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2
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Pearson T, Furstenau T, Wood C, Rigas V, Sahl J, Maltinsky S, Currie BJ, Mayo M, Hall C, Keim P, Fofanov V. Population sequencing for diversity and transmission analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599478. [PMID: 38948873 PMCID: PMC11212992 DOI: 10.1101/2024.06.18.599478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of colonies to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences of Burkholderia pseudomallei from the sputum of a single patient. We also analyzed population sequences of Staphylococcus aureus derived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses of B. pseudomallei populations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses of S. aureus samples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity.
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Affiliation(s)
- Talima Pearson
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara Furstenau
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Colin Wood
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Vanessa Rigas
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jason Sahl
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sara Maltinsky
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Carina Hall
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Viacheslav Fofanov
- Pathogen &Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 PMCID: PMC11090465 DOI: 10.1093/jac/dkae023] [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: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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4
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Bu F, Kagaayi J, Grabowski MK, Ratmann O, Xu J. Inferring HIV transmission patterns from viral deep-sequence data via latent typed point processes. Biometrics 2024; 80:ujad015. [PMID: 38372402 PMCID: PMC10875513 DOI: 10.1093/biomtc/ujad015] [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: 02/23/2023] [Revised: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024]
Abstract
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, providing higher resolution compared to standard Sanger sequencing. To more fully utilize these rich data and account for the uncertainties in outcomes from phylogenetic analyses, we propose a spatial Poisson process model to uncover human immunodeficiency virus (HIV) transmission flow patterns at the population level. We represent pairings of individuals with viral sequence data as typed points, with coordinates representing covariates such as gender and age and point types representing the unobserved transmission statuses (linkage and direction). Points are associated with observed scores on the strength of evidence for each transmission status that are obtained through standard deep-sequence phylogenetic analysis. Our method is able to jointly infer the latent transmission statuses for all pairings and the transmission flow surface on the source-recipient covariate space. In contrast to existing methods, our framework does not require preclassification of the transmission statuses of data points, and instead learns them probabilistically through a fully Bayesian inference scheme. By directly modeling continuous spatial processes with smooth densities, our method enjoys significant computational advantages compared to previous methods that rely on discretization of the covariate space. We demonstrate that our framework can capture age structures in HIV transmission at high resolution, bringing valuable insights in a case study on viral deep-sequencing data from Southern Uganda.
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Affiliation(s)
- Fan Bu
- Department of Biostatistics, University of California - Los Angeles, Los Angeles, CA 90024, United States
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Joseph Kagaayi
- School of Public Health, Makerere University, Kampala, Uganda
| | - Mary Kate Grabowski
- School of Medicine, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jason Xu
- Department of Statistical Science, Duke University, Durham, NC 27708, United States
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Raghuram V, Gunoskey JJ, Hofstetter KS, Jacko NF, Shumaker MJ, Hu YJ, Read TD, David MZ. Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures. Microb Genom 2023; 9:001111. [PMID: 37934072 PMCID: PMC10711313 DOI: 10.1099/mgen.0.001111] [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: 06/14/2023] [Accepted: 09/21/2023] [Indexed: 11/08/2023] Open
Abstract
The most common approach to sampling the bacterial populations within an infected or colonized host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. Sequencing a mixture of several colonies (pool-seq) is a better approach to detect population heterogeneity, but it is more complex to analyse due to different types of heterogeneity, such as within-clone polymorphisms, multi-strain mixtures, multi-species mixtures and contamination. Here, we compared 8 single-colony isolates (singles) and pool-seq on a set of 2286 Staphylococcus aureus culture samples to identify features that can distinguish pure samples, samples undergoing intraclonal variation and mixed strain samples. The samples were obtained by swabbing 3 body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jessica J. Gunoskey
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Katrina S. Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F. Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Margot J. Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z. David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
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Yadav D, Patil-Takbhate B, Khandagale A, Bhawalkar J, Tripathy S, Khopkar-Kale P. Next-Generation sequencing transforming clinical practice and precision medicine. Clin Chim Acta 2023; 551:117568. [PMID: 37839516 DOI: 10.1016/j.cca.2023.117568] [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: 07/08/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.
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Affiliation(s)
- Deepali Yadav
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India; Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Bhagyashri Patil-Takbhate
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Anil Khandagale
- Department of Biotechnology, Dr. D. Y. Patil Arts Science and Commerce College, Pimpri Pune 411018, India
| | - Jitendra Bhawalkar
- Department of Community Medicine, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India
| | - Srikanth Tripathy
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
| | - Priyanka Khopkar-Kale
- Central Research Facility, Dr. D.Y Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri Pune 411018, India.
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Raghuram V, Gunoskey JJ, Hofstetter KS, Jacko NF, Shumaker MJ, Hu YJ, Read TD, David MZ. Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544959. [PMID: 37397999 PMCID: PMC10312683 DOI: 10.1101/2023.06.14.544959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies ("pool-seq"), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286 S. aureus culture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jessica J. Gunoskey
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katrina S. Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F. Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Margot J. Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z. David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Cheng S, Fleres G, Chen L, Liu G, Hao B, Newbrough A, Driscoll E, Shields RK, Squires KM, Chu TY, Kreiswirth BN, Nguyen MH, Clancy CJ. Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia. mBio 2022; 13:e0290622. [PMID: 36445082 PMCID: PMC9765435 DOI: 10.1128/mbio.02906-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated in vitro at 37°C. In conclusion, we identified genotypic and phenotypic variant ST258 CRKP strains from blood cultures of individual patients with BSIs, which were not detected by the clinical laboratory or in seeded blood cultures. The data suggest a new paradigm of CRKP population diversity during BSIs, at least in some patients. If validated for BSIs caused by other bacteria, within-host microbial diversity may have implications for medical, microbiology, and infection prevention practices and for understanding antibiotic resistance and pathogenesis. IMPORTANCE The long-standing paradigm for pathogenesis of bacteremia is that, in most cases, a single organism passes through a bottleneck and establishes itself in the bloodstream (single-organism hypothesis). In keeping with this paradigm, standard practice in processing positive microbiologic cultures is to test single bacterial strains from morphologically distinct colonies. This study is the first genome-wide analysis of within-host diversity of Klebsiella pneumoniae strains recovered from individual patients with bloodstream infections (BSIs). Our finding that positive blood cultures comprised genetically and phenotypically heterogeneous carbapenem-resistant K. pneumoniae strains challenges the single-organism hypothesis and suggests that at least some BSIs are caused by mixed bacterial populations that are unrecognized by the clinical laboratory. The data support a model of pathogenesis in which pressures in vivo select for strain variants with particular antibiotic resistance or virulence attributes and raise questions about laboratory protocols and treatment decisions directed against single strains.
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Affiliation(s)
- Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Binghua Hao
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Ryan K. Shields
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Ting-yu Chu
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cornelius J. Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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9
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Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis. THE LANCET MICROBE 2022; 3:e652-e662. [PMID: 35803292 PMCID: PMC9869340 DOI: 10.1016/s2666-5247(22)00115-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 03/31/2022] [Accepted: 04/19/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND A crucial barrier to the routine application of whole-genome sequencing (WGS) for infection prevention is the insufficient criteria for determining whether a genomic linkage is consistent with transmission within the facility. We evaluated the use of single-nucleotide variant (SNV) thresholds, as well as a novel threshold-free approach, for inferring transmission linkages in a high-transmission setting. METHODS We did a retrospective genomic epidemiology analysis of samples previously collected in the context of an intervention study at a long-term acute care hospital in the USA. We performed WGS on 435 isolates of Klebsiella pneumoniae harbouring the blaKPC carbapenemase (KPC-Kp) collected from 256 patients through admission and surveillance culturing (once every 2 weeks) of almost every patient who was admitted to hospital over a 1-year period. FINDINGS Our analysis showed that the standard approach of using an SNV threshold to define transmission would lead to false-positive and false-negative inferences. False-positive inferences were driven by the frequent importation of closely related strains, which were presumably linked via transmission at connected health-care facilities. False-negative inferences stemmed from the diversity of colonising populations that were spread among patients, with multiple examples of hypermutator strain emergence within patients and, as a result, putative transmission links separated by large genetic distances. Motivated by limitations of an SNV threshold, we implemented a novel threshold-free transmission cluster inference approach, in which each of the acquired KPC-Kp isolates were linked back to the imported KPC-Kp isolate with which it shared the most variants. This approach yielded clusters that varied in levels of genetic diversity but where 105 (81%) of 129 unique strain acquisition events were associated with epidemiological links in the hospital. Of 100 patients who acquired KPC-Kp isolates that were included in a cluster, 47 could be linked to a single patient who was positive for KPC-Kp at admission, compared with 31 and 25 using 10 SNV and 20 SNV thresholds, respectively. Holistic examination of clusters highlighted extensive variation in the magnitude of onward transmission stemming from more than 100 importation events and revealed patterns in cluster propagation that could inform improvements to infection prevention strategies. INTERPRETATION Our results show how the integration of culture surveillance data into genomic analyses can overcome limitations of cluster detection based on SNV-thresholds and improve the ability to track pathways of pathogen transmission in health-care settings. FUNDING US Center for Disease Control and Prevention and University of Michigan.
