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Dalmieda J, Hitchcock M, Xu J. High diversity within and low but significant genetic differentiation among geographic and temporal populations of the global Streptococcus pneumoniae. Can J Microbiol 2024; 70:226-237. [PMID: 38422492 DOI: 10.1139/cjm-2023-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Streptococcus pneumoniae is the major cause of invasive pneumococcal disease. However, the global population structure remains largely unexplored. In this study, we investigated the spatial and temporal patterns of genetic variation of S. pneumoniae based on archived multilocus sequence typing data from PubMLST.org. Our analyses demonstrated both shared and unique distributions of sequence types (STs) and allele types among regional populations. Among the 17 915 global STs, 36 representing 15 263 isolates were broadly shared among all six continents, consistent with recent clonal dispersal and expansion of this pathogen. The analysis of molecular variance revealed that >96% genetic variations were found within individual regional populations. However, though low (<4%), statistically significant genetic differentiation among regional populations was observed. Comparisons between non-clone-corrected and clone-corrected datasets showed that localized clonal expansion contributed significantly to the observed genetic differentiations among regions. Temporal analyses of the isolates showed that implementation of pneumococcal conjugate vaccine impacted the distributions of STs, but the effect on population structure was relatively limited. Linkage disequilibrium analyses identified evidence for recombination in all continental populations; however, the inferred recombination was not random. We discussed the limitations and implications of our analyses to the global epidemiology and future vaccine developments for S. pneumoniae.
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Affiliation(s)
- Jezreel Dalmieda
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Megan Hitchcock
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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2
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Cella E, Sutcliffe CG, Grant LR, Tso C, Weatherholtz RC, Littlepage S, Becenti L, Jubair M, Simons BC, Harker-Jones M, Reid R, Yazzie D, Santosham M, O'Brien KL, Hammitt LL, Azarian T. Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001-2018. Microb Genom 2024; 10. [PMID: 38498591 DOI: 10.1099/mgen.0.001196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024] Open
Abstract
Background. Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.Methods. We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (n=61) or IPD (n=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.Results. The serotype 3 population structure was characterized by three dominant subpopulations: clade II (n=90, 46.9 %) and clade Iα (n=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (n=43, 22.4 %). The proportion of clade II-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; P<0.001) but not in children (27.3-33.3 %; P=0.84). Over the same period, the proportion of clade II-associated carriage increased; this was statistically significant among children (23.3-52.6 %; P=0.04) but not adults (0-50.0 %, P=0.08).Conclusions. In this setting with persistent serotype 3 IPD and carriage, clade II has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.
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Affiliation(s)
- Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida
| | - Catherine G Sutcliffe
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Lindsay R Grant
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Carol Tso
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Robert C Weatherholtz
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Shea Littlepage
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ladonna Becenti
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mohammad Jubair
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida
| | - Brenna C Simons
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska
| | - Marcella Harker-Jones
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, Alaska
| | - Raymond Reid
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Del Yazzie
- Navajo Epidemiology Center, Window Rock, Arizona
| | - Mathuram Santosham
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katherine L O'Brien
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L Hammitt
- Center for Indigenous Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida
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3
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Dao TH, Echlin H, McKnight A, Marr ES, Junker J, Jia Q, Hayden R, van Opijnen T, Isberg RR, Cooper VS, Rosch JW. Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones. mBio 2024; 15:e0282823. [PMID: 38193698 PMCID: PMC10865975 DOI: 10.1128/mbio.02828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Streptococcus pneumoniae is a major human pathogen of global health concern and the rapid emergence of antibiotic resistance poses a serious public health problem worldwide. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage and has remained rare. Our data indicate that deleterious fitness costs in the mammalian host constrain the emergence of fluoroquinolone resistance both by de novo mutation and recombination. S. pneumoniae was able to circumvent such deleterious fitness costs via the development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, resulting in a fitness benefit during infection of mice treated with fluoroquinolones. These data suggest that the emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes are an important contributor to the evasion of antibiotic-mediated killing.IMPORTANCEThe increasing prevalence of antibiotic resistant bacteria is a major global health concern. While many species have the potential to develop antibiotic resistance, understanding the barriers to resistance emergence in the clinic remains poorly understood. A prime example of this is fluroquinolone resistance in Streptococcus pneumoniae, whereby, despite continued utilization, resistance to this class of antibiotic remains rare. In this study, we found that the predominant pathways for developing resistance to this antibiotic class severely compromised the infectious capacity of the pneumococcus, providing a key impediment for the emergence of resistance. Using in vivo models of experimental evolution, we found that S. pneumoniae responds to repeated fluoroquinolone exposure by modulating key metabolic pathways involved in the generation of redox molecules, which leads to antibiotic treatment failure in the absence of appreciable shifts in resistance levels. These data underscore the complex pathways available to pathogens to evade antibiotic mediating killing via antibiotic tolerance.
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Affiliation(s)
- Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Abigail McKnight
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Enolia S. Marr
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Julia Junker
- Nationales Referenzzentrum für Streptokokken Abteilung Medizinische Mikrobiologie, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ralph R. Isberg
- Deptartment of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Vaughn S. Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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4
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German EL, Nabwera HM, Robinson R, Shiham F, Liatsikos K, Parry CM, McNamara C, Kattera S, Carter K, Howard A, Pojar S, Hamilton J, Matope A, Read JM, Allen SJ, Hill H, Hawcutt DB, Urban BC, Collins AM, Ferreira DM, Nikolaou E. Participant perceptions and experiences of a novel community-based respiratory longitudinal sampling method in Liverpool, UK: A mixed methods feasibility study. PLoS One 2023; 18:e0294133. [PMID: 37943741 PMCID: PMC10635470 DOI: 10.1371/journal.pone.0294133] [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: 07/12/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
Longitudinal, community-based sampling is important for understanding prevalence and transmission of respiratory pathogens. Using a minimally invasive sampling method, the FAMILY Micro study monitored the oral, nasal and hand microbiota of families for 6 months. Here, we explore participant experiences and opinions. A mixed methods approach was utilised. A quantitative questionnaire was completed after every sampling timepoint to report levels of discomfort and pain, as well as time taken to collect samples. Participants were also invited to discuss their experiences in a qualitative structured exit interview. We received questionnaires from 36 families. Most adults and children >5y experienced no pain (94% and 70%) and little discomfort (73% and 47% no discomfort) regardless of sample type, whereas children ≤5y experienced variable levels of pain and discomfort (48% no pain but 14% hurts even more, whole lot or worst; 38% no discomfort but 33% moderate, severe, or extreme discomfort). The time taken for saliva and hand sampling decreased over the study. We conducted interviews with 24 families. Families found the sampling method straightforward, and adults and children >5y preferred nasal sampling using a synthetic absorptive matrix over nasopharyngeal swabs. It remained challenging for families to fit sampling into their busy schedules. Adequate fridge/freezer space and regular sample pick-ups were found to be important factors for feasibility. Messaging apps proved extremely effective for engaging with participants. Our findings provide key information to inform the design of future studies, specifically that self-sampling at home using minimally invasive procedures is feasible in a family context.
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Affiliation(s)
- Esther L. German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Helen M. Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Ryan Robinson
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | - Farah Shiham
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kostas Liatsikos
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom
| | | | | | | | - Katie Carter
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
| | - Ashleigh Howard
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joshua Hamilton
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Agnes Matope
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jonathan M. Read
- Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Stephen J. Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Edward Francis Small Teaching Hospital, Banjul, The Gambia
| | - Helen Hill
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Daniel B. Hawcutt
- Alder Hey Children’s Hospital, Liverpool, United Kingdom
- University of Liverpool, Liverpool, United Kingdom
| | - Britta C. Urban
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea M. Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Daniela M. Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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5
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Wyllie AL, Rots NY, Wijmenga-Monsuur AJ, van Houten MA, Sanders EAM, Trzciński K. Saliva as an alternative sample type for detection of pneumococcal carriage in young children. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001394. [PMID: 37819029 PMCID: PMC10634364 DOI: 10.1099/mic.0.001394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
For children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillance of pneumococcal colonization and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of paired nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular detection methods. Nasopharyngeal and saliva samples were collected from 288 24-month-old children during the autumn/winter, 2012/2013. All samples were first processed by conventional diagnostic culture. Next, DNA extracted from all plate growth was tested by qPCR for the presence of the pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 161/288 (60 %) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture plates. By qPCR, 155/288 (54 %) culture-enriched saliva samples and 187/288 (65 %) nasopharyngeal swabs tested positive. Altogether, 219/288 (76 %) infants tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture (P<0.001) or qPCR detection of saliva (P=0.002). However, 32/219 (15 %) carriers were only positive in saliva, contributing significantly to the overall number of carriers detected (P=0.002). While testing nasopharyngeal swabs by qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes that may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling of study participants.
