1
|
Sitkiewicz I, Borek A, Gryko M, Karpińska A, Kozińska A, Obszańska K, Wilemska-Dziaduszycka J, Walory J, Bańska A, Belkiewicz K, Foryś M, Gołębiewska A, Hryniewicz W, Kadłubowski M, Kiedrowska M, Klarowicz A, Matynia B, Ronkiewicz P, Szczypa K, Waśko I, Wawszczak M, Wróbel-Pawelczyk I, Zieniuk B. Epidemiology of Streptococcus pyogenes upper respiratory tract infections in Poland (2003-2017). J Appl Genet 2024; 65:635-644. [PMID: 38760644 PMCID: PMC11310251 DOI: 10.1007/s13353-024-00875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) is a major human pathogen and causes every year over 600 millions upper respiratory tract onfections worldwide. Untreated or repeated infections may lead to post-infectional sequelae such as rheumatic heart disease, a major cause of GAS-mediated mortality. There is no comprehensive, longitudinal analysis of the M type distribution of upper respiratory tract strains isolated in Poland. Single reports describe rather their antibiotic resistance patterns or focus on the invasive isolates. Our goal was to analyse the clonal structure of the upper respiratory tract GAS isolated over multiple years in Poland. Our analysis revealed a clonal structure similar to the ones observed in high-income countries, with M1, M12, M89, M28, and M77 serotypes constituting over 80% of GAS strains. The M77 serotype is a major carrier of erythromycin resistance and is more often correlated with upper respiratory tract infections than other serotypes.
Collapse
Affiliation(s)
- Izabela Sitkiewicz
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Anna Borek
- National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138, Warsaw, Poland
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Monika Gryko
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Aneta Karpińska
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | | | - Katarzyna Obszańska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 01-106, Warsaw, Poland
| | | | - Jarosław Walory
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Agata Bańska
- ALAB Laboratory, Mikrobiologia, Ul. Stępińska 22/30, 00-739, Warsaw, Poland
| | - Katarzyna Belkiewicz
- National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138, Warsaw, Poland
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Małgorzata Foryś
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | | | - Waleria Hryniewicz
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
- Centre of Quality Control in Microbiology (Polmicro), Rydygiera 8, 01-793, Warsaw, Poland
| | | | | | - Anna Klarowicz
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Bożena Matynia
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | | | - Katarzyna Szczypa
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Izabela Waśko
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Monika Wawszczak
- National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | | | | |
Collapse
|
2
|
Butler TA, Story C, Green E, Williamson KM, Newton P, Jenkins F, Varadhan H, van Hal S. Insights gained from sequencing Australian non-invasive and invasive Streptococcus pyogenes isolates. Microb Genom 2024; 10:001152. [PMID: 38197886 PMCID: PMC10868607 DOI: 10.1099/mgen.0.001152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024] Open
Abstract
Epidemiological data have indicated that invasive infections caused by the Gram-positive cocci Streptococcus pyogenes (group A streptococcus, GAS) have increased in many Australian states over the past two decades. In July 2022, invasive GAS (iGAS) infections became nationally notifiable in Australia via public-health agencies. Surveillance for S. pyogenes infections has been sporadic within the state of New South Wales (NSW). This has led to a lack of genetic data on GAS strains in circulation, particularly for non-invasive infections, which are the leading cause of GAS's burden on the Australian healthcare system. To address this gap, we used whole-genome sequencing to analyse the genomes of 318 S. pyogenes isolates collected within two geographical regions of NSW. Invasive isolates were collected in 2007-2017, whilst non-invasive isolates were collected in 2019-2021. We found that at least 66 different emm-types were associated with clinical disease within NSW. There was no evidence of any Australian-specific clones in circulation. The M1UK variant of the emm1 global pandemic clone (M1global) has been detected in our isolates from 2013 onwards. We detected antimicrobial-resistance genes (mainly tetM, ermA or ermB genes) in less than 10 % of our 318 isolates, which were more commonly associated with non-invasive infections. Superantigen virulence gene carriage was reasonably proportionate between non-invasive and invasive infection isolates. Our study adds rich data on the genetic makeup of historical S. pyogenes infections within Australia. Ongoing surveillance of invasive and non-invasive GAS infections within NSW by whole-genome sequencing is warranted to inform on outbreaks, antimicrobial resistance and vaccine coverage.