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10
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Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young BC, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife 2022; 11:e77195. [PMID: 35699423 PMCID: PMC9270034 DOI: 10.7554/elife.77195] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- Department of Infectious Diseases, Austin HealthHeidelbergAustralia
- Victorian Infectious Diseases Service, Royal Melbourne HospitalMelbourneAustralia
| | - Romain Guérillot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
| | - Sebastian Duchene
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
| | - Diane Daniel
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter HospitalNewcastle, New South WalesAustralia
- Menzies School of Health Research, Charles Darwin UniversityCasuarina, Northern TerritoryAustralia
| | - Steven YC Tong
- Menzies School of Health Research, Charles Darwin UniversityCasuarina, Northern TerritoryAustralia
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, University of OxfordOxfordUnited Kingdom
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
| | - Benjamin P Howden
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneAustralia
- Department of Infectious Diseases, Austin HealthHeidelbergAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Doherty Institute for Infection and ImmunityMelbourneAustralia
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11
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Zhou Y, Zhao XC, Wang LQ, Chen CW, Hsu MH, Liao WT, Deng X, Yan Q, Zhao GP, Chen CL, Zhang L, Chiu CH. Detecting Genetic Variation of Colonizing Streptococcus agalactiae Genomes in Humans: A Precision Protocol. FRONTIERS IN BIOINFORMATICS 2022; 2:813599. [PMID: 36304301 PMCID: PMC9580942 DOI: 10.3389/fbinf.2022.813599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Deciphering the genotypic diversity of within-individual pathogens and verifying the evolutionary model can help elucidate resistant genotypes, virulent subpopulations, and the mechanism of opportunistic pathogenicity. However, observed polymorphic mutations (PMs) are rare and difficult to be detected in the “dominant-lineage” model of bacterial infection due to the low frequency. The four pooled group B Streptococcus (GBS) samples were collected from the genital tracts of healthy pregnant women, and the pooled samples and the isogenic controls were genomically sequenced. Using the PMcalling program, we detected the PMs in samples and compared the results between two technical duplicates, GBS-M001T and GBS-M001C. Tested with simulated datasets, the PMcalling program showed high sensitivity especially in low-frequency PMs and reasonable specificity. The genomic sequence data from pooled samples of GBS colonizing carrier pregnant women were analyzed, and few high-frequency PMs and some low-frequency PMs were discovered, indicating a dominant-lineage evolution model. The PMs mainly were nonsynonymous and enriched in quorum sensing, glycolysis/gluconeogenesis, ATP-binding cassette (ABC) transporters, etc., suggesting antimicrobial or environmental selective pressure. The re-analysis of the published Burkholderia dolosa data showed a diverse-community model, and only a few low-frequency PMs were shared between different individuals. Genes of general control non-repressible 5-related N-acetyltransferases family, major facilitator superfamily (MFS) transporter, and ABC transporter were positive selection candidates. Our findings indicate an unreported nature of the dominant-lineage model of GBS colonization in healthy women, and a formerly not observed mutation pool in a colonized microbial community, possibly maintained by selection pressure.
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Affiliation(s)
- Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- *Correspondence: Yan Zhou, ; Liang Zhang, ; Cheng-Hsun Chiu,
| | - Xue-Chao Zhao
- The Institutes of Biology and Medical Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Lin-Qi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Cheng-Wen Chen
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Mei-Hua Hsu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Wan-Ting Liao
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Xiao Deng
- The Institutes of Biology and Medical Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Qing Yan
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Guo-Ping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- *Correspondence: Yan Zhou, ; Liang Zhang, ; Cheng-Hsun Chiu,
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
- *Correspondence: Yan Zhou, ; Liang Zhang, ; Cheng-Hsun Chiu,
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12
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Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection. BMC Infect Dis 2022; 22:400. [PMID: 35462538 PMCID: PMC9036699 DOI: 10.1186/s12879-022-07371-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Healthcare-associated infections pose a potentially fatal threat to patients worldwide and Staphylococcus aureus is one of the most common causes of healthcare-associated infections. S. aureus is a common commensal pathogen and a frequent cause of bacteremia, with studies demonstrating that nasal and blood isolates from single patients match more than 80% of the time. Here we report on a contemporary collection of colonizing isolates from those with methicillin-resistant S. aureus (MRSA) bloodstream infections to evaluate the diversity within hosts, and detail the clinical features associated with concomitant nasal colonization.
Methods
Swabs of the bilateral anterior nares were obtained from patients diagnosed with MRSA bacteremia. A single colony culture from the blood and an average of 6 colonies from the nares were evaluated for MRSA growth. For the nares cultures, we typed multiple isolates for staphylococcal protein A (spa) and derived the clonal complexes. Demographic and clinical data were obtained retrospectively from the electronic medical record system and analysed using univariate and multivariable regression models.
Results
Over an 11-month period, 68 patients were diagnosed with MRSA bloodstream infection, 53 were swabbed, and 37 (70%) were colonized with MRSA in the anterior nares. We performed molecular typing on 213 nasal colonies. Spa types and clonal complexes found in the blood were also detected in the nares in 95% of the cases. We also found that 11% of patients carried more than one clone of MRSA in the nares. Male sex and history of prior hospitalization within the past 90 days increased odds for MRSA colonization.
Conclusion
The molecular epidemiological landscape of colonization in the setting of invasive disease is diverse and defining the interplay between colonization and invasive disease is critical to combating invasive MRSA disease.
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13
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Forde TL, Dennis TPW, Aminu OR, Harvey WT, Hassim A, Kiwelu I, Medvecky M, Mshanga D, Van Heerden H, Vogel A, Zadoks RN, Mmbaga BT, Lembo T, Biek R. Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microb Genom 2022; 8:000759. [PMID: 35188453 PMCID: PMC8942019 DOI: 10.1099/mgen.0.000759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/10/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.
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Affiliation(s)
- Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - O. Rhoda Aminu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - William T. Harvey
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ayesha Hassim
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Matej Medvecky
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - Henriette Van Heerden
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Adeline Vogel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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14
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Stone MJ, Swales C, Bond S, Muthayya P, Sarma JB. An outbreak of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 in a Regional Burns Centre. J Hosp Infect 2021; 122:1-8. [PMID: 34902497 DOI: 10.1016/j.jhin.2021.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND MRSA outbreaks have previously been reported in burns centres with resulting mortality and morbidity. We describe the first human associated outbreak in the UK caused by a strain of mupirocin-resistant (MuR) livestock-associated meticillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) in an Adult Burns Centre. The centre historically had a very low prevalence of MRSA infections. AIM This report describes the clinical and epidemiological context of how the outbreak was identified and contained using a range of infection prevention and control (IPC) measures guided by both traditional and genetic methods. METHODS A cluster of MuR-MRSA led to an outbreak investigation. Cases were detected via retrospective search and real-time laboratory surveillance. Isolates were sent continuously for whole genome sequencing (WGS). A live timeline of cases and interventions was produced throughout the period. FINDINGS The outbreak consisted of twelve cases, seven males and five females, aged between 22 to 70 years. Patients were identified between May and October 2020. All patients were colonized rather than infected. The strain acquired the plasmid bearing MupA while colonizing the index case before dissemination. The index case was found to be a chicken farmer. This outbreak was eventually controlled using IPC measures, audits and blind staff decolonization guided by the insight from WGS. CONCLUSION We could not determine how the strain entered the centre or if a staff carrier was involved. The outbreak demonstrated the potential for continued transmissions for months despite active surveillance and stringent control measures.