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Affiliation(s)
- Anne L. Wyllie
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nynke Y. Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Alienke J. Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Elisabeth A. M. Sanders
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Krzysztof Trzciński
- Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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6
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Watkins ER, Kalizang'Oma A, Gori A, Gupta S, Heyderman RS. Factors affecting antimicrobial resistance in Streptococcus pneumoniae following vaccination introduction. Trends Microbiol 2022; 30:1135-1145. [PMID: 35843855 DOI: 10.1016/j.tim.2022.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/13/2023]
Abstract
Streptococcus pneumoniae is a major cause of pneumonia, meningitis, and septicaemia worldwide. Pneumococcal antimicrobial resistance (AMR) has been highlighted by the WHO as an important public health concern, with emerging serotypes showing resistance to multiple antibiotics. Indeed, although the introduction of pneumococcal conjugate vaccines (PCVs) has been associated with an overall decline in pneumococcal AMR, there have been increases in prevalence of potentially disease-causing AMR serotypes not targeted by vaccination. Here, we discuss a variety of evolutionary mechanisms at the host, pathogen, and environmental levels that may contribute to changes in the prevalence of pneumococcal AMR in the post-vaccination era. The relative importance of these factors may vary by population, pneumococcal lineage, geography, and time, leading to the complex relationship between vaccination, antibiotic use, and AMR.
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Affiliation(s)
| | - Akuzike Kalizang'Oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
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7
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Stanojković A, Skoupý S, Škaloud P, Dvořák P. High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genus Laspinema (cyanobacteria). Front Microbiol 2022; 13:977454. [PMID: 36160208 PMCID: PMC9500459 DOI: 10.3389/fmicb.2022.977454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.
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Affiliation(s)
| | - Svatopluk Skoupý
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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8
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Preska Steinberg A, Lin M, Kussell E. Core genes can have higher recombination rates than accessory genes within global microbial populations. eLife 2022; 11:78533. [PMID: 35801696 PMCID: PMC9444244 DOI: 10.7554/elife.78533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/30/2022] [Indexed: 11/24/2022] Open
Abstract
Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, assessing the impact of homologous recombination on accessory genes which are only present in a subset of strains of a given species remains challenging due to their complex phylogenetic relationships. Quantifying homologous recombination for accessory genes (which are important for niche-specific adaptations) in comparison to core genes (which are present in all strains and have essential functions) is critical to understanding how selection acts on variation to shape species diversity and genome structures of bacteria. Here, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome using >100,000 whole genome sequences from Streptococcus pneumoniae and several additional species. By analyzing diverse sets of sequence clusters, we show that core genes often have higher recombination rates than accessory genes, and for some bacterial species the associated effect sizes for these differences are pronounced. In a subset of species, we find that gene frequency and homologous recombination rate are positively correlated. For S. pneumoniae and several additional species, we find that while the recombination rate is higher for the core genome, the mutational divergence is lower, indicating that divergence-based homologous recombination barriers could contribute to differences in recombination rates between the core and accessory genome. Homologous recombination may therefore play a key role in increasing the efficiency of selection in the most conserved parts of the genome.
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Affiliation(s)
| | - Mingzhi Lin
- Department of Biology, New York University, New York, United States
| | - Edo Kussell
- Department of Biology, New York University, New York, United States
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9
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Chaguza C, Yang M, Jacques LC, Bentley SD, Kadioglu A. Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms. Trends Microbiol 2022; 30:581-592. [PMID: 34949516 PMCID: PMC7613904 DOI: 10.1016/j.tim.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Darwin College, University of Cambridge, Silver Street, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
| | - Laura C Jacques
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
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10
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Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A, McGee L, Breiman RF, Klugman KP, Kadioglu A, Everett DB, Mackenzie G, Croucher NJ, Roca A, Kwambana-Adams BA, Antonio M, Bentley SD. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci. Genome Biol Evol 2022; 14:evac052. [PMID: 35439297 PMCID: PMC9048925 DOI: 10.1093/gbe/evac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa. We found no consensus evidence that certain genomic variation is overrepresented among isolates from patients with invasive disease than asymptomatic carriage. Overall, the genomic variation explained negligible phenotypic variability, suggesting a minimal effect on the disease status. Furthermore, changes in lineage distribution were seen with lineages replacing each other over time, highlighting the importance of continued pathogen surveillance. Our findings suggest that the hyper-invasiveness is an intrinsic property of the serotype 1 strains, not specific for a "disease-associated" subpopulation disproportionately harboring unique genomic variation.
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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
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - 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
| | - Rebecca A. Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Archibald Worwui
- 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, GA, USA
| | - Robert F. Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dean B. Everett
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Grant Mackenzie
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Murdoch Children’s Research Institute, Parkville, Melbourne, VIC, Australia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anna Roca
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, 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
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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11
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Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microb Genom 2022; 8. [PMID: 35225216 PMCID: PMC8942026 DOI: 10.1099/mgen.0.000753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mitis group Streptococcus are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in S. pneumoniae, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group Streptococcus.
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Affiliation(s)
- Sophie Belman
- Department of Genetics, University of Cambridge, Cambridge, UK
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Chrispin Chaguza
- Yale School of Medicine, New Haven, CT, USA
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie Lo
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
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12
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Comparative pangenome analysis of capsulated Haemophilus influenzae serotype f highlights their high genomic stability. Sci Rep 2022; 12:3189. [PMID: 35210526 PMCID: PMC8873416 DOI: 10.1038/s41598-022-07185-5] [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: 11/18/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Haemophilus influenzae is an opportunistic pathogen adapted to the human respiratory tract. Non-typeable H. influenzae are highly heterogeneous, but few studies have analysed the genomic variability of capsulated strains. This study aims to examine the genetic diversity of 37 serotype f isolates from the Netherlands, Portugal, and Spain, and to compare all capsulated genomes available on public databases. Serotype f isolates belonged to CC124 and shared few single nucleotide polymorphisms (SNPs) (n = 10,999), but a high core genome (> 80%). Three main clades were identified by the presence of 75, 60 and 41 exclusive genes for each clade, respectively. Multi-locus sequence type analysis of all capsulated genomes revealed a reduced number of clonal complexes associated with each serotype. Pangenome analysis showed a large pool of genes (n = 6360), many of which were accessory genome (n = 5323). Phylogenetic analysis revealed that serotypes a, b, and f had greater diversity. The total number of SNPs in serotype f was significantly lower than in serotypes a, b, and e (p < 0.0001), indicating low variability within the serotype f clonal complexes. Capsulated H. influenzae are genetically homogeneous, with few lineages in each serotype. Serotype f has high genetic stability regardless of time and country of isolation.
