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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.
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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.
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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
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53
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Deriving group A Streptococcus typing information from short-read whole-genome sequencing data. J Clin Microbiol 2014; 52:1871-6. [PMID: 24648555 DOI: 10.1128/jcm.00029-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typing of group A Streptococcus (GAS) is crucial for infection control and epidemiology. While whole-genome sequencing (WGS) is revolutionizing the way that bacterial organisms are typed, it is necessary to provide backward compatibility with currently used typing schemas to facilitate comparisons and understanding of epidemiological trends. Here, we sequenced the genomes of 191 GAS isolates representing 42 different emm types and used bioinformatics tools to derive commonly used GAS typing information directly from the short-read WGS data. We show that emm typing and multilocus sequence typing can be achieved rapidly and efficiently using this approach, which also permits the determination of the presence or absence of genes associated with GAS tissue tropism. We also report on how the WGS data analysis was instrumental in identifying ambiguities present in the commonly used emm type database hosted by the U.S. Centers for Disease Control and Prevention.
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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.
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55
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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: 51] [Impact Index Per Article: 4.3] [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'.
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Affiliation(s)
- M W Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Man., Canada.
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Scott J, Nguyen SV, King CJ, Hendrickson C, McShan WM. Phage-Like Streptococcus pyogenes Chromosomal Islands (SpyCI) and Mutator Phenotypes: Control by Growth State and Rescue by a SpyCI-Encoded Promoter. Front Microbiol 2012; 3:317. [PMID: 22969756 PMCID: PMC3430984 DOI: 10.3389/fmicb.2012.00317] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/13/2012] [Indexed: 11/13/2022] Open
Abstract
We recently showed that a prophage-like Streptococcus pyogenes chromosomal island (SpyCI) controls DNA mismatch repair and other repair functions in M1 genome strain SF370 by dynamic excision and reintegration into the 5' end of mutL in response to growth, causing the cell to alternate between a wild type and mutator phenotype. Nine of the 16 completed S. pyogenes genomes contain related SpyCI integrated into the identical attachment site in mutL, and in this study we examined a number of these strains to determine whether they also had a mutator phenotype as in SF370. With the exception of M5 genome strain Manfredo, all demonstrated a mutator phenotype as compared to SpyCI-free strain NZ131. The integrase gene (int) in the SpyCIM5 contains a deletion that rendered it inactive, and this deletion predicts that Manfredo would have a pronounced mutator phenotype. Remarkably, this was found not to be the case, but rather a cryptic promoter within the int ORF was identified that ensured constitutive expression of mutL and the downstream genes encoded on the same mRNA, providing a striking example of rescue of gene function following decay of a mobile genetic element. The frequent occurrence of SpyCI in the group A streptococci may facilitate bacterial survival by conferring an inducible mutator phenotype that promotes adaptation in the face of environmental challenges or host immunity.
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Affiliation(s)
- Julie Scott
- Department of Pharmaceutical Sciences, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
| | - Scott V. Nguyen
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
| | - Catherine J. King
- Department of Pharmaceutical Sciences, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
| | - Christina Hendrickson
- Department of Pharmaceutical Sciences, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
| | - W. Michael McShan
- Department of Pharmaceutical Sciences, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences CenterOklahoma City, OK, USA
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Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012; 8:e1002824. [PMID: 22876174 PMCID: PMC3410874 DOI: 10.1371/journal.ppat.1002824] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
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Fittipaldi N, Olsen RJ, Beres SB, Van Beneden C, Musser JM. Genomic analysis of emm59 group A Streptococcus invasive strains, United States. Emerg Infect Dis 2012; 18:650-2. [PMID: 22469010 PMCID: PMC3309687 DOI: 10.3201/eid1804.111803] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genomic analysis of type emm59 group A Streptococcus invasive strains isolated in the United States discovered higher than anticipated genetic heterogeneity among strains and identified a heretofore unrecognized monoclonal cluster of invasive infections in the San Francisco Bay area. Heightened monitoring for a potential shift in the epidemic behavior of emm59 group A Streptococcus is warranted.
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Affiliation(s)
- Nahuel Fittipaldi
- The Methodist Hospital Research Institute, Houston, Texas 77030, USA
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Bessen DE. Population genomics: an investigative tool for epidemics. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:1358-1361. [PMID: 22386771 PMCID: PMC3378846 DOI: 10.1016/j.ajpath.2012.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 01/19/2012] [Indexed: 05/31/2023]
Abstract
This Commentary highlights the article by Fittipaldi et al describing the emergence and epidemic spread of an emm59 strain of group A streptococcus.
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Affiliation(s)
- Debra E Bessen
- Department of Microbiology and Immunology, New York Medical College, Valhalla, New York 10595, USA.
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60
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Olsen RJ, Long SW, Musser JM. Bacterial genomics in infectious disease and the clinical pathology laboratory. Arch Pathol Lab Med 2012; 136:1414-22. [PMID: 22439809 DOI: 10.5858/arpa.2012-0025-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Throughout history, technologic advancements have fueled the engine of innovation, which, in turn, has driven discovery. Accordingly, recent advancements in DNA sequencing technology are revolutionizing bacterial genomics. OBJECTIVE To review important developments from the literature. The current state of bacterial genomics, with an emphasis on human pathogens and the clinical pathology laboratory, will be discussed. DATA SOURCES A comprehensive review was performed of the relevant literature indexed in PubMed (National Library of Medicine) and referenced medical texts. CONCLUSIONS Many important discoveries bearing on infectious disease research and pathology laboratory practice have been achieved through whole-genome sequencing strategies. Bacterial genomics has improved our understanding of molecular pathogenesis, host-pathogen interactions, and antibiotic-resistance mechanisms. Bacterial genomics has also facilitated the study of population structures, epidemics and outbreaks, and newly identified pathogens. Many opportunities now exist for clinical pathologists to contribute to bacterial genomics, including in the design of new diagnostic tests, therapeutic agents, and vaccines.
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Affiliation(s)
- Randall J Olsen
- Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX 77030, USA.
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Abstract
Diseases caused by Streptococcus pyogenes (Group A streptococcus, GAS) range from superficial infections such as pharyngitis and impetigo to potentially fatal rheumatic heart disease and invasive disease. Studies spanning emm-typing surveillance to population genomics are providing new insights into the epidemiology, pathogenesis, and biology of this organism. Such studies have demonstrated the differences that exist in the epidemiology of streptococcal disease between developing and developed nations. In developing nations, where streptococcal disease is endemic, the diversity of GAS emm-types circulating is much greater than that found in developed nations. An association between emm-type and disease, as observed in developed countries is also lacking. Intriguingly, comparative genetic studies suggest that emm-type is not always a good predictor of the evolutionary relatedness of geographically distant isolates. A view of GAS as a highly dynamic organism, in possession of a core set of virulence genes that contribute to host niche specialization and common pathogenic processes, augmented by accessory genes that change the relative virulence of specific lineages is emerging. Our inability to definitively identify genetic factors that contribute to specific disease outcome underscores the complex nature of streptococcal diseases.
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