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Affiliation(s)
- Matthew James Stone
- Department of Burns and Plastic Surgery, The Mid Yorkshire Hospitals NHS Trust, UK
| | - Claire Swales
- Department of Burns and Plastic Surgery, The Mid Yorkshire Hospitals NHS Trust, UK
| | - Stuart Bond
- Pharmacy Department, The Mid Yorkshire Hospitals NHS Trust, UK
| | - Preetha Muthayya
- Department of Burns and Plastic Surgery, The Mid Yorkshire Hospitals NHS Trust, UK
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15
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Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E, Honkela A. Bacterial genomic epidemiology with mixed samples. Microb Genom 2021; 7:000691. [PMID: 34779765 PMCID: PMC8743562 DOI: 10.1099/mgen.0.000691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jarno Alanko
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - 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, UT The Arctic University of Norway, Tromsø, Norway
| | - 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, UT The Arctic University of Norway, Tromsø, Norway
| | - Veli Mäkinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Eva Heinz
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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16
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Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J, Honkela A. High-resolution sweep metagenomics using fast probabilistic inference. Wellcome Open Res 2021; 5:14. [PMID: 34746439 PMCID: PMC8543175 DOI: 10.12688/wellcomeopenres.15639.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 01/13/2023] Open
Abstract
Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Christine J. Boinett
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David M. Aanensen
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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17
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Long DR, Wolter DJ, Lee M, Precit M, McLean K, Holmes E, Penewit K, Waalkes A, Hoffman LR, Salipante SJ. Polyclonality, Shared Strains, and Convergent Evolution in Chronic Cystic Fibrosis Staphylococcus aureus Airway Infection. Am J Respir Crit Care Med 2021; 203:1127-1137. [PMID: 33296290 DOI: 10.1164/rccm.202003-0735oc] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rationale: Staphylococcus aureus is the most common respiratory pathogen isolated from patients with cystic fibrosis (CF) in the United States. Although modes of acquisition and genetic adaptation have been described for Pseudomonas aeruginosa, resulting in improved diagnosis and treatment, these features remain more poorly defined for S. aureus.Objectives: To characterize the molecular epidemiology and genetic adaptation of S. aureus during chronic CF airway infection and in response to antibiotic therapy.Methods: We performed whole-genome sequencing of 1,382 S. aureus isolates collected longitudinally over a mean 2.2 years from 246 children with CF at five U.S. centers between 2008 and 2017. Results were integrated with clinical and demographic data to characterize bacterial population dynamics and identify common genetic targets of in vivo adaptation.Measurements and Main Results: Results showed that 45.5% of patients carried multiple, coexisting S. aureus lineages, often having different antibiotic susceptibility profiles. Adaptation during the course of infection commonly occurred in a set of genes related to persistence and antimicrobial resistance. Individual sequence types demonstrated wide geographic distribution, and we identified limited strain-sharing among children linked by common household or clinical exposures. Unlike P. aeruginosa, S. aureus genetic diversity was unconstrained, with an ongoing flow of new genetic elements into the population of isolates from children with CF.Conclusions: CF airways are frequently coinfected by multiple, genetically distinct S. aureus lineages, indicating that current clinical procedures for sampling isolates and selecting antibiotics are likely inadequate. Strains can be shared by patients in close domestic or clinical contact and can undergo convergent evolution in key persistence and antimicrobial-resistance genes, suggesting novel diagnostic and therapeutic approaches for future study.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine
| | - Daniel J Wolter
- Department of Pediatrics.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | | | | | - Kathryn McLean
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Elizabeth Holmes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
| | - Lucas R Hoffman
- Department of Pediatrics.,Department of Microbiology, and.,Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington; and
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18
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Yamamoto T, Sawai K, Nishi T, Fukai K, Kato T, Hayama Y, Murato Y, Shimizu Y, Yamaguchi E. Subgrouping and analysis of relationships between classical swine fever virus identified during the 2018-2020 epidemic in Japan by a novel approach using shared genomic variants. Transbound Emerg Dis 2021; 69:1166-1177. [PMID: 33730417 DOI: 10.1111/tbed.14076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF) is a worldwide devastating disease of the pig industry caused by classical swine fever virus (CSFV). In September 2018, an outbreak of CSF occurred in Japan where the disease had been eradicated and was officially designated a CSF-free country since 2015. Following the detection of the first 2018 case on a farm in Gifu Prefecture, the disease spread among both farm pigs and wild boars and still continues. Epigenome analysis using whole-genome information is helpful in identifying the infection route, but the current approaches provide an insufficient resolution. In this study, a novel method of using single-nucleotide variants (SNVs) was employed to identify the associations among 158 isolates (65 from farms and 93 from wild boars). The identified groups of CSFV strains were plotted in different colours on a map, identifying the location where each strain was collected. The lack of an SNV set shared between the index case and the other strains suggested the first infection in Japan during the outbreak occurred in wild boars, not at the index farm. For the Atsumi Peninsula outbreaks, where nine farms were found infected within a 10-km radius area, the farm strains were assembled into three groups, suggesting these outbreaks resulted from at least three different infection events in this area. For the infections in the area around Saitama Prefecture, an area remote from the epicentre, strains from both the farms and wild boars were identified as being in the same group, suggesting they resulted from one viral introduction. Likewise, seven infected farms in Okinawa Prefecture, almost 1,500 km from Gifu Prefecture, were identified as being in a common, but separate group. By demonstrating the variety of transmission routes and possibility of long-distance infection, these results will help improve disease control measures.
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Affiliation(s)
- Takehisa Yamamoto
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Kotaro Sawai
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Tatsuya Nishi
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Katsuhiko Fukai
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Tomoko Kato
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Yoko Hayama
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yoshinori Murato
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yumiko Shimizu
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Emi Yamaguchi
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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19
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Xanthopoulou K, Wille J, Zweigner J, Lucaßen K, Wille T, Seifert H, Higgins PG. Characterization of a vancomycin-resistant Enterococcus faecium isolate and a vancomycin-susceptible E. faecium isolate from the same blood culture. J Antimicrob Chemother 2021; 76:883-886. [PMID: 33370443 DOI: 10.1093/jac/dkaa532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/25/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To characterize two Enterococcus faecium isolates with different resistance phenotypes obtained from the same blood culture. METHODS The isolates were identified by MALDI-TOF MS and antimicrobial susceptibility testing (AST) was performed using a VITEK® 2 AST P592 card and Etest. WGS was performed on the MiSeq and MinION sequencer platforms. Core-genome MLST (cgMLST) and seven-loci MLST were performed. Plasmid analysis was performed using S1-PFGE followed by Southern-blot hybridization. RESULTS Both E. faecium isolates were ST203. AST revealed that one was a vancomycin-resistant E. faecium (VREfm) isolate and the other was a vancomycin-susceptible E. faecium (VSEfm) isolate. The VREfm isolate harboured the vanA gene cluster as part of a Tn1546-type transposon encoded on a 49 kb multireplicon (rep1, rep2 and rep7a) plasmid (pAML0157.1). On the same plasmid, ant(6)-Ia, cat-like and erm(B) were encoded. The VSEfm isolate harboured a rep2 plasmid (pAML0158.1), 12 kb in size, which was present in full length as part of pAML0157.1 from the VREfm isolate. The vanA-encoding pAML0157.1 was a chimera of the rep2 pAML0158.1 and a second DNA segment harbouring vanA, ant(6)-Ia, erm(B) and cat-like, as well as the replicons rep1 and rep7a. By cgMLST analysis, the VREfm and VSEfm isolates were identical. CONCLUSIONS Our results demonstrate that the VREfm and VSEfm blood culture isolates represented ST203 and were identical. The investigated heterogeneous resistance phenotypes resulted from the acquisition or loss of plasmid segments in the enterococcal isolates. These data illustrate that mobile genetic elements may contribute to the spread of vancomycin resistance among enterococci and to the genotypic and phenotypic variation within clonal isolates.