Collapse
Affiliation(s)
- Trent A.J. Butler
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Chloe Story
- Microbiology, NSW Health Pathology, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - Emily Green
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Kirsten M. Williamson
- Hunter New England Population Health, Hunter New England Local Health District, Newcastle, New South Wales, Australia
| | - Peter Newton
- Microbiology, NSW Health Pathology, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - Frances Jenkins
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia
| | - Hemalatha Varadhan
- Microbiology, NSW Health Pathology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Sebastiaan van Hal
- Department of Infectious Diseases and Microbiology, NSW Health Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia
- Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
3
|
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: 26] [Impact Index Per Article: 5.2] [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.
Collapse
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.
| |
Collapse
|
4
|
Abstract
Active surveillance of invasive group A Streptococcus (iGAS) disease indicates that its incidence in the US general population is low, but limited studies show rates for American Indians and Alaska Natives (AI/AN) are severalfold higher. Major disparities in rates of iGAS exist between Indigenous and non-Indigenous populations of Australia, New Zealand, and Canada, but much less is understood about iGAS among AI/AN in the United States. Although complex host-pathogen interactions influence the rates of iGAS, including strain variation and virulence, the number and type of concurrent conditions, and socioeconomic status, the relative contribution of each remains unclear. We highlight the poor correlation between the substantial effect of iGAS among Indigenous persons in industrialized countries and the current understanding of factors that influence iGAS disease in these populations. Prospective, large-scale, population-based studies of iGAS are needed that include AI/AN as a necessary first step to understanding the effects of iGAS.
Collapse
|
5
|
Bubba L, Bundle N, Kapatai G, Daniel R, Balasegaram S, Anderson C, Chalker V, Lamagni T, Brown C, Ready D, Efstratiou A, Coelho J. Genomic sequencing of a national emm66 group A streptococci (GAS) outbreak among people who inject drugs and the homeless community in England and Wales, January 2016–May 2017. J Infect 2019; 79:435-443. [DOI: 10.1016/j.jinf.2019.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 08/09/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
|
6
|
Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015). Clin Microbiol Infect 2018; 25:96-101. [PMID: 29698817 DOI: 10.1016/j.cmi.2018.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 03/02/2018] [Accepted: 04/13/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVES To analyse genomic sequence data of referred Streptococcus pyogenes isolates and those pertaining to selected elderly/nursing care or maternity clusters from 2010 to 2015 to ascertain genomic differences between epidemiologically related isolates and unrelated isolates from outbreaks of disease. METHODS The genomic sequences of 134 S. pyogenes isolates from 21 clusters of infection in elderly care or maternity settings from 2010 to 2015 were analysed using bioinformatics to ascertain genomic phylogeny, single nucleotide polymorphism (SNP) differences and statistical outliers from epidemiologically defined outbreaks. Analysis was undertaken within clusters and compared with sporadic isolates from geographically distinct outbreaks of S. pyogenes infection. RESULTS Genomic sequence analysis of 21 outbreaks of S. pyogenes infection ranged in size from a single patient (with colonized healthcare worker link) to 18 patient cases of group A streptococcus (GAS) infection in a single setting. Seventeen healthcare workers were identified in 8 of 21 outbreaks with the associated outbreak strain, with multiple staff in 2 of 21 outbreaks. Genomic sequences from epidemiologically linked isolates from patients, staff and healthcare environmental settings were highly conserved, differing by 0-1 SNP in some cases and mirrored geographical data. Four of 21 outbreaks had environmental contamination with the outbreak strain, indistinguishable or of limited SNP difference to the patient isolates. Genomic SNP analysis enabled exclusion of ten isolates from epidemiological outbreaks. CONCLUSIONS Genomic discrimination can be applied to assist outbreak investigation. It enabled confirmation or exclusion of GAS cases from epidemiologically defined outbreaks. Colonization of healthcare workers and environmental contamination with the outbreak strain was demonstrated for several outbreaks.