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13
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Wu X, Zhao S, Jiang Y, Xiang X, Ge L, Chen Q, Wang Y, Vidal JE, Yu Y. Effect of pneumococcal conjugate vaccine availability on Streptococcus pneumoniae infections and genetic recombination in Zhejiang, China from 2009 to 2019. Emerg Microbes Infect 2022; 11:606-615. [PMID: 35135440 PMCID: PMC8865111 DOI: 10.1080/22221751.2022.2040921] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Pneumococcal pneumonia is one of the main reasons for child death worldwide. Pneumococcal conjugate vaccines (PCVs) are considered the most effective strategy for pneumococcal disease (PD) prevention, but how a pause in PCV vaccination affects the prevalence of PD or the genetic evolution of Streptococcus pneumoniae genetic evolution is unknown. Based on the unique PCV introduction timeline (vaccine unavailable during April 2015-April 2017) in China, we aimed to evaluate the effect of interrupted PCV availability on PD and pneumococcal genome variation. Pneumococcal isolates (n = 386) were collected retrospectively from eight sites in Zhejiang, China from 2009 to 2019 in which 184 pathogenic (isolates from sterile and infection sites) strains were identified. An interrupted time series analysis was conducted to estimate changes in PD and the recombination frequency of whole genome-sequenced strains was estimated via SNP calling. We found that both PD and pneumococcal genome variation were affected by interrupted PCV availability. The proportion (∼70%) of vaccine-type pneumococcal LRTI (VT-LRTI) in all LRTI cases decreased to ∼30% in the later PCV7 period and rebounded to ∼70% in children once PCV7 became unavailable in April 2015 (p = 0.0007). The major clone CC271 strains showed slowed (p = 0.0293) recombination frequency (decreased from 2.82 ± 1.16–0.72 ± 0.21) upon PCV removal. Our study illustrated for the first time that VT-LRTI fluctuated upon interrupted vaccine availability in China and causing a decreased of recombination frequency of vaccine types. Promoting a nationwide continuous vaccination programme and strengthening S. pneumoniae molecular epidemiology surveillance are essential for PD prevention.
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Affiliation(s)
- Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Shanshan Zhao
- Department of Clinical Laboratory, Shangyu People's Hospital, Shaoxing 312300, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, Zhejiang, China
| | - Lihong Ge
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health. Hangzhou 310052, Zhejiang, China
| | - Qiong Chen
- Department of Clinical laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang, China
| | - Yanfei Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Jorge E Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, Zhejiang, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
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14
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Lee IPA, Andam CP. Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis. Sci Rep 2022; 12:1515. [PMID: 35087075 PMCID: PMC8795270 DOI: 10.1038/s41598-022-04995-5] [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: 07/13/2021] [Accepted: 01/05/2022] [Indexed: 11/08/2022] Open
Abstract
Streptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.
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Affiliation(s)
| | - Cheryl P Andam
- University at Albany, State University of New York, New York, 12222, USA.
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15
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Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microb Genom 2021; 7. [PMID: 34550067 PMCID: PMC8715442 DOI: 10.1099/mgen.0.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, World Health Organization, Collaborating Centre for New Vaccines Surveillance, Banjul, Gambia
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Atlanta, GA, USA
| | - David Goldblatt
- University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | | | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
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16
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Zeng HL, Aurell E. Inferring genetic fitness from genomic data. Phys Rev E 2021; 101:052409. [PMID: 32575265 DOI: 10.1103/physreve.101.052409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/04/2020] [Indexed: 11/07/2022]
Abstract
The genetic composition of a naturally developing population is considered as due to mutation, selection, genetic drift, and recombination. Selection is modeled as single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). The problem is posed to infer epistatic fitness from population-wide whole-genome data from a time series of a developing population. We generate such data in silico and show that in the quasilinkage equilibrium phase of Kimura, Neher, and Shraiman, which pertains at high enough recombination rates and low enough mutation rates, epistatic fitness can be quantitatively correctly inferred using inverse Ising-Potts methods.
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Affiliation(s)
- Hong-Li Zeng
- School of Science, and New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing 210023, China.,Nordita, Royal Institute of Technology, and Stockholm University, SE-10691 Stockholm, Sweden
| | - Erik Aurell
- KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.,Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 Kraków, Poland
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17
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Tsang RSW. A Narrative Review of the Molecular Epidemiology and Laboratory Surveillance of Vaccine Preventable Bacterial Meningitis Agents: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae and Streptococcus agalactiae. Microorganisms 2021; 9:449. [PMID: 33671611 PMCID: PMC7926440 DOI: 10.3390/microorganisms9020449] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
This narrative review describes the public health importance of four most common bacterial meningitis agents, Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, and S. agalactiae (group B Streptococcus). Three of them are strict human pathogens that normally colonize the nasopharynx and may invade the blood stream to cause systemic infections and meningitis. S. agalactiae colonizes the genito-gastrointestinal tract and is an important meningitis agent in newborns, but also causes invasive infections in infants or adults. These four bacteria have polysaccharide capsules that protect them against the host complement defense. Currently licensed conjugate vaccines (against S. pneumoniae, H. influenza, and N. meningitidis only but not S. agalactiae) can induce protective serum antibodies in infants as young as two months old offering protection to the most vulnerable groups, and the ability to eliminate carriage of homologous serotype strains in vaccinated subjects lending further protection to those not vaccinated through herd immunity. However, the serotype-specific nature of these vaccines have driven the bacteria to adapt by mechanisms that affect the capsule antigens through either capsule switching or capsule replacement in addition to the possibility of unmasking of strains or serotypes not covered by the vaccines. The post-vaccine molecular epidemiology of vaccine-preventable bacterial meningitis is discussed based on findings obtained with newer genomic laboratory surveillance methods.
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Affiliation(s)
- Raymond S W Tsang
- Laboratory for Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
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18
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Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021; 22:39. [PMID: 33413118 PMCID: PMC7792055 DOI: 10.1186/s12864-020-07316-0] [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: 07/19/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype. RESULTS The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa. CONCLUSIONS The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.
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Affiliation(s)
- Néhémie Nzoyikorera
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco.
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco.
| | - Idrissa Diawara
- Faculty of Sciences and Health Techniques, Mohammed VI University of Health Sciences (UM6SS) of Casablanca, Casablanca, Morocco
| | - Pablo Fresia
- Institut Pasteur de Montevideo, Pasteur + INIA Joint Unit (UMPI), Montevideo, Uruguay
- Institut Pasteur de Montevideo, Microbial Genomics Laboratory, Montevideo, Uruguay
| | - Fakhreddine Maaloum
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Katfy
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Kaotar Nayme
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Mossaab Maaloum
- Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Houria Belabess
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Zerouali
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
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19
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Jespersen MG, Lacey JA, Tong SYC, Davies MR. Global genomic epidemiology of Streptococcus pyogenes. INFECTION GENETICS AND EVOLUTION 2020; 86:104609. [PMID: 33147506 DOI: 10.1016/j.meegid.2020.104609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 02/04/2023]
Abstract
Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide causing a range of clinical manifestations in humans. Colonizing a range of ecological niches within its sole host, the human, is key to the ability of this opportunistic pathogen to cause direct and post-infectious manifestations. The expansion of genome sequencing capabilities and data availability over the last decade has led to an improved understanding of the evolutionary dynamics of this pathogen within a global framework where epidemiological relationships and evolutionary mechanisms may not be universal. This review uses the recent publication by Davies et al., 2019 as an updated global framework to address S. pyogenes population genomics, highlighting how genomics is being used to gain new insights into evolutionary processes, transmission pathways, and vaccine design.
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Affiliation(s)
- Magnus G Jespersen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, VIC, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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20
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Hanachi M, Kiran A, Cornick J, Harigua-Souiai E, Everett D, Benkahla A, Souiai O. Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13. Bioinform Biol Insights 2020; 14:1177932220962106. [PMID: 33088176 PMCID: PMC7545519 DOI: 10.1177/1177932220962106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus (cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity.