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Affiliation(s)
- Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Janine Zweigner
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.,Department of Infection Control and Hospital Hygiene, University Hospital Cologne, Cologne, Germany
| | - Kai Lucaßen
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Thorsten Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
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20
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Penna B, Silva MB, Soares AER, Vasconcelos ATR, Ramundo MS, Ferreira FA, Silva-Carvalho MC, de Sousa VS, Rabello RF, Bandeira PT, de Souza VS, Planet PJ, Vieira-da-Motta O, Botelho AMN, Figueiredo AMS. Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire. Sci Rep 2021; 11:4724. [PMID: 33633263 PMCID: PMC7907190 DOI: 10.1038/s41598-021-83993-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.
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Affiliation(s)
- Bruno Penna
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Marcella B. Silva
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - André E. R. Soares
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Ana T. R. Vasconcelos
- grid.452576.70000 0004 0602 9007Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Mariana S. Ramundo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabienne A. Ferreira
- grid.411237.20000 0001 2188 7235Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina Brazil
| | - Maria C. Silva-Carvalho
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Sousa
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renata F. Rabello
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Paula T. Bandeira
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Viviane S. de Souza
- grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paul J. Planet
- grid.25879.310000 0004 1936 8972Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Olney Vieira-da-Motta
- grid.412331.60000 0000 9087 6639Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Ana M. N. Botelho
- grid.411173.10000 0001 2184 6919Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil ,grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Agnes M. S. Figueiredo
- grid.8536.80000 0001 2294 473XDepartment of Medical Microbiology, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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21
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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22
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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23
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Rose R, Nolan DJ, Moot S, Rodriguez C, Cross S, McCarter YS, Neilsen C, Lamers SL. Molecular surveillance of methicillin-resistant Staphylococcus aureus genomes in hospital unexpectedly reveals discordance between temporal and genetic clustering. Am J Infect Control 2021; 49:59-64. [PMID: 32565273 DOI: 10.1016/j.ajic.2020.06.180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The objective of this study was to identify sources and linkages among methicillin-resistant Staphylococcus aureus infections using whole-genome sequencing (WGS). METHODS A total of 56 samples were obtained from all patients with a confirmed MRSA infection over 6 months at University of Florida-Health Jacksonville. Samples were cultured and sequenced; data was analyzed on an automated cloud-based platform. Genetic Clusters were defined as <40 single nucleotide polymorphisms. Temporal Clusters were defined as ≥5 MRSA cases over 3 days. RESULTS We found 7 Genetic Clusters comprising 15 samples. Four Genetic Clusters contained patients with non-overlapping stays (3-10 weeks apart), 3 of which contained patients who shared the same Unit. We also found 5 Temporal Clusters comprising 23 samples, although none of the samples were genetically related. DISCUSSION Results showed that temporal clustering may be a poor indicator of genetic linkage. Shared epidemiological characteristics between patients in Genetic Clusters may point toward previously unidentified hospital sources. Repeated observation of related strains is also consistent with ongoing MRSA transmission within the surrounding high-risk community. CONCLUSIONS WGS is a valuable tool for hospital infection prevention and control.
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Affiliation(s)
| | | | | | | | | | - Yvette S McCarter
- Department of Pathology and Laboratory Medicine, UF Health Jacksonville, Jacksonville, FL
| | - Chad Neilsen
- Department of Infection Prevention & Control, UF Health Jacksonville, Jacksonville, FL
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24
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Vanegas JM, Salazar-Ospina L, Gallego MA, Jiménez JN. A longitudinal study shows intermittent colonization by Staphylococcus aureus with a high genetic diversity in hemodialysis patients. Int J Med Microbiol 2020; 311:151471. [PMID: 33373839 DOI: 10.1016/j.ijmm.2020.151471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/29/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus colonization increases the risk of invasive infections in different groups of patients. We analyzed the dynamics and factors associated with S. aureus colonization in hemodialysis patients. A longitudinal study was conducted at a dialysis center associated with a tertiary health care institution. S. aureus colonization was assessed three times in nostrils and on the skin and was classified as absent, intermittent or persistent. The molecular analysis included pulsed-field gel electrophoresis (PFGE) and spa-typing. Clonal complex was inferred from spa-typing. A model of generalized estimating equations was performed to determine the factors associated with colonization. A total of 210 patients were included. Colonization by methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) isolates was 29.1 % vs. 4.8 %, 29.2 % vs. 6.7 % and 24.1 % vs. 7.1 % in the first, second and third screenings respectively. Most of the colonized patients were intermittent carriers (77.8 %, n = 63). PFGE and spa-typing revealed a high genetic diversity. One third (33.3 %) of the carriers classified as persistent had different clones during follow-up. Clonal complex 8 was frequent among MSSA (28 %) and MRSA (59 %) isolates. Current smoking (OR:7.22, 95 %CI 2.24-23.27), Charlson index (OR:1.22, 95 %CI 1.03-1.43) and previous infection by S. aureus (OR:2.41; 95 %CI:1.09-5.30) were associated with colonization by this microorganism. Colonization increased the risk of bacteremia (HR = 4.9; 95 % CI: 1.9-12.9). In conclusion, the colonization by S. aureus in hemodialysis patients changes over time and acquisition of new clones is a frequent event. These results evidence that patients are repeatedly recolonizing from hospitals, dialysis units and their homes. On the other hand, factors not associated with healthcare, as smoking, can increase the risk of colonization.
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Affiliation(s)
- Johanna M Vanegas
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Lorena Salazar-Ospina
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Marlon A Gallego
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - J Natalia Jiménez
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia.
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25
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Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch DA, Brown NM, Parkhill J, Peacock SJ. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. LANCET MICROBE 2020; 1:e328-e335. [PMID: 33313577 PMCID: PMC7721685 DOI: 10.1016/s2666-5247(20)30149-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Whole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide polymorphisms (SNP), for meticillin-resistant Staphylococcus aureus (MRSA), above which recent (ie, within 6 months) patient-to-patient transmission could be ruled out. Methods We did a retrospective genomic and epidemiological analysis of MRSA data from two prospective observational cohort studies in the UK to establish SNP cutoffs for genetic relatedness, above which recent transmission was unlikely. We used three separate approaches to calculate these thresholds. First, we applied a linear mixed model to estimate the S aureus substitution rate and 95th percentile within-host diversity in a cohort in which multiple isolates were sequenced per individual. Second, we applied a simulated transmission model to this same genomic dataset. Finally, in a second cohort, we determined the genetic distance (ie, the number of SNPs) that would capture 95% of epidemiologically linked cases. We applied the three approaches to both whole-genome and core-genome sequences. Findings In the linear mixed model, the estimated substitution rate was roughly 5 whole-genome SNPs (wgSNPs) or 3 core-genome SNPs (cgSNPs) per genome per year, and the 95th percentile within-host diversity was 19 wgSNPs or 10 cgSNPs. The combined SNP cutoffs for detection of MRSA transmission within 6 months per this model were thus 24 wgSNPs or 13 cgSNPs. The simulated transmission model suggested that cutoffs of 17 wgSNPs or 12 cgSNPs would detect 95% of MRSA transmission events within the same timeframe. Finally, in the second cohort, cutoffs of 22 wgSNPs or 11 cgSNPs captured 95% of epidemiologically linked cases within 6 months. Interpretation On the basis of our results, we propose conservative cutoffs of 25 wgSNPs or 15 cgSNPS above which transmission of MRSA within the previous 6 months can be ruled out. These cutoffs could potentially be used as part of a genomic sequencing approach to the management of outbreaks of MRSA in conjunction with traditional epidemiological techniques. Funding UK Department of Health, Wellcome Trust, UK National Institute for Health Research.