Collapse
|
7
|
Teatero S, McGeer A, Tyrrell GJ, Hoang L, Smadi H, Domingo MC, Levett PN, Finkelstein M, Dewar K, Plevneshi A, Athey TBT, Gubbay JB, Mulvey MR, Martin I, Demczuk W, Fittipaldi N. Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease. Open Forum Infect Dis 2018; 5:ofy085. [PMID: 29780850 DOI: 10.1093/ofid/ofy085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Abstract
Background The number of invasive group A Streptococcus (iGAS) infections due to hitherto extremely rare type emm74 strains has increased in several Canadian provinces since late 2015. We hypothesized that the cases recorded in the different provinces are linked and caused by strains of an emm74 clone that recently emerged and expanded explosively. Methods We analyzed both active and passive surveillance data for iGAS infections and used whole-genome sequencing to investigate the phylogenetic relationships of the emm74 strains responsible for these invasive infections country-wide. Results Genome analysis showed that highly clonal emm74 strains, genetically different from emm74 organisms previously circulating in Canada, were responsible for a country-wide epidemic of >160 invasive disease cases. The emerging clone belonged to multilocus sequence typing ST120. The analysis also revealed dissemination patterns of emm74 subclonal lineages across Canadian provinces. Clinical data analysis indicated that the emm74 epidemic disproportionally affected middle-aged or older male individuals. Homelessness, alcohol abuse, and intravenous drug usage were significantly associated with invasive emm74 infections. Conclusions In a period of 20 months, an emm74 GAS clone emerged and rapidly spread across several Canadian provinces located more than 4500 km apart, causing invasive infections primarily among disadvantaged persons.
Collapse
Affiliation(s)
- Sarah Teatero
- Public Health Ontario Laboratory, Toronto, ON, Canada
| | - Allison McGeer
- Sinai Health System, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gregory J Tyrrell
- Alberta Provincial Laboratory for Public Health, and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Linda Hoang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Hanan Smadi
- New Brunswick Department of Health, Communicable Disease and Control, Fredericton, NB, Canada
| | - Marc-Christian Domingo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Ste-Anne de Bellevue, QC, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, Regina, SK, Canada
| | | | - Ken Dewar
- Genome Québec Innovation Centre, and McGill University, Montreal, QC, Canada
| | | | | | - Jonathan B Gubbay
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario Laboratory, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
8
|
Beres SB, Olsen RJ, Ojeda Saavedra M, Ure R, Reynolds A, Lindsay DSJ, Smith AJ, Musser JM. Genome sequence analysis of emm89 Streptococcus pyogenes strains causing infections in Scotland, 2010-2016. J Med Microbiol 2017; 66:1765-1773. [PMID: 29099690 PMCID: PMC5845742 DOI: 10.1099/jmm.0.000622] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose Strains of type emm89 Streptococcus pyogenes have recently increased in frequency as a cause of human infections in several countries in Europe and North America. This increase has been molecular epidemiologically linked with the emergence of a new genetically distinct clone, designated clade 3. We sought to extend our understanding of this epidemic behavior by the genetic characterization of type emm89 strains responsible in recent years for an increased frequency of infections in Scotland. Methodology We sequenced the genomes of a retrospective cohort of 122 emm89 strains recovered from patients with invasive and noninvasive infections throughout Scotland during 2010 to 2016. Results All but one of the 122 emm89 infection isolates are of the recently emerged epidemic clade 3 clonal lineage. The Scotland isolates are closely related to and not genetically distinct from recent emm89 strains from England, they constitute a single genetic population. Conclusions The clade 3 clone causes virtually all-contemporary emm89 infections in Scotland. These findings add Scotland to a growing list of countries of Europe and North America where, by whole genome sequencing, emm89 clade 3 strains have been demonstrated to be the cause of an ongoing epidemic of invasive infections and to be genetically related due to descent from a recent common progenitor.
Collapse
Affiliation(s)
- Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA
| | - Roisin Ure
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Arlene Reynolds
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Diane S J Lindsay
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK
| | - Andrew J Smith
- Scottish Haemophilus Legionella Meningococcus Pneumococcus Reference Laboratory, New Lister Building, Glasgow, G31 2ER, Scotland, UK.,College of Medical, Veterinary and Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, 378 Sauchiehall Street, Glasgow, G2 3JZ, Scotland, UK
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, TX 77030, USA.,Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| |
Collapse
|
9
|
Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, Daniel R, Dhami C, Laranjeira M, Chambers T, Guy R, Lamagni T, Harrison T, Chand M, Johnson AP, Underwood A, The Scarlet Fever Incident Management Team. Genome analysis following a national increase in Scarlet Fever in England 2014. BMC Genomics 2017; 18:224. [PMID: 28283023 PMCID: PMC5345146 DOI: 10.1186/s12864-017-3603-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 02/24/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1st April 2014 to 18th June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics. RESULTS 555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95%CI 37.5-48.5; 14.7% higher than the percentage of emm3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS (p < 0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a "meta-ssa" phage defined by the presence of :315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360.vir phage was not detected yet the HKU360.ssa phage was present in 43/63 emm12 isolates but not found to be over-represented in isolates from patients with SF. CONCLUSIONS There is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.