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Affiliation(s)
- Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Anmol Kiran
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.,Departement of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology-LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Dean Everett
- Queens Research Institute, University of Edinburgh, Edinburgh, UK.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.,Institut Supérieur des Technologies Médicales de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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21
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Golden AR, Baxter MR, Davidson RJ, Martin I, Demczuk W, Mulvey MR, Karlowsky JA, Hoban DJ, Zhanel GG, Adam HJ. Comparison of antimicrobial resistance patterns in Streptococcus pneumoniae from respiratory and blood cultures in Canadian hospitals from 2007-16. J Antimicrob Chemother 2020; 74:iv39-iv47. [PMID: 31505644 DOI: 10.1093/jac/dkz286] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To compare the epidemiology and antimicrobial susceptibility patterns of Streptococcus pneumoniae collected from respiratory and blood culture samples in Canada between 2007 and 2016. METHODS S. pneumoniae strains were obtained from Canadian hospitals as part of the ongoing national surveillance study, CANWARD. Isolates were serotyped using the Quellung method. Antimicrobial susceptibility testing was performed using the CLSI broth microdilution method. MDR and XDR were defined as resistance to three or more and five or more classes of antimicrobials, respectively. RESULTS Of the 2581 S. pneumoniae isolates collected, 1685 (65.3%) and 896 (34.7%) were obtained from respiratory and blood samples, respectively. Respiratory isolates demonstrated lower rates of antimicrobial susceptibility than blood isolates to penicillin, ceftriaxone, clarithromycin, clindamycin, doxycycline and trimethoprim/sulfamethoxazole (P ≤ 0.03). From 2007 to 2016, invasive isolates demonstrated trends towards increasing penicillin susceptibility and decreasing clarithromycin susceptibility. MDR was significantly higher in respiratory S. pneumoniae compared with blood (9.1% versus 4.5%, P < 0.0001). Serotypes 11A, 16F, 19F, 23A/B/F, 34, 35B and non-typeable strains were more commonly isolated from respiratory specimens, while 4, 5, 7F, 8, 12F, 14 and 19A were more commonly invasive serotypes. Numerous serotypes, including 3 and 22F, were isolated frequently from both specimen sources. CONCLUSIONS S. pneumoniae from respiratory samples demonstrated lower antimicrobial susceptibilities and higher MDR in a greater diversity of serotypes than isolates obtained from blood. Many serotypes were associated with one specific specimen source, while others were associated with both; genetic characterization is necessary to elucidate the specific factors influencing the ability of these serotypes to commonly cause both invasive and non-invasive disease.
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Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Ross J Davidson
- Queen Elizabeth II Health Sciences Centre, Dalhousie University, 5788 University Avenue, Halifax, Nova Scotia, Canada
| | - Irene Martin
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - Walter Demczuk
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Department of Clinical Microbiology, Health Sciences Centre, Diagnostic Services - Shared Health Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
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22
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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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23
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Rodgers E, Bentley SD, Borrow R, Bratcher HB, Brisse S, Brueggemann AB, Caugant DA, Findlow J, Fox L, Glennie L, Harrison LH, Harrison OB, Heyderman RS, van Rensburg MJ, Jolley KA, Kwambana-Adams B, Ladhani S, LaForce M, Levin M, Lucidarme J, MacAlasdair N, Maclennan J, Maiden MCJ, Maynard-Smith L, Muzzi A, Oster P, Rodrigues CMC, Ronveaux O, Serino L, Smith V, van der Ende A, Vázquez J, Wang X, Yezli S, Stuart JM. The global meningitis genome partnership. J Infect 2020; 81:510-520. [PMID: 32615197 DOI: 10.1016/j.jinf.2020.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 10/24/2022]
Abstract
Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data.
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Affiliation(s)
- Elizabeth Rodgers
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK.
| | - Stephen D Bentley
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Ray Borrow
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Angela B Brueggemann
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jamie Findlow
- Pfizer Limited, Walton Oaks, Dorking Road, Tadworth, Surrey KT20 7NS, UK
| | - LeAnne Fox
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Linda Glennie
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Robert S Heyderman
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | | | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - Shamez Ladhani
- Public Health England, Immunisation and Countermeasures Division, 61 Colindale Avenue, London NW9 5EQ, UK; Paediatric Infectious Diseases Research Group (PIDRG), St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Jay Lucidarme
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | - Neil MacAlasdair
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Jenny Maclennan
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | | | | | | | | | | | | | | | - Vinny Smith
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam UMC and, the Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | | | - Xin Wang
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Saber Yezli
- Ministry of Health, The Global Centre for Mass Gatherings Medicine, Riyadh, Saudi Arabia
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24
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Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJ. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. SCIENCE ADVANCES 2020; 6:eaaz6137. [PMID: 32671212 PMCID: PMC7314567 DOI: 10.1126/sciadv.aaz6137] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in Streptococcus pneumoniae. We analyze microbiological, genomic, and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is little evidence of HGT playing a major role in determining resistance frequencies. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.
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Affiliation(s)
- Sonja Lehtinen
- Big Data Institute, University of Oxford, Oxford, UK
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Claire Chewapreecha
- Wellcome Sanger Institute, Hinxton, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - John Lees
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nicholas J. Croucher
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | | | - Rafał J. Mostowy
- Big Data Institute, University of Oxford, Oxford, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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25
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Streptococcus pneumoniae Elaborates Persistent and Prolonged Competent State during Pneumonia-Derived Sepsis. Infect Immun 2020; 88:IAI.00919-19. [PMID: 31988172 DOI: 10.1128/iai.00919-19] [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] [Received: 12/06/2019] [Accepted: 01/21/2020] [Indexed: 01/18/2023] Open
Abstract
The competence regulon of pneumococcus regulates both genetic transformation and virulence. However, competence induction during host infection has not been examined. By using the serotype 2 strain D39, we transcriptionally fused the firefly luciferase (luc) to competence-specific genes and spatiotemporally monitored the competence development in a mouse model of pneumonia-derived sepsis. In contrast to the universally reported short transient burst of competent state in vitro, the naturally developed competent state was prolonged and persistent during pneumonia-derived sepsis. The competent state began at approximately 20 h postinfection (hpi) and facilitated systemic invasion and sepsis development and progressed in different manners. In some mice, acute pneumonia quickly led to sepsis and death, accompanied by increasing intensity of the competence signal. In the remaining mice, pneumonia lasted longer, with the competence signal decreasing at first but increasing as the infection became septic. The concentration of pneumococcal inoculum (1 × 106 to 1 × 108 CFU/mouse) and postinfection lung bacterial burden did not appreciably impact the kinetics of competence induction. Exogenously provided competence stimulating peptide 1 (CSP1) failed to modulate the onset kinetics of competence development in vivo The competence shutoff regulator DprA was highly expressed during pneumonia-derived sepsis but failed to turn off the competent state in mice. Competent D39 bacteria propagated the competence signal through cell-to-cell contact rather than the classically described quorum-sensing mechanism. Finally, clinical pneumococcal strains of different serotypes were also able to develop natural competence during pneumonia-derived sepsis.
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26
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Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ, Holden MTG, David S, Giffard PM, Worthing KA, Seale AC, Berkley JA, Harris SR, Rivera-Hernandez T, Berking O, Cork AJ, Torres RSLA, Lithgow T, Strugnell RA, Bergmann R, Nitsche-Schmitz P, Chhatwal GS, Bentley SD, Fraser JD, Moreland NJ, Carapetis JR, Steer AC, Parkhill J, Saul A, Williamson DA, Currie BJ, Tong SYC, Dougan G, Walker MJ. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics. Nat Genet 2019; 51:1035-1043. [PMID: 31133745 DOI: 10.1038/s41588-019-0417-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 04/10/2019] [Indexed: 11/09/2022]
Abstract
Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies.