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Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Correspondence to: Dr Francesc Coll, Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Danielle Leek
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Public Health England, London, UK
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26
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McLean K, Balada-Llasat JM, Waalkes A, Pancholi P, Salipante SJ. Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing. J Hosp Infect 2020; 108:64-71. [PMID: 33227298 DOI: 10.1016/j.jhin.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays. AIM To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers. METHODS Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies. FINDINGS Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events. CONCLUSION These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.
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Affiliation(s)
- K McLean
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - J-M Balada-Llasat
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA
| | - A Waalkes
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - P Pancholi
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
| | - S J Salipante
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
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27
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Wee BA, Muloi DM, van Bunnik BAD. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics. Clin Microbiol Infect 2020; 26:1612-1616. [PMID: 32979568 PMCID: PMC7721588 DOI: 10.1016/j.cmi.2020.09.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. OBJECTIVES To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. SOURCES Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli. CONTENT We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface. IMPLICATIONS A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
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Affiliation(s)
- Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; International Livestock Research Institute, Nairobi, Kenya
| | - Bram A D van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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28
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Avberšek J, Golob M, Papić B, Dermota U, Grmek Košnik I, Kušar D, Ocepek M, Zdovc I. Livestock-associated methicillin-resistant Staphylococcus aureus: Establishing links between animals and humans on livestock holdings. Transbound Emerg Dis 2020; 68:789-801. [PMID: 32687685 DOI: 10.1111/tbed.13745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 12/01/2022]
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) represents a concern in both human and veterinary medicine. The aim of this study was to investigate potential LA-MRSA transmission between animals and humans in rural settings. To this aim, a study was designed to include 14 farms in Slovenia, which were selected on the basis of a farmer (initial patient) with confirmed LA-MRSA infection and regular animal contacts. On all farms, the initial patients, their household members, animals and barn environment were analysed for the presence of LA-MRSA. In addition, the epidemiologically linked hospital-related LA-MRSA isolates were included to investigate possible nosocomial transmissions. On five farms, LA-MRSA was discovered both in animals and in humans. In total, 49 LA-MRSA isolates of different origins underwent whole-genome sequencing, antimicrobial susceptibility testing and spa typing. All 49 isolates belonged to the sequence type 398 (ST398), spa types t011 and t034, and harboured staphylococcal chromosomal cassette mec Vc. High levels of concordance between resistance phenotypes and genotypes were observed. No transmission pairs between animals and initial patients were discovered. However, several isolates originating from farm animals and other household members formed clusters with pairwise distances of ≤14 single nucleotide polymorphisms (SNPs), indicating recent transmission events. In addition, three closely related isolates (0 SNP) form hospitalized patients were observed, indicating a possible nosocomial transmission. Two hospital-related isolates harboured the immune evasion cluster genes, which are associated with adaptation to the human host; however, these two isolates differed in >30 SNPs from the remaining isolates. Characteristics of LA-MRSA from Slovenia reflect those observed previously in other European studies. Immune evasion cluster-positive LA-MRSA ST398 suggests its re-adaptation to the human host and calls for a closer monitoring of such emerging LA-MRSA lineages, in addition to monitoring and preventing the introduction of LA-MRSA from farms to hospitals where transmission is highly plausible.
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Affiliation(s)
- Jana Avberšek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Majda Golob
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Bojan Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Urška Dermota
- National Laboratory of Health, Environment and Food, Kranj, Slovenia
| | | | - Darja Kušar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Matjaž Ocepek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
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29
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Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nat Commun 2020; 11:3442. [PMID: 32651390 PMCID: PMC7351774 DOI: 10.1038/s41467-020-17327-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK.
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebrima Bojang
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rowan E Bancroft
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebenezer Foster-Nyarko
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatima Ceesay
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Catherine Okoi
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | | | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Richard A Adegbola
- RAMBICON Immunisation & Global Health Consulting, 6A Platinum Close, Lekki, Lagos State, Nigeria
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Brenda A Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.
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30
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Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J, Honkela A. High-resolution sweep metagenomics using fast probabilistic inference. Wellcome Open Res 2020; 5:14. [PMID: 34746439 PMCID: PMC8543175 DOI: 10.12688/wellcomeopenres.15639.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2020] [Indexed: 12/29/2022] Open
Abstract
Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.
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Affiliation(s)
- Tommi Mäklin
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Christine J. Boinett
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David M. Aanensen
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jukka Corander
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
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31
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Matuszewska M, Murray GGR, Harrison EM, Holmes MA, Weinert LA. The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends Microbiol 2020; 28:465-477. [PMID: 31948727 DOI: 10.1016/j.tim.2019.12.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/18/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Ewan M Harrison
- Wellcome Sanger Institute, University of Cambridge, Cambridge, CB10 1SA, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
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32
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Kronbichler A, Blane B, Holmes MA, Wagner J, Parkhill J, Peacock SJ, Jayne DRW, Harrison EM. Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis. Rheumatology (Oxford) 2020; 58:548-550. [PMID: 30412252 PMCID: PMC6381761 DOI: 10.1093/rheumatology/key317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Andreas Kronbichler
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge, UK.,Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Beth Blane
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Josef Wagner
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - David R W Jayne
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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33
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Steinig EJ, Duchene S, Robinson DA, Monecke S, Yokoyama M, Laabei M, Slickers P, Andersson P, Williamson D, Kearns A, Goering RV, Dickson E, Ehricht R, Ip M, O'Sullivan MVN, Coombs GW, Petersen A, Brennan G, Shore AC, Coleman DC, Pantosti A, de Lencastre H, Westh H, Kobayashi N, Heffernan H, Strommenger B, Layer F, Weber S, Aamot HV, Skakni L, Peacock SJ, Sarovich D, Harris S, Parkhill J, Massey RC, Holden MTG, Bentley SD, Tong SYC. Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent. mBio 2019; 10:e01105-19. [PMID: 31772058 PMCID: PMC6879714 DOI: 10.1128/mbio.01105-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole-genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the emergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth, and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (MRSA). Our study demonstrates the importance of whole-genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally, resulting in small-scale community and health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. This study demonstrates the importance of whole-genome sequencing for the surveillance of highly antibiotic-resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.