Collapse
Affiliation(s)
- Victoria Chalker
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Aleksey Jironkin
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Juliana Coelho
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Ali Al-Shahib
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Steve Platt
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Georgia Kapatai
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Roger Daniel
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Chenchal Dhami
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Marisa Laranjeira
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Timothy Chambers
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Rebecca Guy
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Theresa Lamagni
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Timothy Harrison
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Meera Chand
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
- Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Alan P. Johnson
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | - Anthony Underwood
- National Infection Service, Public Health England, 61 Colindale Avenue, London, NW9 5HT UK
| | | |
Collapse
|
10
|
Engelthaler DM, Valentine M, Bowers J, Pistole J, Driebe EM, Terriquez J, Nienstadt L, Carroll M, Schumacher M, Ormsby ME, Brady S, Livar E, Yazzie D, Waddell V, Peoples M, Komatsu K, Keim P. Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States. Emerg Infect Dis 2016; 22:734-8. [PMID: 26982330 PMCID: PMC4806960 DOI: 10.3201/eid2204.151582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hyper-virulent emm59 genotype of invasive group A Streptococcus was identified in northern Arizona in 2015. Eighteen isolates belonging to a genomic cluster grouped most closely with recently identified isolates in New Mexico. The continued transmission of emm59 in the southwestern United States poses a public health concern.
Collapse
|
11
|
Euler CW, Juncosa B, Ryan PA, Deutsch DR, McShan WM, Fischetti VA. Targeted Curing of All Lysogenic Bacteriophage from Streptococcus pyogenes Using a Novel Counter-selection Technique. PLoS One 2016; 11:e0146408. [PMID: 26756207 PMCID: PMC4710455 DOI: 10.1371/journal.pone.0146408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/16/2015] [Indexed: 01/21/2023] Open
Abstract
Streptococcus pyogenes is a human commensal and a bacterial pathogen responsible for a wide variety of human diseases differing in symptoms, severity, and tissue tropism. The completed genome sequences of >37 strains of S. pyogenes, representing diverse disease-causing serotypes, have been published. The greatest genetic variation among these strains is attributed to numerous integrated prophage and prophage-like elements, encoding several virulence factors. A comparison of isogenic strains, differing in prophage content, would reveal the effects of these elements on streptococcal pathogenesis. However, curing strains of prophage is often difficult and sometimes unattainable. We have applied a novel counter-selection approach to identify rare S. pyogenes mutants spontaneously cured of select prophage. To accomplish this, we first inserted a two-gene cassette containing a gene for kanamycin resistance (KanR) and the rpsL wild-type gene, responsible for dominant streptomycin sensitivity (SmS), into a targeted prophage on the chromosome of a streptomycin resistant (SmR) mutant of S. pyogenes strain SF370. We then applied antibiotic counter-selection for the re-establishment of the KanS/SmR phenotype to select for isolates cured of targeted prophage. This methodology allowed for the precise selection of spontaneous phage loss and restoration of the natural phage attB attachment sites for all four prophage-like elements in this S. pyogenes chromosome. Overall, 15 mutants were constructed that encompassed every permutation of phage knockout as well as a mutant strain, named CEM1ΔΦ, completely cured of all bacteriophage elements (a ~10% loss of the genome); the only reported S. pyogenes strain free of prophage-like elements. We compared CEM1ΔΦ to the WT strain by analyzing differences in secreted DNase activity, as well as lytic and lysogenic potential. These mutant strains should allow for the direct examination of bacteriophage relationships within S. pyogenes and further elucidate how the presence of prophage may affect overall streptococcal survival, pathogenicity, and evolution.
