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Yi S, Zhou K, Xu X. Characterization of erm(B)-Carrying Integrative and Conjugative Elements Transferred from Streptococcus anginosus to Other Streptococci and Enterococci. Microb Drug Resist 2024; 30:243-253. [PMID: 38608246 DOI: 10.1089/mdr.2023.0342] [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: 04/14/2024] Open
Abstract
Integrative and conjugative elements (ICEs) are important vectors of lateral gene transfer and contribute to the evolution of bacterial pathogens. However, studies on the transfer among species and the physiological consequences of ICEs are rare. The objective of this study was to investigate the cross-species transferability of newly identified erm(B)-carried ICE in Streptococcus anginosus San95 and its physiological consequences after transfer. The erm(B)-carried ICE, characterized by a triple serine integrase module, integrated into hsdM genes, thus designated ICESan95_hsdM. Analysis of ICESan95_hsdM revealed 32 additional ICESan95-like ICEs in the available NCBI genome (n = 24) and sequence of clinical isolates (n = 8). Polymerase chain reaction (PCR) was used to evaluate the 467 clinical isolates, of which 84 were positive for core genes (integrase, relaxase, and T4SS genes) of ICESan95_hsdM. Cross-species transfer experiments demonstrated that ICESan95_hsdM could transfer from S. anginosus to different streptococcal and enterococcal recipients. Growth and competitive culture assays showed acquisition of ICESan95_hsdM incurred no fitness cost. Our work discovered a group of ICEs in Streptococci and Enterococci. For the first time, we demonstrated the broad cross-species transferability to different species or genera of ICEs with no fitness cost that enables commensal S. anginosus to deliver antimicrobial resistance genes to other streptococci and enterococci.
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Affiliation(s)
- Sida Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Kaixin Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
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2
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Novazzi F, Colombini L, Perniciaro S, Genoni A, Agosti M, Santoro F, Mancini N. A family cluster of Streptococcus pyogenes associated with a fatal early-onset neonatal sepsis. Clin Microbiol Infect 2024; 30:830-832. [PMID: 38432434 DOI: 10.1016/j.cmi.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Affiliation(s)
- Federica Novazzi
- University of Insubria, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, Laboratory of Medical Microbiology and Virology, Italy.
| | | | - Simona Perniciaro
- Ospedale Filippo del Ponte Ostetricia e Ginecologia, Neonatology and NICU, Del Ponte Hospital, Varese, Italy
| | - Angelo Genoni
- University of Insubria, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, Laboratory of Medical Microbiology and Virology, Italy
| | - Massimo Agosti
- University of Insubria, Department of Medicine and Surgery, Italy
| | | | - Nicasio Mancini
- University of Insubria, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, Laboratory of Medical Microbiology and Virology, Italy
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3
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Nysten J, Sofras D, Van Dijck P. One species, many faces: The underappreciated importance of strain diversity. PLoS Pathog 2024; 20:e1011931. [PMID: 38271302 PMCID: PMC10810500 DOI: 10.1371/journal.ppat.1011931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Affiliation(s)
- Jana Nysten
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Dimitrios Sofras
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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4
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Zhang Y, Lv F, Su Y, Zhang H, Zhang B. Complete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates. Front Microbiol 2023; 14:1285027. [PMID: 38029076 PMCID: PMC10646407 DOI: 10.3389/fmicb.2023.1285027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery. Methods Three S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes. Results Whole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains. Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase. Discussion In summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.
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Affiliation(s)
| | | | - Yan Su
- Department of Microbiology and Immunology, College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, Xinjiang, China
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5
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Expression of the Group A Streptococcus Fibrinogen-Binding Protein Mrp Is Negatively Regulated by the Small Regulatory RNA FasX. J Bacteriol 2022; 204:e0025122. [PMID: 36286516 PMCID: PMC9664951 DOI: 10.1128/jb.00251-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small regulatory RNAs (sRNAs) represent a major class of regulatory molecule that promotes the ability of the group A
Streptococcus
(GAS) and other pathogens to regulate virulence factor expression. Despite FasX being the best-described sRNA in GAS, there remains much to be learned.