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Affiliation(s)
- Eike J Steinig
- Menzies School of Health Research, Darwin, Australia
- Australian Institute of Tropical Health and Medicine, Townsville, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Technical University of Dresden, Dresden, Germany
| | - Maho Yokoyama
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Peter Slickers
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | | | - Deborah Williamson
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Angela Kearns
- Public Health England, National Infection Service, London, United Kingdom
| | | | - Elizabeth Dickson
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- Technical University of Dresden, Dresden, Germany
| | - Margaret Ip
- The Chinese University of Hong Kong, Hong Kong
| | - Matthew V N O'Sullivan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia, and New Wales Health Pathology, Westmead Hospital, Sydney, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Laboratory Sciences, Murdoch University, Murdoch, Australia
| | | | - Grainne Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Anna C Shore
- Microbiology Research Unit, School of Dental Science, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - David C Coleman
- Microbiology Research Unit, School of Dental Science, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | | | - Herminia de Lencastre
- Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
- The Rockefeller University, New York, New York, USA
| | - Henrik Westh
- University of Copenhagen, Copenhagen, Denmark
- Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Helen Heffernan
- Institute of Environmental Science and Research, Wellington, New Zealand
| | | | | | - Stefan Weber
- Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | | | - Leila Skakni
- King Fahd Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Derek Sarovich
- Menzies School of Health Research, Darwin, Australia
- Sunshine Coast University, Sippy Downs, Australia
| | - Simon Harris
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mathew T G Holden
- Wellcome Sanger Institute, Cambridge, United Kingdom
- University of St. Andrews, St. Andrews, United Kingdom
| | | | - Steven Y C Tong
- Menzies School of Health Research, Darwin, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, and Doherty Department, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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34
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Abstract
Staphylococci, and in particular Staphylococcus aureus, cause an extensive variety of infections in a range of hosts. The comprehensive analysis of staphylococcal genomes reveals mechanisms controlling the organism's biology, pathobiology, and dissemination. Whole-genome sequencing technologies led to a quantum leap in our understanding of bacterial genomes. The recent cost reduction of sequencing has resulted in unprecedented volumes of genomic information about S. aureus, one of the most sequenced bacterial species. Collecting, comparing, and interpreting big data is challenging, but fascinating insights have emerged. For example, it is becoming clearer which selective pressures staphylococci face in their habitats and which mechanisms allow this pathogen to adapt, survive, and spread. A key theme is the constant evolution of staphylococci as they alter their genome, exchange DNA, and adapt to new environments, leading to the emergence of increasingly successful, antibiotic-resistant, immune-evading, and host-adapted colonizers and pathogens. This article introduces the structure of staphylococcal genomes, details how genomes vary between strains, outlines the mechanisms of genetic variation, and describes the features of successful clones.
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Affiliation(s)
- Jodi A Lindsay
- St. George's, University of London, Institute of Infection and Immunity, London, United Kingdom
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35
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Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis. Nat Commun 2019; 10:1411. [PMID: 30926780 PMCID: PMC6441045 DOI: 10.1038/s41467-019-09139-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022] Open
Abstract
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these 'source' populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8-28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.
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Affiliation(s)
- Oliver Ratmann
- Department of Mathematics, Imperial College London, London, SW72AZ, UK.
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK.
| | - M Kate Grabowski
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Matthew Hall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Tanya Golubchik
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris Wymant
- Department of Infectious Disease, Epidemiology School of Public Health, Imperial College London, London, W21PG, UK
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Lucie Abeler-Dörner
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - David Bonsall
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Andrew Leigh Brown
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Tulio de Oliveira
- College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Paul Kellam
- Department of Medicine, Imperial College London, London, W12 0HS, UK
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
- Africa Health Research Institute, Private Bag X7, Durban, 4013, South Africa
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Godfrey Kigozi
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
| | - Thomas C Quinn
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - Maria J Wawer
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892-9806, USA
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Makerere University School of Public Health, Kampala, 8HQG+3V, Uganda
| | - Ronald H Gray
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205-2196, USA
- Rakai Health Sciences Program, Entebbe, P.O.Box 49, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Christophe Fraser
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford, OX3 7BN, UK
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36
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Hawken SE, Snitkin ES. Genomic epidemiology of multidrug-resistant Gram-negative organisms. Ann N Y Acad Sci 2019; 1435:39-56. [PMID: 29604079 PMCID: PMC6167210 DOI: 10.1111/nyas.13672] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 12/12/2022]
Abstract
The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.
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Affiliation(s)
- Shawn E Hawken
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
- Division of Infectious Diseases/Department of Medicine, University of Michigan Medical School, Michigan, USA
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37
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Johnson RC, Deming C, Conlan S, Zellmer CJ, Michelin AV, Lee-Lin S, Thomas PJ, Park M, Weingarten RA, Less J, Dekker JP, Frank KM, Musser KA, McQuiston JR, Henderson DK, Lau AF, Palmore TN, Segre JA. Investigation of a Cluster of Sphingomonas koreensis Infections. N Engl J Med 2018; 379:2529-2539. [PMID: 30586509 PMCID: PMC6322212 DOI: 10.1056/nejmoa1803238] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. METHODS We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions. RESULTS The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses. CONCLUSIONS This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).
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Affiliation(s)
- Ryan C Johnson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Clay Deming
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Sean Conlan
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Caroline J Zellmer
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Angela V Michelin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - ShihQueen Lee-Lin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Pamela J Thomas
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Morgan Park
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Rebecca A Weingarten
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John Less
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John P Dekker
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Karen M Frank
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Kimberlee A Musser
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John R McQuiston
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - David K Henderson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Anna F Lau
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Tara N Palmore
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Julia A Segre
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
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Antão EM, Vincze S, Hanke R, Klimmek L, Suchecka K, Lübke-Becker A, Wieler LH. Antibiotic resistance, the 3As and the road ahead. Gut Pathog 2018; 10:52. [PMID: 30598701 PMCID: PMC6303944 DOI: 10.1186/s13099-018-0280-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance is by far one of the most important health threats of our time. Only a global concerted effort of several disciplines based on the One-Health concept will help in slowing down this process and potentially mitigate the ruin of healthcare we have come to enjoy. In this review, we attempt to summarize the most basic and important topics that serve as good information tools to create Awareness. The Availability of antibiotics or the lack thereof is another significant factor that must be given thought, and finally because antibiotic resistance is a problem that will not go away, it is important to have Alternatives. Together, we have the 3As, essential concepts, in dealing with this growing and complex problem.
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Affiliation(s)
- Esther-Maria Antão
- 1Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany.,2Robert-Koch-Institute, Nordufer 20, 13353 Berlin, Germany
| | - Szilvia Vincze
- 1Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany.,4Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Regina Hanke
- Lindgrün GmbH, Cuxhavener Str. 12, 10557 Berlin, Germany
| | - Lukas Klimmek
- Lindgrün GmbH, Cuxhavener Str. 12, 10557 Berlin, Germany
| | | | - Antina Lübke-Becker
- 1Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany
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Giulieri SG, Baines SL, Guerillot R, Seemann T, Gonçalves da Silva A, Schultz M, Massey RC, Holmes NE, Stinear TP, Howden BP. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Med 2018; 10:65. [PMID: 30103826 PMCID: PMC6090636 DOI: 10.1186/s13073-018-0574-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/27/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Large-scale genomic studies of within-host diversity in Staphylococcus aureus bacteraemia (SAB) are needed to understanding bacterial adaptation underlying persistence and thus refining the role of genomics in management of SAB. However, available comparative genomic studies of sequential SAB isolates have tended to focus on selected cases of unusually prolonged bacteraemia, where secondary antimicrobial resistance has developed. METHODS To understand bacterial genetic diversity during SAB more broadly, we applied whole genome sequencing to a large collection of sequential isolates obtained from patients with persistent or relapsing bacteraemia. After excluding genetically unrelated isolates, we performed an in-depth genomic analysis of point mutations and chromosome structural variants arising within individual SAB episodes. RESULTS We show that, while adaptation pathways are heterogenous and episode-specific, isolates from persistent bacteraemia have a distinctive molecular signature, characterised by a low mutation frequency and high proportion of non-silent mutations. Analysis of structural genomic variants revealed that these often overlooked genetic events are commonly acquired during SAB. We discovered that IS256 insertion may represent the most effective driver of within-host microevolution in selected lineages, with up to three new insertion events per isolate even in the absence of other mutations. Genetic mechanisms resulting in significant phenotypic changes, such as increases in vancomycin resistance, development of small colony phenotypes, and decreases in cytotoxicity, included mutations in key genes (rpoB, stp, agrA) and an IS256 insertion upstream of the walKR operon. CONCLUSIONS This study provides for the first time a large-scale analysis of within-host genomic changes during invasive S. aureus infection and describes specific patterns of adaptation that will be informative for both understanding S. aureus pathoadaptation and utilising genomics for management of complicated S. aureus infections.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia.,Infectious Disease Department, Austin Health, Melbourne, Australia.,Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia.,Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Mark Schultz
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Natasha E Holmes
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Australia. .,Infectious Disease Department, Austin Health, Melbourne, Australia. .,Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Doherty Institute of Infection and Immunity, Melbourne, Australia.