Collapse
Affiliation(s)
- Chad W. Euler
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, NY, NY, 10065, United States of America
- Department of Medical Laboratory Sciences, Belfer Research Building, Hunter College, CUNY, New York, NY, 10065, United States of America
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, United States of America
- * E-mail: ;
| | - Barbara Juncosa
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, NY, NY, 10065, United States of America
| | - Patricia A. Ryan
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, NY, NY, 10065, United States of America
| | - Douglas R. Deutsch
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, NY, NY, 10065, United States of America
| | - W. Michael McShan
- Department of Pharmaceutical Sciences and Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73117, United States of America
| | - Vincent A. Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, NY, NY, 10065, United States of America
| |
Collapse
|
12
|
High Incidence of Invasive Group A Streptococcus Disease Caused by Strains of Uncommon emm Types in Thunder Bay, Ontario, Canada. J Clin Microbiol 2015; 54:83-92. [PMID: 26491184 DOI: 10.1128/jcm.02201-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/15/2015] [Indexed: 12/26/2022] Open
Abstract
An outbreak of type emm59 invasive group A Streptococcus (iGAS) disease was declared in 2008 in Thunder Bay District, Northwestern Ontario, 2 years after a countrywide emm59 epidemic was recognized in Canada. Despite a declining number of emm59 infections since 2010, numerous cases of iGAS disease continue to be reported in the area. We collected clinical information on all iGAS cases recorded in Thunder Bay District from 2008 to 2013. We also emm typed and sequenced the genomes of all available strains isolated from 2011 to 2013 from iGAS infections and from severe cases of soft tissue infections. We used whole-genome sequencing data to investigate the population structure of GAS strains of the most frequently isolated emm types. We report an increased incidence of iGAS in Thunder Bay compared to the metropolitan area of Toronto/Peel and the province of Ontario. Illicit drug use, alcohol abuse, homelessness, and hepatitis C infection were underlying diseases or conditions that might have predisposed patients to iGAS disease. Most cases were caused by clonal strains of skin or generalist emm types (i.e., emm82, emm87, emm101, emm4, emm83, and emm114) uncommonly seen in other areas of the province. We observed rapid waxing and waning of emm types causing disease and their replacement by other emm types associated with the same tissue tropisms. Thus, iGAS disease in Thunder Bay District predominantly affects a select population of disadvantaged persons and is caused by clonally related strains of a few skin and generalist emm types less commonly associated with iGAS in other areas of Ontario.
Collapse
|
13
|
The majority of 9,729 group A streptococcus strains causing disease secrete SpeB cysteine protease: pathogenesis implications. Infect Immun 2015; 83:4750-8. [PMID: 26416912 DOI: 10.1128/iai.00989-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022] Open
Abstract
Group A streptococcus (GAS), the causative agent of pharyngitis and necrotizing fasciitis, secretes the potent cysteine protease SpeB. Several lines of evidence suggest that SpeB is an important virulence factor. SpeB is expressed in human infections, protects mice from lethal challenge when used as a vaccine, and contributes significantly to tissue destruction and dissemination in animal models. However, recent descriptions of mutations in genes implicated in SpeB production have led to the idea that GAS may be under selective pressure to decrease secreted SpeB protease activity during infection. Thus, two divergent hypotheses have been proposed. One postulates that SpeB is a key contributor to pathogenesis; the other, that GAS is under selection to decrease SpeB during infection. In order to distinguish between these alternative hypotheses, we performed casein hydrolysis assays to measure the SpeB protease activity secreted by 6,775 GAS strains recovered from infected humans. The results demonstrated that 84.3% of the strains have a wild-type SpeB protease phenotype. The availability of whole-genome sequence data allowed us to determine the relative frequencies of mutations in genes implicated in SpeB production. The most abundantly mutated genes were direct transcription regulators. We also sequenced the genomes of 2,954 GAS isolates recovered from nonhuman primates with experimental necrotizing fasciitis. No mutations that would result in a SpeB-deficient phenotype were identified. Taken together, these data unambiguously demonstrate that the great majority of GAS strains recovered from infected humans secrete wild-type levels of SpeB protease activity. Our data confirm the important role of SpeB in GAS pathogenesis and help end a long-standing controversy.
Collapse
|
14
|
Bessen DE, McShan WM, Nguyen SV, Shetty A, Agrawal S, Tettelin H. Molecular epidemiology and genomics of group A Streptococcus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 33:393-418. [PMID: 25460818 PMCID: PMC4416080 DOI: 10.1016/j.meegid.2014.10.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/11/2014] [Accepted: 10/13/2014] [Indexed: 12/15/2022]
Abstract
Streptococcus pyogenes (group A Streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed.
Collapse
Affiliation(s)
- Debra E Bessen
- Department of Microbiology & Immunology, New York Medical College, Valhalla, NY 10595, USA.
| | - W Michael McShan
- University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences, College of Pharmacy, Oklahoma City, OK 73117, USA.
| | - Scott V Nguyen
- University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences, College of Pharmacy, Oklahoma City, OK 73117, USA.