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Affiliation(s)
- Mark R Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia. .,The Wellcome Trust Sanger Institute, Hinxton, UK. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
| | - Liam McIntyre
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ankur Mutreja
- The Wellcome Trust Sanger Institute, Hinxton, UK.,GSK Vaccines Institute for Global Health, Siena, Italy
| | - Jake A Lacey
- Doherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Rebecca J Towers
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Sebastián Duchêne
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Pierre R Smeesters
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pediatrics, Queen Fabiola Childrens University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Hannah R Frost
- Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pediatrics, Queen Fabiola Childrens University Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - David J Price
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Matthew T G Holden
- The Wellcome Trust Sanger Institute, Hinxton, UK.,School of Medicine, University of St Andrews, St Andrews, UK
| | - Sophia David
- The Wellcome Trust Sanger Institute, Hinxton, UK
| | - Philip M Giffard
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Kate A Worthing
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | - James A Berkley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tania Rivera-Hernandez
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Olga Berking
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda J Cork
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Rosângela S L A Torres
- Laboratory of Bacteriology, Epidemiology Laboratory and Disease Control Division, Laboratório Central do Estado do Paraná, Curitiba, Brazil.,Department of Medicine, Universidade Positivo, Curitiba, Brazil
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Rene Bergmann
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | | | - John D Fraser
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jonathan R Carapetis
- Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, Western Australia, Australia
| | - Andrew C Steer
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | | | - Allan Saul
- GSK Vaccines Institute for Global Health, Siena, Italy
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Bart J Currie
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Steven Y C Tong
- Doherty Department, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Menzies School of Health Research, Darwin, Northern Territory, Australia.,Victorian Infectious Disease Service, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
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27
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Abstract
The polysaccharide capsule of Streptococcus pneumoniae is the dominant surface structure of the organism and plays a critical role in virulence, principally by interfering with host opsonophagocytic clearance mechanisms. The capsule is the target of current pneumococcal vaccines, but there are 98 currently recognised polysaccharide serotypes and protection is strictly serotype-specific. Widespread use of these vaccines is driving changes in serotype prevalence in both carriage and disease. This chapter summarises current knowledge on the role of the capsule and its regulation in pathogenesis, the mechanisms of capsule synthesis, the genetic basis for serotype differences, and provides insights into how so many structurally distinct capsular serotypes have evolved. Such knowledge will inform ongoing refinement of pneumococcal vaccination strategies.
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28
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Gao CY, Cecconi F, Vulpiani A, Zhou HJ, Aurell E. DCA for genome-wide epistasis analysis: the statistical genetics perspective. Phys Biol 2019; 16:026002. [PMID: 30605896 DOI: 10.1088/1478-3975/aafbe0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the quasi-linkage equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of clonal competition. We discuss how the exponential (Potts model) distributions emerge in QLE, and compare couplings to correlations obtained in a study of about 3000 genomes of the human pathogen Streptococcus pneumoniae.
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Affiliation(s)
- Chen-Yi Gao
- Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China. School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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29
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Rendueles O, de Sousa JAM, Bernheim A, Touchon M, Rocha EPC. Genetic exchanges are more frequent in bacteria encoding capsules. PLoS Genet 2018; 14:e1007862. [PMID: 30576310 PMCID: PMC6322790 DOI: 10.1371/journal.pgen.1007862] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/07/2019] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred pan-genomes and thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. We found that bacteria encoding capsules have larger pan-genomes, higher rates of horizontal gene transfer, and higher rates of homologous recombination in their core genomes. Accordingly, genomes encoding capsules have more plasmids, conjugative elements, transposases, prophages, and integrons. Furthermore, capsular loci are frequent in plasmids, and can be found in prophages. These results are valid for Bacteria, independently of their ability to be naturally transformable. Since we have shown previously that capsules are commonly present in nosocomial pathogens, we analysed their co-occurrence with antibiotic resistance genes. Genomes encoding capsules have more antibiotic resistance genes, especially those encoding efflux pumps, and they constitute the majority of the most worrisome nosocomial bacteria. We conclude that bacteria with capsule systems are more genetically diverse and have fast-evolving gene repertoires, which may further contribute to their success in colonizing novel niches such as humans under antibiotic therapy. Previous works showed that bacteria encoding capsules are better colonizers and are dominant in most environments suggesting a positive role for capsules in the genetic diversification of bacteria. Yet, it has been repeatedly suggested, based almost exclusively studies in few model species, that such bacteria are less diverse and engage in fewer genetic exchanges. Here, we reverse the current paradigm and show that bacteria encoding capsules have larger and more diverse gene repertoires, which change faster by horizontal gene transfer and recombination. Our study alters the traditional view of the capsule as a barrier to gene flow and raises novel questions about the role of capsules in bacterial adaptation.
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Affiliation(s)
- Olaya Rendueles
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
- * E-mail:
| | - Jorge A. Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- UMR 3525, CNRS, Paris, France
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Kayansamruaj P, Soontara C, Unajak S, Dong HT, Rodkhum C, Kondo H, Hirono I, Areechon N. Comparative genomics inferred two distinct populations of piscine pathogenic Streptococcus agalactiae, serotype Ia ST7 and serotype III ST283, in Thailand and Vietnam. Genomics 2018; 111:1657-1667. [PMID: 30453061 DOI: 10.1016/j.ygeno.2018.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 11/16/2022]
Abstract
The genomes of Streptococcus agalactiae (group B streptococcus; GBS) collected from diseased fish in Thailand and Vietnam over a nine-year period (2008-2016) were sequenced and compared (n = 21). Based on capsular serotype and multilocus sequence typing (MLST), GBS isolates are divided into 2 groups comprised of i) serotype Ia; sequence type (ST)7 and ii) serotype III; ST283. Population structure inferred by core genome (cg)MLST and Bayesian clustering analysis also strongly indicated distribution of two GBS populations in both Thailand and Vietnam. Deep phylogenetic analysis implied by CRISPR array's spacer diversity was able to cluster GBS isolates according to their temporal and geographic origins, though ST7 has varying CRISPR1-spacer profiles when compared to ST283 strains. Based on overall genotypic features, Thai ST283 strains were closely related to the Singaporean ST283 strain causing foodborne illness in humans in 2015, thus, signifying zoonotic potential of this GBS population in the country.
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Affiliation(s)
| | - Chayanit Soontara
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ha Thanh Dong
- Department of Science, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Channarong Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Research Unit of Fish Infectious Diseases (RU-FIDs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Nontawith Areechon
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
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Hiller NL, Sá-Leão R. Puzzling Over the Pneumococcal Pangenome. Front Microbiol 2018; 9:2580. [PMID: 30425695 PMCID: PMC6218428 DOI: 10.3389/fmicb.2018.02580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.
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Affiliation(s)
- N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Dube FS, Ramjith J, Gardner-Lubbe S, Nduru P, Robberts FJL, Wolter N, Zar HJ, Nicol MP. Longitudinal characterization of nasopharyngeal colonization with Streptococcus pneumoniae in a South African birth cohort post 13-valent pneumococcal conjugate vaccine implementation. Sci Rep 2018; 8:12497. [PMID: 30131607 PMCID: PMC6104038 DOI: 10.1038/s41598-018-30345-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage and impact on health. We longitudinally investigated pneumococcal carriage dynamics in infants. Pneumococcal isolates were obtained from nasopharyngeal (NP) swabs collected 2-weekly from 137 infants enrolled from birth through their first year of life. Pneumococci were serotyped by sequetyping, confirmed by Quellung. Pneumococci were isolated from 54% (1809/3331) of infants. Median time to first acquisition was 63 days. Serotype-specific acquisition rates ranged from 0.01 to 0.88 events/child-year and did not differ between PCV13 and non-PCV13 serotypes (0.11 events/child-year [95% CI 0.07-0.18] vs. 0.11 events/child-year [95% CI 0.06-0.18]). There was no difference in carriage duration between individual PCV13 and non-PCV13 serotypes (40.6 days [95% CI 31.9-49.4] vs. 38.6 days [95% CI 35.1-42.1]), however cumulatively the duration of carriage of non-PCV13 serotypes was greater than PCV13 serotypes (141.2 days (95% CI 126.6-155.8) vs. 30.7 days (95% CI 22.3-39.0). Frequently carried PCV13 serotypes included 19F, 9V, 19A and 6A, while non-PCV13 serotypes included 15B/15C, 21, 10A, 16F, 35B, 9N and 15A. Despite high immunization coverage in our setting, PCV13 serotypes remain in circulation in this cohort, comprising 22% of isolates. Individual PCV13 serotypes were acquired, on average, at equivalent rate to non-PCV13 serotypes, and carried for a similar duration, although the most common non-PCV13 serotypes were more frequently acquired than PCV13 serotypes.