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Le TT, Nadimpalli M, Wu J, Heaney CD, Stewart JR. Challenges in Estimating Characteristics of Staphylococcus aureus Nasal Carriage Among Humans Enrolled in Surveillance Studies. Front Public Health 2018; 6:163. [PMID: 29911098 PMCID: PMC5992268 DOI: 10.3389/fpubh.2018.00163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Evaluating carriage of Staphylococcus aureus, an opportunistic pathogen of humans and animals capable of causing antibiotic-resistant infections, is epidemiologically important. However, clinical and epidemiological surveillance studies of S. aureus typically rely on characterizing one isolate per individual, which may not represent the actual population diversity in a carrier. The objective of this study was to determine if one isolate is sufficient for determining carrier status of particular strains or characteristics of S. aureus in a healthy (non-hospitalized) human population. We compared spa types, genetic markers (mecA, scn), and antibiotic resistance profiles of 10 S. aureus isolates recovered from a single nasal swab for each of 19 participants (190 isolates total) selected from a cohort of industrial hog operation workers and their household members. Participants included both persistent (n = 10) and intermediate (n = 9) carriers of S. aureus. Among the participants, 17 (89%) carried a single S. aureus spa type intranasally and the other two carried dominant spa types. Less similarity was observed for genes encoded on mobile genetic elements (mecA, scn) and antibiotic resistance profiles. Statistical modeling, based on receiving operating characteristic curves, suggests that three to five isolates may be necessary to accurately assign nasal carriage status for these more variable characteristics. Variability was observed for both persistent and intermediate carriers of S. aureus. These results suggest that surveillance studies that rely on testing one S. aureus isolate are likely to identify predominant spa types but may not fully capture more variable characteristics of S. aureus, including antibiotic resistance. Surveillance studies that rely on testing one isolate may underestimate prevalence of nasal carriage of S. aureus with these more variable characteristics.
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Affiliation(s)
- Thanh-Thao Le
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Maya Nadimpalli
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Jianyong Wu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States
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Loeffler A, Lloyd D. What has changed in canine pyoderma? A narrative review. Vet J 2018; 235:73-82. [DOI: 10.1016/j.tvjl.2018.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 12/28/2022]
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You Y, Song L, Nonyane BAS, Price LB, Silbergeld EK. Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities. PLoS One 2018; 13:e0193820. [PMID: 29509797 PMCID: PMC5839586 DOI: 10.1371/journal.pone.0193820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/20/2018] [Indexed: 01/31/2023] Open
Abstract
New human pathogens can emerge from the livestock-human interface and spread into human populations through many pathways including livestock products. Occupational contact with livestock is a risk factor for exposure to those pathogens and may cause further spreading of those pathogens in the community. The current study used whole genome sequencing to explore nasal Staphylococcus aureus obtained from hog slaughterhouse workers and their community members, all of whom resided in a livestock-dense region in rural North Carolina. Sequence data were analyzed for lineage distribution, pathogenicity-related genomic features, and mobile genetic elements. We observed evidence of nasal S. aureus differences between hog workers and non-workers. Nasal S. aureus from hog workers showed a greater lineage diversity than nasal S. aureus from community residents. Hog worker isolates were less likely to carry the φSa3 prophage and human-specific immune evasion cluster genes than community resident isolates (φSa3 prophage: 54.5% vs. 91.7%, Benjamini-Hochberg (BH) corrected p = 0.035; immune evasion cluster genes: 66.7% vs. 100%, BH p = 0.021). Hog worker isolates had a lower prevalence and diversity of enterotoxins than community resident isolates, particularly lacking the enterotoxin gene cluster (39.4% vs. 70.8%, BH p = 0.125). Moreover, hog worker isolates harbored more diverse antibiotic resistance genes, with a higher prevalence of carriage of multiple resistance genes, than community resident isolates (75.8% vs. 29.2%, BH p = 0.021). Phylogenetic analysis of all ST5 isolates, the most abundant lineage in the collection, further supported separation of isolates from hog workers and non-workers. Together, our observations suggest impact of occupational contact with livestock on nasal S. aureus colonization and highlight the need for further research on the complex epidemiology of S. aureus at the livestock-human interface.
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Affiliation(s)
- Yaqi You
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Li Song
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Bareng A. S. Nonyane
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lance B. Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Ellen K. Silbergeld
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Worby CJ, Lipsitch M, Hanage WP. Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. Am J Epidemiol 2017; 186:1209-1216. [PMID: 29149252 PMCID: PMC5860558 DOI: 10.1093/aje/kwx182] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/18/2017] [Indexed: 12/11/2022] Open
Abstract
Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection control. Genomic data shed new light on transmission dynamics and can be used to identify clusters of individuals likely to be linked by direct transmission. However, identification of individual routes of infection via single genome samples typically remains uncertain. We investigated the potential of deep sequence data to provide greater resolution on transmission routes, via the identification of shared genomic variants. We assessed several easily implemented methods to identify transmission routes using both shared variants and genetic distance, demonstrating that shared variants can provide considerable additional information in most scenarios. While shared-variant approaches identify relatively few links in the presence of a small transmission bottleneck, these links are highly accurate. Furthermore, we propose a hybrid approach that also incorporates phylogenetic distance to provide greater resolution. We applied our methods to data collected during the 2014 Ebola outbreak, identifying several likely routes of transmission. Our study highlights the power of data from deep sequencing of pathogens as a component of outbreak investigation and epidemiologic analyses.
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Affiliation(s)
- Colin J Worby
- Correspondence to Dr. Colin J. Worby, Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (e-mail: )
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Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Sci Transl Med 2017; 9:eaak9745. [PMID: 29070701 PMCID: PMC5683347 DOI: 10.1126/scitranslmed.aak9745] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/24/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022]
Abstract
Genome sequencing has provided snapshots of the transmission of methicillin-resistant Staphylococcus aureus (MRSA) during suspected outbreaks in isolated hospital wards. Scale-up to populations is now required to establish the full potential of this technology for surveillance. We prospectively identified all individuals over a 12-month period who had at least one MRSA-positive sample processed by a routine diagnostic microbiology laboratory in the East of England, which received samples from three hospitals and 75 general practitioner (GP) practices. We sequenced at least 1 MRSA isolate from 1465 individuals (2282 MRSA isolates) and recorded epidemiological data. An integrated epidemiological and phylogenetic analysis revealed 173 transmission clusters containing between 2 and 44 cases and involving 598 people (40.8%). Of these, 118 clusters (371 people) involved hospital contacts alone, 27 clusters (72 people) involved community contacts alone, and 28 clusters (157 people) had both types of contact. Community- and hospital-associated MRSA lineages were equally capable of transmission in the community, with instances of spread in households, long-term care facilities, and GP practices. Our study provides a comprehensive picture of MRSA transmission in a sampled population of 1465 people and suggests the need to review existing infection control policy and practice.
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Affiliation(s)
- Francesc Coll
- London School of Hygiene and Tropical Medicine, London, UK.
| | | | - Michelle S Toleman
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | | | | | | | | | - A Ruth M Kappeler
- Public Health England, London, UK
- Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Public Health England, London, UK
| | - M Estée Török
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, UK.
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
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45
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Woksepp H, Ryberg A, Berglind L, Schön T, Söderman J. Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing. APMIS 2017; 125:1117-1124. [PMID: 28960453 DOI: 10.1111/apm.12753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/23/2017] [Indexed: 01/05/2023]
Abstract
Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.