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Sonia Agrawal
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| |
Collapse
|
15
|
Phosphorylation events in the multiple gene regulator of group A Streptococcus significantly influence global gene expression and virulence. Infect Immun 2015; 83:2382-95. [PMID: 25824840 DOI: 10.1128/iai.03023-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/21/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome sequencing analysis of ∼800 strains of group A Streptococcus (GAS) found that the gene encoding the multiple virulence gene regulator of GAS (mga) is highly polymorphic in serotype M59 strains but not in strains of other serotypes. To help understand the molecular mechanism of gene regulation by Mga and its contribution to GAS pathogenesis in serotype M59 GAS, we constructed an isogenic mga mutant strain. Transcriptome studies indicated a significant regulatory influence of Mga and altered metabolic capabilities conferred by Mga-regulated genes. We assessed the phosphorylation status of Mga in GAS cell lysates with Phos-tag gels. The results revealed that Mga is phosphorylated at histidines in vivo. Using phosphomimetic and nonphosphomimetic substitutions at conserved phosphoenolpyruvate:carbohydrate phosphotransferase regulation domain (PRD) histidines of Mga, we demonstrated that phosphorylation-mimicking aspartate replacements at H207 and H273 of PRD-1 and at H327 of PRD-2 are inhibitory to Mga-dependent gene expression. Conversely, non-phosphorylation-mimicking alanine substitutions at H273 and H327 relieved inhibition, and the mutant strains exhibited a wild-type phenotype. The opposing regulatory profiles observed for phosphorylation- and non-phosphorylation-mimicking substitutions at H273 extended to global gene regulation by Mga. Consistent with these observations, the H273D mutant strain attenuated GAS virulence, whereas the H273A strain exhibited a wild-type virulence phenotype in a mouse model of necrotizing fasciitis. Together, our results demonstrate phosphoregulation of Mga and its direct link to virulence in M59 GAS strains. These data also lay a foundation toward understanding how naturally occurring gain-of-function variations in mga, such as H201R, may confer an advantage to the pathogen and contribute to M59 GAS pathogenesis.
Collapse
|
16
|
Full-Length Genome Sequence of Type M/emm83 Group A Streptococcus pyogenes Strain STAB1101, Isolated from Clustered Cases in Brittany. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01459-14. [PMID: 25614568 PMCID: PMC4319592 DOI: 10.1128/genomea.01459-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we announce the complete annotated genome sequence of a Streptococcus pyogenes M/emm83 strain, STAB1101, isolated from clustered cases in homeless persons in Brittany (France). The genome is composed of 1,709,790 bp, with a G+C content of 38.4% and 1,550 identified coding sequences (CDS), and it harbors a Tn916-like transposon.
Collapse
|
17
|
Brown CC, Olsen RJ, Fittipaldi N, Morman ML, Fort PL, Neuwirth R, Majeed M, Woodward WB, Musser JM. Spread of virulent group A Streptococcus type emm59 from Montana to Wyoming, USA. Emerg Infect Dis 2014; 20:679-81. [PMID: 24655919 PMCID: PMC3966365 DOI: 10.3201/eid2004.130564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Full-genome sequencing showed that a recently emerged and hypervirulent clone of group A Streptococcus type emm59 active in Canada and parts of the United States has now caused severe invasive infections in rural northeastern Wyoming. Phylogenetic analysis of genome data indicated that the strain was likely introduced from Montana.
Collapse
|
18
|
Sanson M, O'Neill BE, Kachroo P, Anderson JR, Flores AR, Valson C, Cantu CC, Makthal N, Karmonik C, Fittipaldi N, Kumaraswami M, Musser JM, Olsen RJ. A naturally occurring single amino acid replacement in multiple gene regulator of group A Streptococcus significantly increases virulence. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 185:462-71. [PMID: 25476528 DOI: 10.1016/j.ajpath.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 12/27/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common source of genetic variation within a species; however, few investigations demonstrate how naturally occurring SNPs may increase strain virulence. We recently used group A Streptococcus as a model pathogen to study bacteria strain genotype-patient disease phenotype relationships. Whole-genome sequencing of approximately 800 serotype M59 group A Streptococcus strains, recovered during an outbreak of severe invasive infections across North America, identified a disproportionate number of SNPs in the gene encoding multiple gene regulator of group A Streptococcus (mga). Herein, we report results of studies designed to test the hypothesis that the most commonly occurring SNP, encoding a replacement of arginine for histidine at codon 201 of Mga (H201R), significantly increases virulence. Whole transcriptome analysis revealed that the H201R replacement significantly increased expression of mga and 54 other genes, including many proven virulence factors. Compared to the wild-type strain, a H201R isogenic mutant strain caused significantly larger skin lesions in mice. Serial quantitative bacterial culture and noninvasive magnetic resonance imaging also demonstrated that the isogenic H201R strain was significantly more virulent in a nonhuman primate model of joint infection. These findings show that the H201R replacement in Mga increases the virulence of M59 group A Streptococcus and provide new insight to how a naturally occurring SNP in bacteria contributes to human disease phenotypes.