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Affiliation(s)
- Felix S Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa. .,Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jordache Ramjith
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistical Sciences, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Polite Nduru
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - F J Lourens Robberts
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis (CRDM), National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.,SAMRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.,Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Cowley LA, Petersen FC, Junges R, Jimson D. Jimenez M, Morrison DA, Hanage WP. Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet 2018; 14:e1007410. [PMID: 29897968 PMCID: PMC6016952 DOI: 10.1371/journal.pgen.1007410] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/25/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent ‘target’ cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs. Experiments designed to explore the effect of environment on large scale recombination events used saturating purified donor DNA, short-term cell assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22 recombinants for each environment mapped all SNPs that were identical between the recombinant and the donor but not the recipient. The mean recombination event size was found to be significantly larger in cell-to-cell contact cultures (4051 bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with saturating DNA). Up to 5.8% of the genome was transferred, through 20 recombination events, to a single recipient, with the largest single event incorporating 29,971 bp. We also found that some recombination events are clustered, that these clusters are more likely to occur in cell-to-cell contact environments, and that they cause significantly increased linkage of genes as far apart as 60,000 bp. We conclude that pneumococcal evolution through homologous recombination is more likely to occur on a larger scale in environments that permit cell-to-cell contact. Bacteria shuffle their genes far less often than humans do and genes or traits are more directly linked with the singular bacterial parent cell rather than the two parents that are involved in sexual reproduction. However, bacteria do occasionally have sex in the form of homologous recombination by taking up external DNA and incorporating it into their genomes. This happens far less regularly than sexual reproduction happens in human generations but is a known way that bacteria undergo ‘Horizontal gene transfer’. This means that genes can be acquired without being inherited. In this study we show that this form of horizontal gene transfer is more likely to happen in certain environments over others in Streptococcus pneumoniae. In particular, we show that this is more likely to happen in environments that closely mirror the nasopharynx which is the natural habitat of S. pneumoniae.
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Affiliation(s)
- Lauren A. Cowley
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States of America
- * E-mail:
| | | | - Roger Junges
- Department of Oral Biology, University of Oslo, Oslo, Norway
| | - Med Jimson D. Jimenez
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States of America
| | - Donald A. Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States of America
| | - William P. Hanage
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States of America
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Stress Suppressor Screening Leads to Detection of Regulation of Cyclic di-AMP Homeostasis by a Trk Family Effector Protein in Streptococcus pneumoniae. J Bacteriol 2018; 200:JB.00045-18. [PMID: 29483167 DOI: 10.1128/jb.00045-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/21/2018] [Indexed: 02/07/2023] Open
Abstract
Cyclic di-AMP (c-di-AMP) is a newly discovered bacterial second messenger. However, regulation of c-di-AMP homeostasis is poorly understood. In Streptococcus pneumoniae, a sole diadenylate cyclase, CdaA, produces c-di-AMP and two phosphodiesterases, Pde1 and Pde2, cleave the signaling dinucleotide. To expand our knowledge of the pneumococcal c-di-AMP signaling network, we performed whole-genome sequencing of Δpde1 Δpde2 heat shock suppressors. In addition to their effects on surviving heat shock, these suppressor mutations restored general stress resistance and improved growth in rich medium. Mutations in CdaA or in the potassium transporter TrkH paired with an insertion leading to a frameshift at the C terminus of CdaA significantly reduced c-di-AMP levels. These observations indicate that the elevated c-di-AMP levels in the Δpde1 Δpde2 mutant enhance susceptibility of S. pneumoniae to the stress conditions. Interestingly, we have previously shown that TrkH complexes with a Trk family c-di-AMP-binding protein, CabP, to mediate potassium uptake. In this study, we found that deletion of cabP significantly reduced pneumococcal c-di-AMP levels. This is the first observation that a c-di-AMP effector protein modulates bacterial c-di-AMP homeostasis.IMPORTANCE Second messengers, including c-di-AMP, are prevalent among bacterial species. In S. pneumoniae, c-di-AMP phosphodiesterase-encoding gene null mutants are attenuated during mouse models of infection, but the role of c-di-AMP signaling in pneumococcal pathogenesis is enigmatic. In this work, we found that heat shock suppressor mutations converge on undermining c-di-AMP toxicity by changing intracellular c-di-AMP concentrations. These mutations improve the growth and restore the stress response generally in c-di-AMP phosphodiesterase-deficient pneumococci, thereby demonstrating the essentiality for tight regulation of c-di-AMP homeostasis in order to respond to stress. Likewise, this work demonstrates that a c-di-AMP effector protein, CabP, affects c-di-AMP homeostasis, which provides new perception into c-di-AMP regulation. This study has implications for c-di-AMP-producing bacteria since many species contain CabP homologs.
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Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens. BMC Genomics 2018; 19:379. [PMID: 29788909 PMCID: PMC5964661 DOI: 10.1186/s12864-018-4771-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022] Open
Abstract
Background Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome. Results Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis. Conclusions The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.
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A Mechanism of Unidirectional Transformation, Leading to Antibiotic Resistance, Occurs within Nasopharyngeal Pneumococcal Biofilm Consortia. mBio 2018; 9:mBio.00561-18. [PMID: 29764945 PMCID: PMC5954218 DOI: 10.1128/mbio.00561-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2Tet and S4Str in a bioreactor simulating the human nasopharynx led to the generation of SpnTet/Str recombinants. Double-resistant pneumococci emerged soon after 4 h postinoculation at a recombination frequency (rF) of 2.5 × 10−4 while peaking after 8 h at a rF of 1.1 × 10−3. Acquisition of antibiotic resistance genes by transformation was confirmed by treatment with DNase I. A high-throughput serotyping method demonstrated that all double-resistant pneumococci belonged to one serotype lineage (S2Tet/Str) and therefore that unidirectional transformation had occurred. Neither heterolysis nor availability of DNA for transformation was a factor for unidirectional transformation given that the density of each strain and extracellular DNA (eDNA) released from both strains were similar. Unidirectional transformation occurred regardless of the antibiotic-resistant gene carried by donors or acquired by recipients and regardless of whether competence-stimulating peptide-receptor cross talk was allowed. Moreover, unidirectional transformation occurred when two donor strains (e.g., S4Str and S19FTmp) were incubated together, leading to S19FStr/Tmp but at a rF 3 orders of magnitude lower (4.9 × 10−6). We finally demonstrated that the mechanism leading to unidirectional transformation was due to inhibition of transformation of the donor by the recipient. Pneumococcal transformation in the human nasopharynx may lead to the acquisition of antibiotic resistance genes or genes encoding new capsular variants. Antibiotics and vaccines are currently putting pressure on a number of strains, leading to an increase in antibiotic resistance and serotype replacement. These pneumococcal strains are also acquiring virulence traits from vaccine types via transformation. In this study, we recapitulated multiple-strain colonization with strains carrying a resistance marker and selected for those acquiring resistance to two or three antibiotics, such as would occur in the human nasopharynx. Strains acquiring dual and triple resistance originated from one progenitor, demonstrating that transformation was unidirectional. Unidirectional transformation was the result of inhibition of transformation of donor strains. Unidirectional transformation has implications for the understanding of acquisition patterns of resistance determinants or capsule-switching events.