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Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci. mSphere 2021; 6:e0079921. [PMID: 34787444 PMCID: PMC8597746 DOI: 10.1128/msphere.00799-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although prokaryotic DNA methylation investigations have long focused on immunity against exogenous DNA, it has been recently recognized that DNA methylation impacts gene expression and phase variation in Streptococcus pneumoniae and Streptococcus suis. A comprehensive analysis of DNA methylation is lacking for beta-hemolytic streptococci, and thus we sought to examine DNA methylation in the major human pathogen group A Streptococcus (GAS). Using a database of 224 GAS genomes encompassing 80 emm types, we found that nearly all GAS strains encode a type I restriction modification (RM) system that lacks the hsdS′ alleles responsible for impacting gene expression in S. pneumoniae and S. suis. The GAS type I system is located on the core chromosome, while sporadically present type II orphan methyltransferases were identified on prophages. By combining single-molecule real-time (SMRT) analyses of 10 distinct emm types along with phylogenomics of 224 strains, we were able to assign 13 methylation patterns to the GAS population. Inactivation of the type I RM system, occurring either naturally through phage insertion or through laboratory-induced gene deletion, abrogated DNA methylation detectable via either SMRT or MinION sequencing. Contrary to a previous report, inactivation of the type I system did not impact transcript levels of the gene (mga) encoding the key multigene activator protein (Mga) or Mga-regulated genes. Inactivation of the type I system significantly increased plasmid transformation rates. These data delineate the breadth of the core chromosomal type I RM system in the GAS population and clarify its role in immunity rather than impacting Mga regulon expression. IMPORTANCE The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci. The data described herein are from the first systematic analysis of DNA methylation in a beta-hemolytic streptococcus and one of the few analyses to comprehensively characterize DNA methylation across hundreds of strains of the same bacterial species. We clarify that DNA methylation in group A Streptococcus (GAS) is primarily due to a type I restriction modification (RM) system present in the core genome and does not impact mga-regulated virulence gene expression, but does impact immunity against exogenous DNA. The identification of the DNA motifs recognized by each type I RM system may assist with optimizing methods for GAS genetic manipulation and help us understand how bacterial pathogens acquire exogenous DNA elements.
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7
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Berbel D, Càmara J, González-Díaz A, Cubero M, López de Egea G, Martí S, Tubau F, Domínguez MA, Ardanuy C. Deciphering mobile genetic elements disseminating macrolide resistance in Streptococcus pyogenes over a 21 year period in Barcelona, Spain. J Antimicrob Chemother 2021; 76:1991-2003. [PMID: 34015100 DOI: 10.1093/jac/dkab130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/23/2021] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To phenotypically and genetically characterize the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among macrolide-resistant (MR) Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates collected in Barcelona, Spain. METHODS Antibiotic susceptibility testing was performed by microdilution. Isolates were emm and MLST typed and 55 were whole-genome sequenced to determine the nature of the macrolide resistance (MR) determinants and their larger MGE and chromosomal context. RESULTS Between 1998 and 2018, 142 of 1028 GAS (13.8%) were MR. Among 108 isolates available for molecular characterization, 41.7% had cMLSB, 30.5% iMLSB and 27.8% M phenotype. Eight erm(B)-containing strains were notable in having an MDR phenotype conferred by an MGE encoding several antibiotic resistance genes. MR isolates were comprised of several distinct genetic lineages as defined by the combination of emm and ST. Although most lineages were only transiently present, the emm11/ST403 clone persisted throughout the period. Two lineages, emm9/ST75 with erm(B) and emm77/ST63 with erm(TR), emerged in 2016-18. The erm(B) was predominantly encoded on the Tn916 family of transposons (21/31) with different genetic contexts, and in other MGEs (Tn6263, ICESpHKU372 and one harbouring an MDR cluster called ICESp1070HUB). The erm(TR) was found in ICESp2905 (8/17), ICESp1108-like (4/17), ICESpHKU165 (3/17) and two structures described in this study (IMESp316HUB and ICESp3729HUB). The M phenotype [mef(A)-msr(D)] was linked to phage φ1207.3. Eight integrative conjugative element/integrative mobilizable element (ICE/IME) cluster groups were classified on the basis of gene content within conjugation modules. These groups were found among MGEs, which corresponded with the MR-containing element or the site of integration. CONCLUSIONS We detected several different MGEs harbouring erm(B) or erm(TR). This is the first known description of Tn6263 in GAS and three MGEs [IMESp316HUB, ICESp3729HUB and ICESp1070HUB] associated with MR. Periods of high MR rates in our area were mainly associated with the expansion of certain predominant lineages, while in low MR periods different sporadic and low prevalence lineages were more frequent.