Collapse
Affiliation(s)
- Misu Sanson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas; School of Biotechnology, School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Brian E O'Neill
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Priyanka Kachroo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Jeff R Anderson
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Anthony R Flores
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas; Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Chandni Valson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Concepcion C Cantu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Nishanth Makthal
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Christof Karmonik
- Department of Translational Imaging, MRI Core, Houston Methodist Research Institute, Houston, Texas
| | - Nahuel Fittipaldi
- Department of Laboratory Medicine and Pathobiology, Public Health Ontario, University of Toronto, Toronto, Ontario, Canada
| | - Muthiah Kumaraswami
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Center for Molecular and Translational Human Infectious Diseases Research, Houston, Texas.
| |
Collapse
|
19
|
Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study. J Clin Microbiol 2014; 52:4210-6. [PMID: 25253790 DOI: 10.1128/jcm.02164-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Large hospital-based clinical laboratories must be prepared to rapidly investigate potential infectious disease outbreaks. To challenge the ability of our molecular diagnostics laboratory to use whole-genome sequencing in a potential outbreak scenario and identify impediments to these efforts, we studied 84 invasive serotype emm59 group A streptococcus (GAS) strains collected in the United States. We performed a rapid-response exercise to the mock outbreak scenario using whole-genome sequencing, genome-wide transcript analysis, and mouse virulence studies. The protocol changes installed in response to the lessons learned were tested in a second iteration. The initial investigation was completed in 9 days. Whole-genome sequencing showed that the invasive infections were caused by multiple subclones of epidemic emm59 GAS strains likely spread to the United States from Canada. The phylogenetic tree showed a strong temporal-spatial structure with diversity in mobile genetic element content, features that are useful for identifying closely related strains and possible transmission events. The genome data informed the epidemiology, identifying multiple patients who likely acquired the organisms through direct person-to-person transmission. Transcriptome analysis unexpectedly revealed significantly altered expression of genes encoding a two-component regulator and the hyaluronic acid capsule virulence factor. Mouse infection studies confirmed a high-virulence capacity of these emm59 organisms. Whole-genome sequencing, coupled with transcriptome analysis and animal virulence studies, can be rapidly performed in a clinical environment to effectively contribute to patient care decisions and public health maneuvers.
Collapse
|
20
|
Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin Microbiol Rev 2014. [PMID: 24696436 DOI: 10.1128/cmr.00101-13)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Streptococcus pyogenes, also known as group A Streptococcus (GAS), causes mild human infections such as pharyngitis and impetigo and serious infections such as necrotizing fasciitis and streptococcal toxic shock syndrome. Furthermore, repeated GAS infections may trigger autoimmune diseases, including acute poststreptococcal glomerulonephritis, acute rheumatic fever, and rheumatic heart disease. Combined, these diseases account for over half a million deaths per year globally. Genomic and molecular analyses have now characterized a large number of GAS virulence determinants, many of which exhibit overlap and redundancy in the processes of adhesion and colonization, innate immune resistance, and the capacity to facilitate tissue barrier degradation and spread within the human host. This improved understanding of the contribution of individual virulence determinants to the disease process has led to the formulation of models of GAS disease progression, which may lead to better treatment and intervention strategies. While GAS remains sensitive to all penicillins and cephalosporins, rising resistance to other antibiotics used in disease treatment is an increasing worldwide concern. Several GAS vaccine formulations that elicit protective immunity in animal models have shown promise in nonhuman primate and early-stage human trials. The development of a safe and efficacious commercial human vaccine for the prophylaxis of GAS disease remains a high priority.