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Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser C. Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination. Mol Biol Evol 2017; 34:2537-2554. [PMID: 28595308 PMCID: PMC5850285 DOI: 10.1093/molbev/msx173] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diversity of the polysaccharide capsule in Streptococcus pneumoniae-main surface antigen and the target of the currently used pneumococcal vaccines-constitutes a major obstacle in eliminating pneumococcal disease. Such diversity is genetically encoded by almost 100 variants of the capsule biosynthesis locus, cps. However, the evolutionary dynamics of the capsule remains not fully understood. Here, using genetic data from 4,519 bacterial isolates, we found cps to be an evolutionary hotspot with elevated substitution and recombination rates. These rates were a consequence of relaxed purifying selection and positive, diversifying selection acting at this locus, supporting the hypothesis that the capsule has an increased potential to generate novel diversity compared with the rest of the genome. Diversifying selection was particularly evident in the region of wzd/wze genes, which are known to regulate capsule expression and hence the bacterium's ability to cause disease. Using a novel, capsule-centered approach, we analyzed the evolutionary history of 12 major serogroups. Such analysis revealed their complex diversification scenarios, which were principally driven by recombination with other serogroups and other streptococci. Patterns of recombinational exchanges between serogroups could not be explained by serotype frequency alone, thus pointing to nonrandom associations between co-colonizing serotypes. Finally, we discovered a previously unobserved mosaic serotype 39X, which was confirmed to carry a viable and structurally novel capsule. Adding to previous discoveries of other mosaic capsules in densely sampled collections, these results emphasize the strong adaptive potential of the bacterium by its ability to generate novel antigenic diversity by recombination.
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Affiliation(s)
- Rafał J. Mostowy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Institute for Emerging Infections, Oxford Martin School, Oxford, United Kingdom
| | - Claire Chewapreecha
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Susannah J. Salter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Turner
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - David M. Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D. Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Nuffield Department of Medicine, Li Ka Shing Centre for Health Information and Discovery, Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom
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A Quorum-Sensing System That Regulates Streptococcus pneumoniae Biofilm Formation and Surface Polysaccharide Production. mSphere 2017; 2:mSphere00324-17. [PMID: 28932816 PMCID: PMC5597970 DOI: 10.1128/msphere.00324-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022] Open
Abstract
Quorum sensing regulates bacterial social behaviors by production, secretion, and sensing of pheromones. In this study, we characterized a new quorum-sensing system of the Rgg/SHP class in S. pneumoniae D39. The system was found to directly induce the expression of a single gene cluster comprising the gene for the SHP pheromone and genes with putative functions in capsule synthesis. Capsule size, as measured by dextran exclusion, was increased by SHP exposure in R36A, an unencapsulated derivative of D39. In the encapsulated parent strain, overexpression of the gene cluster increased capsule size, supporting the role of Rgg/SHP in the synthesis of surface polysaccharides. Further, we found that biofilm formation on epithelial cells was reduced by overexpression of the system and increased in a mutant with an rgg deletion. Placing surface polysaccharide expression under quorum-sensing regulation may enable S. pneumoniae to tune interactions with the host and other bacteria in accordance with environmental and cell density conditions. Despite vaccines, Streptococcus pneumoniae kills more than a million people yearly. Thus, understanding how pneumococci transition from commensals to pathogens is particularly relevant. Quorum sensing regulates collective behaviors and thus represents a potential driver of commensal-to-pathogen transitions. Rgg/small hydrophobic peptide (SHP) quorum-sensing systems are widespread in streptococci, yet they remain largely uncharacterized in S. pneumoniae. Using directional transcriptome sequencing, we show that the S. pneumoniae D39 Rgg0939/SHP system induces the transcription of a single gene cluster including shp and capsule gene homologs. Capsule size measurements determined by fluorescein isothiocyanate-dextran exclusion allowed assignment of the system to the regulation of surface polysaccharide expression. We found that the SHP pheromone induced exopolysaccharide expression in R36A, an unencapsulated derivative of D39. In the encapsulated parent strain, overexpression of the Rgg system resulted in a mutant with increased capsule size. In line with previous studies showing that capsule expression is inversely associated with biofilm formation, we found that biofilm formed on lung epithelial cells was decreased in the overexpression strain and increased in an rgg deletion mutant. Although no significant differences were observed between D39 and the rgg deletion mutant in a mouse model of lung infection, in competitive assays, overexpression reduced fitness. This is the first study to reveal a quorum-sensing system in streptococci that regulates exopolysaccharide synthesis from a site distinct from the original capsule locus. IMPORTANCE Quorum sensing regulates bacterial social behaviors by production, secretion, and sensing of pheromones. In this study, we characterized a new quorum-sensing system of the Rgg/SHP class in S. pneumoniae D39. The system was found to directly induce the expression of a single gene cluster comprising the gene for the SHP pheromone and genes with putative functions in capsule synthesis. Capsule size, as measured by dextran exclusion, was increased by SHP exposure in R36A, an unencapsulated derivative of D39. In the encapsulated parent strain, overexpression of the gene cluster increased capsule size, supporting the role of Rgg/SHP in the synthesis of surface polysaccharides. Further, we found that biofilm formation on epithelial cells was reduced by overexpression of the system and increased in a mutant with an rgg deletion. Placing surface polysaccharide expression under quorum-sensing regulation may enable S. pneumoniae to tune interactions with the host and other bacteria in accordance with environmental and cell density conditions.
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39
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Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L. Strain Level Streptococcus Colonization Patterns during the First Year of Life. Front Microbiol 2017; 8:1661. [PMID: 28932211 PMCID: PMC5592222 DOI: 10.3389/fmicb.2017.01661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/16/2017] [Indexed: 01/20/2023] Open
Abstract
Pneumococcal pneumonia has decreased significantly since the implementation of the pneumococcal conjugate vaccine (PCV), nevertheless, in many developing countries pneumonia mortality in infants remains high. We have undertaken a study of the nasopharyngeal (NP) microbiome during the first year of life in infants from The Philippines and South Africa. The study entailed the determination of the Streptococcus sp. carriage using a lytA qPCR assay, whole metagenomic sequencing, and in silico serotyping of Streptococcus pneumoniae, as well as 16S rRNA amplicon based community profiling. The lytA carriage in both populations increased with infant age and lytA+ samples ranged from 24 to 85% of the samples at each sampling time point. We next developed informatic tools for determining Streptococcus community composition and pneumococcal serotype from metagenomic sequences derived from a subset of longitudinal lytA-positive Streptococcus enrichment cultures from The Philippines (n = 26 infants, 50% vaccinated) and South African (n = 7 infants, 100% vaccinated). NP samples from infants were passaged in enrichment media, and metagenomic DNA was purified and sequenced. In silico capsular serotyping of these 51 metagenomic assemblies assigned known serotypes in 28 samples, and the co-occurrence of serotypes in 5 samples. Eighteen samples were not typeable using known serotypes but did encode for capsule biosynthetic cluster genes similar to non-encapsulated reference sequences. In addition, we performed metagenomic assembly and 16S rRNA amplicon profiling to understand co-colonization dynamics of Streptococcus sp. and other NP genera, revealing the presence of multiple Streptococcus species as well as potential respiratory pathogens in healthy infants. A range of virulence and drug resistant elements were identified as circulating in the NP microbiomes of these infants. This study revealed the frequent co-occurrence of multiple S. pneumoniae strains along with Streptococcus sp. and other potential pathogens such as S. aureus in the NP microbiome of these infants. In addition, the in silico serotype analysis proved powerful in determining the serotypes in S. pneumoniae carriage, and may lead to developing better targeted vaccines to prevent invasive pneumococcal disease (IPD) in these countries. These findings suggest that NP colonization by S. pneumoniae during the first years of life is a dynamic process involving multiple serotypes and species.