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Affiliation(s)
- Hanna Woksepp
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden.,Department of Medicine and Optometry, Linnaeus University, Kalmar, Sweden
| | - Anna Ryberg
- Department of Clinical Microbiology, Växjö Central Hospital, Växjö, Sweden
| | - Linda Berglind
- Division of Medical Diagnostics, Region Jönköping County, Jönköping, Sweden
| | - Thomas Schön
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden.,Department of Medicine and Optometry, Linnaeus University, Kalmar, Sweden.,Department Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden.,Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Jan Söderman
- Division of Medical Diagnostics, Region Jönköping County, Jönköping, Sweden
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46
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Clausen M, Edslev S, Andersen P, Clemmensen K, Krogfelt K, Agner T. Staphylococcus aureus
colonization in atopic eczema and its association with filaggrin gene mutations. Br J Dermatol 2017; 177:1394-1400. [DOI: 10.1111/bjd.15470] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2017] [Indexed: 12/29/2022]
Affiliation(s)
- M.‐L. Clausen
- Department of Dermatology Bispebjerg University Hospital Copenhagen Denmark
| | - S.M. Edslev
- Department of Microbiology and Infection Control Statens Serum Institut Copenhagen Denmark
| | - P.S. Andersen
- Department of Microbiology and Infection Control Statens Serum Institut Copenhagen Denmark
- Institute of Veterinary Disease Biology University of Copenhagen Copenhagen Denmark
| | - K. Clemmensen
- Department of Dermatology Bispebjerg University Hospital Copenhagen Denmark
| | - K.A. Krogfelt
- Department of Microbiology and Infection Control Statens Serum Institut Copenhagen Denmark
| | - T. Agner
- Department of Dermatology Bispebjerg University Hospital Copenhagen Denmark
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47
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Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR, Rice D, Mather AE, Parkhill J, Brown SJ, Proby CM, Holden MTG. The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare. J Invest Dermatol 2017; 138:336-343. [PMID: 28951239 PMCID: PMC5780352 DOI: 10.1016/j.jid.2017.09.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/11/2017] [Accepted: 09/12/2017] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. A characteristic of atopic eczema (AE) is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the microevolution of S. aureus colonization, we deep sequenced S. aureus populations from nine children with moderate to severe AE and 18 non-atopic children asymptomatically carrying S. aureus nasally. Colonization by clonal S. aureus populations was observed in both AE patients and control participants, with all but one of the individuals carrying colonies belonging to a single sequence type. Phylogenetic analysis showed that disease flares were associated with the clonal expansion of the S. aureus population, occurring over a period of weeks to months. There was a significant difference in the genetic backgrounds of S. aureus colonizing AE cases versus controls (Fisher exact test, P = 0.03). Examination of intra-host genetic heterogeneity of the colonizing S. aureus populations identified evidence of within-host selection in the AE patients, with AE variants being potentially selectively advantageous for intracellular persistence and treatment resistance.
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Affiliation(s)
- Catriona P Harkins
- School of Medicine, University of St Andrews, St Andrews, UK; Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK.
| | | | - Katarina Oravcová
- School of Medicine, University of St Andrews, St Andrews, UK; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - June Gardner
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - R M Ross Hearn
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - Debbie Rice
- Scottish Children's Research Network, MACH 2 Building, Level 5, Ninewells Hospital, Dundee, UK
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sara J Brown
- Department of Dermatology, Ninewells Hospital, Dundee, UK; Skin Research Group, Division of Cancer Research, School of Medicine, University of Dundee, UK
| | - Charlotte M Proby
- Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK
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48
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Morris DO, Loeffler A, Davis MF, Guardabassi L, Weese JS. Recommendations for approaches to meticillin-resistant staphylococcal infections of small animals: diagnosis, therapeutic considerations and preventative measures.: Clinical Consensus Guidelines of the World Association for Veterinary Dermatology. Vet Dermatol 2017; 28:304-e69. [PMID: 28516494 DOI: 10.1111/vde.12444] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Multiple drug resistance (MDR) in staphylococci, including resistance to the semi-synthetic penicillinase-resistant penicillins such as meticillin, is a problem of global proportions that presents serious challenges to the successful treatment of staphylococcal infections of companion animals. OBJECTIVES The objective of this document is to provide harmonized recommendations for the diagnosis, prevention and treatment of meticillin-resistant staphylococcal infections in dogs and cats. METHODS The authors served as a Guideline Panel (GP) and reviewed the literature available prior to September 2016. The GP prepared a detailed literature review and made recommendations on selected topics. The World Association of Veterinary Dermatology (WAVD) provided guidance and oversight for this process. A draft of the document was presented at the 8th World Congress of Veterinary Dermatology (May 2016) and was then made available via the World Wide Web to the member organizations of the WAVD for a period of three months. Comments were solicited and posted to the GP electronically. Responses were incorporated by the GP into the final document. CONCLUSIONS Adherence to guidelines for the diagnosis, laboratory reporting, judicious therapy (including restriction of use policies for certain antimicrobial drugs), personal hygiene, and environmental cleaning and disinfection may help to mitigate the progressive development and dissemination of MDR staphylococci.
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Affiliation(s)
- Daniel O Morris
- Department of Clinical Studies - Philadelphia, School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
| | - Anette Loeffler
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, UK
| | - Meghan F Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Luca Guardabassi
- Department of Biomedical Sciences, School of Veterinary Medicine, Ross University, Basseterre, St Kitts and Nevis, West Indies
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, N1G 2W1
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49
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Grinberg A, Biggs PJ, Zhang J, Ritchie S, Oneroa Z, O'Neill C, Karkaba A, Velathanthiri NS, Coombs GW. Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection. J Infect 2017; 75:326-335. [PMID: 28782565 DOI: 10.1016/j.jinf.2017.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/29/2017] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains. METHODS We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets. RESULTS Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%). CONCLUSIONS In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk.
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Affiliation(s)
- Alex Grinberg
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand.
| | - Patrick J Biggs
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ji Zhang
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Stephen Ritchie
- University of Auckland, Faculty of Medical and Health Sciences, Molecular Medicine and Pathology, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Zachary Oneroa
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Charlotte O'Neill
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ali Karkaba
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Niluka S Velathanthiri
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, Australia
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50
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Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, Martin V, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom. Genome Med 2017; 9:70. [PMID: 28738847 PMCID: PMC5525225 DOI: 10.1186/s13073-017-0457-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare-associated infections. Here, we describe the value derived from a longitudinal epidemiological and genomic surveillance study of drug-resistant Escherichia coli in a LTCF in the United Kingdom (UK). METHODS Forty-five of 90 (50%) residents were recruited and followed for six months in 2014. Participants were screened weekly for carriage of extended-spectrum beta-lactamase (ESBL) producing E. coli. Participants positive for ESBL E. coli were also screened for ESBL-negative E. coli. Phenotypic antibiotic susceptibility of E. coli was determined using the Vitek2 instrument and isolates were sequenced on an Illumina HiSeq2000 instrument. Information was collected on episodes of clinical infection and antibiotic consumption. RESULTS Seventeen of 45 participants (38%) carried ESBL E. coli. Twenty-three of the 45 participants (51%) had 63 documented episodes of clinical infection treated with antibiotics. Treatment with antibiotics was associated with higher risk of carrying ESBL E. coli. ESBL E. coli was mainly sequence type (ST)131 (16/17, 94%). Non-ESBL E. coli from these 17 cases was more genetically diverse, but ST131 was found in eight (47%) cases. Whole-genome analysis of 297 ST131 E. coli from the 17 cases demonstrated highly related strains from six participants, indicating acquisition from a common source or person-to-person transmission. Five participants carried highly related strains of both ESBL-positive and ESBL-negative ST131. Genome-based comparison of ST131 isolates from the LTCF study participants with ST131 associated with bloodstream infection at a nearby acute hospital and in hospitals across England revealed sharing of highly related lineages between the LTCF and a local hospital. CONCLUSIONS This study demonstrates the power of genomic surveillance to detect multidrug-resistant pathogens and confirm their connectivity within a healthcare network.
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Affiliation(s)
- Hayley J. Brodrick
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Kathy E. Raven
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Teemu Kallonen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Nicholas M. Brown
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Veronique Martin
- British Society for Antimicrobial Chemotherapy, 53 Regent Place, Birmingham, B1 3NJ UK
- Department of Medical Microbiology, Pathology Sciences Building 1, Southmead Hospital, Bristol, BS10 5NB UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge Public Health England Microbiology and Public Health Laboratory, Box 236, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Box 157, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
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