Collapse
|
21
|
Walker MJ, Barnett TC, McArthur JD, Cole JN, Gillen CM, Henningham A, Sriprakash KS, Sanderson-Smith ML, Nizet V. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin Microbiol Rev 2014; 27:264-301. [PMID: 24696436 PMCID: PMC3993104 DOI: 10.1128/cmr.00101-13] [Citation(s) in RCA: 612] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pyogenes, also known as group A Streptococcus (GAS), causes mild human infections such as pharyngitis and impetigo and serious infections such as necrotizing fasciitis and streptococcal toxic shock syndrome. Furthermore, repeated GAS infections may trigger autoimmune diseases, including acute poststreptococcal glomerulonephritis, acute rheumatic fever, and rheumatic heart disease. Combined, these diseases account for over half a million deaths per year globally. Genomic and molecular analyses have now characterized a large number of GAS virulence determinants, many of which exhibit overlap and redundancy in the processes of adhesion and colonization, innate immune resistance, and the capacity to facilitate tissue barrier degradation and spread within the human host. This improved understanding of the contribution of individual virulence determinants to the disease process has led to the formulation of models of GAS disease progression, which may lead to better treatment and intervention strategies. While GAS remains sensitive to all penicillins and cephalosporins, rising resistance to other antibiotics used in disease treatment is an increasing worldwide concern. Several GAS vaccine formulations that elicit protective immunity in animal models have shown promise in nonhuman primate and early-stage human trials. The development of a safe and efficacious commercial human vaccine for the prophylaxis of GAS disease remains a high priority.
Collapse
Affiliation(s)
- Mark J. Walker
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Timothy C. Barnett
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Jason D. McArthur
- School of Biological Sciences and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Jason N. Cole
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Christine M. Gillen
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Anna Henningham
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - K. S. Sriprakash
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Martina L. Sanderson-Smith
- School of Biological Sciences and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
| |
Collapse
|
22
|
Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic. Emerg Microbes Infect 2013; 2:e13. [PMID: 26038455 PMCID: PMC3630956 DOI: 10.1038/emi.2013.13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/15/2013] [Accepted: 02/07/2013] [Indexed: 01/06/2023]
Abstract
Analysis of microbial epidemics has been revolutionized by whole-genome sequencing. We recently sequenced the genomes of 601 type emm59 Group A Streptococcus (GAS) organisms responsible for an ongoing epidemic of invasive infections in Canada and some of the United States. The epidemic has been caused by the emergence of a genetically distinct, hypervirulent clone that has genetically diversified. The ease of obtaining genomic data contrasts with the relatively difficult task of translating them into insightful epidemiological information. Here, we sequenced the genomes of 90 additional invasive Canadian emm59 GAS organisms, including 80 isolated recently in 2010–2011. We used an improved bioinformatics pipeline designed to rapidly process and analyze whole-genome data and integrate strain metadata. We discovered that emm59 GAS organisms are undergoing continued multiclonal evolutionary expansion. Previously identified geographic patterns of strain dissemination are being diluted as mixing of subclones over time and space occurs. Our integrated data analysis strategy permits prompt and accurate mapping of the dissemination of bacterial organisms in an epidemic wave, permitting rapid generation of hypotheses that inform public health and virulence studies.
Collapse
|
23
|
Gilmour MW, Graham M, Reimer A, Van Domselaar G. Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics 2013; 16:25-30. [PMID: 23548714 DOI: 10.1159/000342709] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Laboratory methods that can unambiguously fingerprint pathogenic microbes are needed to investigate the transmission of human infectious diseases from diverse sources, such as from the community, from the environment, within hospitals, or from contaminated food or water sources. Public health investigations currently rely on laboratory subtyping methods that ultimately provide only a fraction of the total genetic information of a pathogen, and although there is widespread success using existing subtyping methods, they do not always provide sufficient evidence to link disease cases together into outbreaks or to link these human cases to the culprit source. Alternatively, whole-genome sequencing of bacterial pathogens provides an unabridged examination of the genetic content of individual pathogen isolates, enabling public health laboratories to benefit from comparative analyses of total genetic content. In this context, whole-genome sequencing represents the ultimate epidemiological typing method - a universally applicable, highly detailed typing platform capable of providing the entire genetic blueprint of a pathogen and distinguishing strains to the single nucleotide level. These new genomic methods, if implemented within existing public health laboratory response programs, promise to revolutionize the ability of the laboratory to provide information and evidence on the evolution, transmission and virulence for bacterial pathogens - and this revolution is launching the new field of 'genomicepidemiology'.
Collapse
Affiliation(s)
- M W Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Man., Canada.
| | | | | | | |
Collapse
|