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Affiliation(s)
| | | | | | - Erin Beck
- J. Craig Venter InstituteRockville, MD, United States
| | - Derek Harkins
- J. Craig Venter InstituteRockville, MD, United States
| | - Jyoti Shankar
- J. Craig Venter InstituteRockville, MD, United States
| | | | | | | | - Brian Bacay
- Research Institute of Tropical MedicineMuntinlupa City, Philippines
| | - Susan A Nzenze
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Sheila Z M Kimaro
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Peter Adrian
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Keith P Klugman
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
| | - Marilla G Lucero
- Research Institute of Tropical MedicineMuntinlupa City, Philippines
| | | | - Shabir Madhi
- Respiratory and Meningeal Pathogens Research UnitSoweto, South Africa
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Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine 2017; 35:4594-4602. [PMID: 28711389 PMCID: PMC5571440 DOI: 10.1016/j.vaccine.2017.07.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Pneumococcal infections cause a high death toll in Sub Saharan Africa (SSA) but the recently rolled out pneumococcal conjugate vaccines (PCV) will reduce the disease burden. To better understand the population impact of these vaccines, comprehensive analysis of large collections of pneumococcal isolates sampled prior to vaccination is required. Here we present a population genomic study of the invasive pneumococcal isolates sampled before the implementation of PCV13 in Malawi. MATERIALS AND METHODS We retrospectively sampled and whole genome sequenced 585 invasive isolates from 2004 to 2010. We determine the pneumococcal population genetic structure and assessed serotype prevalence, antibiotic resistance rates, and the occurrence of serotype switching. RESULTS Population structure analysis revealed 22 genetically distinct sequence clusters (SCs), which consisted of closely related isolates. Serotype 1 (ST217), a vaccine-associated serotype in clade SC2, showed highest prevalence (19.3%), and was associated with the highest MDR rate (81.9%) followed by serotype 12F, a non-vaccine serotype in clade SC10 with an MDR rate of 57.9%. Prevalence of serotypes was stable prior to vaccination although there was an increase in the PMEN19 clone, serotype 5 ST289, in clade SC1 in 2010 suggesting a potential undetected local outbreak. Coalescent analysis revealed recent emergence of the SCs and there was evidence of natural capsule switching in the absence of vaccine induced selection pressure. Furthermore, majority of the highly prevalent capsule-switched isolates were associated with acquisition of vaccine-targeted capsules. CONCLUSIONS This study provides descriptions of capsule-switched serotypes and serotypes with potential to cause serotype replacement post-vaccination such as 12F. Continued surveillance is critical to monitor these serotypes and antibiotic resistance in order to design better infection prevention and control measures such as inclusion of emerging replacement serotypes in future conjugate vaccines.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Cheryl P Andam
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Maaike Alaerts
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Patrick Musicha
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Naor Bar-Zeev
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Arox W Kamng'ona
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Anmol M Kiran
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert S Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi; Division of Infection and Immunity, University College London, London, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen D Bentley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Dean B Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
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Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P, Bentley SD. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 2017; 6:e26255. [PMID: 28742023 PMCID: PMC5576492 DOI: 10.7554/elife.26255] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/21/2017] [Indexed: 01/04/2023] Open
Abstract
Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.
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Affiliation(s)
- John A Lees
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease EpidemiologySt. Mary’s Campus, Imperial College LondonLondonUnited Kingdom
| | - David Goldblatt
- Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Julian Parkhill
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Stephen D Bentley
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
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Interbacterial predation as a strategy for DNA acquisition in naturally competent bacteria. Nat Rev Microbiol 2017; 15:621-629. [PMID: 28690319 DOI: 10.1038/nrmicro.2017.66] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Natural competence enables bacteria to take up exogenous DNA. The evolutionary function of natural competence remains controversial, as imported DNA can act as a source of substrates or can be integrated into the genome. Exogenous homologous DNA can also be used for genome repair. In this Opinion article, we propose that predation of non-related neighbouring bacteria coupled with competence regulation might function as an active strategy for DNA acquisition. Competence-dependent kin-discriminated killing has been observed in the unrelated bacteria Vibrio cholerae and Streptococcus pneumoniae. Importantly, both the regulatory networks and the mode of action of neighbour predation differ between these organisms, with V. cholerae using a type VI secretion system and S. pneumoniae secreting bacteriocins. We argue that the forced release of DNA from killed bacteria and the transfer of non-clonal genetic material have important roles in bacterial evolution.
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Bandara M, Skehel JM, Kadioglu A, Collinson I, Nobbs AH, Blocker AJ, Jenkinson HF. The accessory Sec system (SecY2A2) in Streptococcus pneumoniae is involved in export of pneumolysin toxin, adhesion and biofilm formation. Microbes Infect 2017; 19:402-412. [PMID: 28456649 PMCID: PMC5526788 DOI: 10.1016/j.micinf.2017.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/27/2017] [Accepted: 04/17/2017] [Indexed: 01/04/2023]
Abstract
In Streptococcus pneumoniae TIGR4, genes encoding a SecY2A2 accessory Sec system are present within a locus encoding a serine-rich repeat surface protein PsrP. Mutant strains deleted in secA2 or psrP were deficient in biofilm formation, while the ΔsecA2 mutant was reduced in binding to airway epithelial cells. Cell wall protein (CWP) fractions from the ΔsecA2 mutant, but not from the ΔpsrP mutant, were reduced in haemolytic (pneumolysin) activity. Contact-dependent pneumolysin (Ply) activity of wild type TIGR4 cells was ten-fold greater than that of ΔsecA2 mutant cells suggesting that Ply was not active at the ΔsecA2 cell surface. Ply protein was found to be present in the CWP fraction from the ΔsecA2 mutant, but showed aberrant electrophoretic migration indicative of protein modification. Proteomic analyses led to the discovery that the ΔsecA2 mutant CWP fraction was deficient in two glycosidases as well as other enzymes involved in carbohydrate metabolism. Taken collectively the results suggest that positioning of Ply into the cell wall compartment in active form, together with glycosyl hydrolases and adhesins, requires a functional accessory Sec system.
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Affiliation(s)
- Mikaila Bandara
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol, BS1 2LY, UK; School of Cellular & Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK; School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology & Immunology, Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Angela H Nobbs
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol, BS1 2LY, UK
| | - Ariel J Blocker
- School of Cellular & Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK; School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
| | - Howard F Jenkinson
- School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol, BS1 2LY, UK.
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Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases. BMC Microbiol 2017; 17:62. [PMID: 28288567 PMCID: PMC5348806 DOI: 10.1186/s12866-017-0969-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Background Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Results Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes’ contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. Conclusions This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0969-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia.,Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora Inés Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia.
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Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species. Genetics 2017; 206:363-376. [PMID: 28280056 DOI: 10.1534/genetics.116.195784] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/26/2017] [Indexed: 12/31/2022] Open
Abstract
Nontranslated intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements with key functions. Despite this, there are few systematic studies on the strength and direction of selection operating on IGRs in bacteria using whole-genome sequence data sets. Here we exploit representative whole-genome data sets from six diverse bacterial species: Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, Klebsiella pneumoniae, and Escherichia coli We compare patterns of selection operating on IGRs using two independent methods: the proportion of singleton mutations and the dI/dS ratio, where dI is the number of intergenic SNPs per intergenic site. We find that the strength of purifying selection operating over all intergenic sites is consistently intermediate between that operating on synonymous and nonsynonymous sites. Ribosome binding sites and noncoding RNAs tend to be under stronger selective constraint than promoters and Rho-independent terminators. Strikingly, a clear signal of purifying selection remains even when all these major categories of regulatory elements are excluded, and this constraint is highest immediately upstream of genes. While a paucity of variation means that the data for M. tuberculosis are more equivocal than for the other species, we find strong evidence for positive selection within promoters of this species. This points to a key adaptive role for regulatory changes in this important pathogen. Our study underlines the feasibility and utility of gauging the selective forces operating on bacterial IGRs from whole-genome sequence data, and suggests that our current understanding of the functionality of these sequences is far from complete.
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Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infect Dis 2016; 16:649. [PMID: 27821148 PMCID: PMC5100261 DOI: 10.1186/s12879-016-1987-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. RESULTS Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. CONCLUSIONS The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Simon R. Harris
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Cheryl P. Andam
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Laura Bricio-Moreno
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - Feyruz Yalcin
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Sani Ousmane
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Shanil Govindpersad
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Madikay Senghore
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
| | - Chinelo Ebruke
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Mignon Du Plessis
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Anmol M. Kiran
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia GA 30329 USA
| | - Keith P. Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
- Bill and Melinda Gates Foundation, Seattle, WA 98109 USA
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ UK
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
| | - Jean-Marc Collard
- Unité de Biologie, Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Martin Antonio
- Bacterial Diseases Programme, Medical Research Council (MRC), Banjul, The Gambia
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
| | - William P. Hanage
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Massachusetts, MA 02115 USA
| | - Dean B. Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Stephen D. Bentley
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA UK
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