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Affiliation(s)
- Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Guillem López de Egea
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sara Martí
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - M Angeles Domínguez
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,Departament of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain.,CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain.,Departament of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
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8
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Hanage WP, Shelburne SA. Streptococcus pyogenes With Reduced Susceptibility to β-Lactams: How Big an Alarm Bell? Clin Infect Dis 2021; 71:205-206. [PMID: 31630163 DOI: 10.1093/cid/ciz1006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/17/2019] [Indexed: 01/26/2023] Open
Affiliation(s)
- William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Samuel A Shelburne
- Departments of Infectious Diseases and Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
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9
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Remmington A, Haywood S, Edgar J, Green LR, de Silva T, Turner CE. Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage. Microb Genom 2021; 7:mgen000482. [PMID: 33245690 PMCID: PMC8115907 DOI: 10.1099/mgen.0.000482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
The major human pathogen Streptococcus pyogenes shares an intimate evolutionary history with mobile genetic elements, which in many cases carry genes encoding bacterial virulence factors. During recent whole-genome sequencing of a longitudinal sample of S. pyogenes isolates in England, we identified a lineage within emm4 that clustered with the reference genome MEW427. Like MEW427, this lineage was characterized by substantial gene loss within all three prophage regions, compared to MGAS10750 and isolates outside of the MEW427-like lineage. Gene loss primarily affected lysogeny, replicative and regulatory modules, and to a lesser and more variable extent, structural genes. Importantly, prophage-encoded superantigen and DNase genes were retained in all isolates. In isolates where the prophage elements were complete, like MGAS10750, they could be induced experimentally, but not in MEW427-like isolates with degraded prophages. We also found gene loss within the chromosomal island SpyCIM4 of MEW427-like isolates, although surprisingly, the SpyCIM4 element could not be experimentally induced in either MGAS10750-like or MEW427-like isolates. This did not, however, appear to abolish expression of the mismatch repair operon, within which this element resides. The inclusion of further emm4 genomes in our analyses ratified our observations and revealed an international emm4 lineage characterized by prophage degradation. Intriguingly, the USA population of emm4 S. pyogenes appeared to constitute predominantly MEW427-like isolates, whereas the UK population comprised both MEW427-like and MGAS10750-like isolates. The degraded and cryptic nature of these elements may have important phenotypic and fitness ramifications for emm4 S. pyogenes, and the geographical distribution of this lineage raises interesting questions on the population dynamics of the genotype.
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Affiliation(s)
- Alex Remmington
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
| | - Samuel Haywood
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
| | - Julia Edgar
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke R. Green
- Department of Infection, Immunity and Cardiovascular Disease, Florey Institute, University of Sheffield, Sheffield, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Florey Institute, University of Sheffield, Sheffield, UK
| | - Claire E. Turner
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, UK
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10
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Walker MJ, Brouwer S, Forde BM, Worthing KA, McIntyre L, Sundac L, Maloney S, Roberts LW, Barnett TC, Richter J, Cork AJ, Irwin AD, You Y, Zhang J, Dougan G, Yuen KY, Nizet V, Beatson SA, Grimwood K, Davies MR. Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia. Clin Infect Dis 2020; 69:1232-1234. [PMID: 30721938 DOI: 10.1093/cid/ciz099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Sentinel hospital surveillance was instituted in Australia to detect the presence of pandemic group A Streptococcus strains causing scarlet fever. Genomic and phylogenetic analyses indicated the presence of an Australian GAS emm12 scarlet fever isolate related to United Kingdom outbreak strains. National surveillance to monitor this pandemic is recommended.
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Affiliation(s)
- Mark J Walker
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Stephan Brouwer
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Kate A Worthing
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Lana Sundac
- Pathology Queensland, Gold Coast Laboratory, Brisbane, Australia
| | - Sam Maloney
- Pathology Queensland, Gold Coast Laboratory, Brisbane, Australia
| | - Leah W Roberts
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Timothy C Barnett
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Johanna Richter
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, Australia.,Queensland Children's Hospital, Brisbane, Australia
| | - Yuanhai You
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation, Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing
| | - Jianzhong Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation, Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Kwok Y Yuen
- Department of Microbiology, University of Hong Kong, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong Special Administrative Region, China.,State Key Laboratory for Emerging Infectious Diseases, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Victor Nizet
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane
| | - Keith Grimwood
- Menzies Health Institute Queensland, Griffith University, Gold Coast.,Departments of Infectious Diseases and Pediatrics, Gold Coast Health, Queensland, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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Population Genomic Molecular Epidemiological Study of Macrolide-Resistant Streptococcus pyogenes in Iceland, 1995 to 2016: Identification of a Large Clonal Population with a pbp2x Mutation Conferring Reduced In Vitro β-Lactam Susceptibility. J Clin Microbiol 2020; 58:JCM.00638-20. [PMID: 32522827 PMCID: PMC7448646 DOI: 10.1128/jcm.00638-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Resistance to macrolide antibiotics is a global concern in the treatment of Streptococcus pyogenes (group A Streptococcus [GAS]) infections. In Iceland, since the detection of the first macrolide-resistant isolate in 1998, three epidemic waves of macrolide-resistant GAS infections have occurred, with peaks in 1999, 2004, and 2008. We conducted whole-genome sequencing of all 1,575 available GAS macrolide-resistant clinical isolates of all infection types collected at the national reference laboratory in Reykjavik, Iceland, from 1998 to 2016. Among 1,515 erythromycin-resistant isolates, 90.3% were of only three emm types, emm4 (n = 713), emm6 (n = 324), and emm12 (n = 332), with each being predominant in a distinct epidemic peak. The antibiotic efflux pump genes, mef(A) and msr(D), were present on chimeric mobile genetic elements in 99.3% of the macrolide-resistant isolates of these emm types. Of note, in addition to macrolide resistance, virtually all emm12 isolates had a single amino acid substitution in penicillin-binding protein PBP2X that conferred a 2-fold increased penicillin G and ampicillin MIC among the isolates tested. We conclude that each of the three large epidemic peaks of macrolide-resistant GAS infections occurring in Iceland since 1998 was caused by the emergence and clonal expansion of progenitor strains, with macrolide resistance being conferred predominantly by inducible Mef(A) and Msr(D) drug efflux pumps. The occurrence of emm12 strains with macrolide resistance and decreased beta-lactam susceptibility was unexpected and is of public health concern.
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12
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Eraso JM, Kachroo P, Olsen RJ, Beres SB, Zhu L, Badu T, Shannon S, Cantu CC, Saavedra MO, Kubiak SL, Porter AR, DeLeo FR, Musser JM. Genetic heterogeneity of the Spy1336/R28-Spy1337 virulence axis in Streptococcus pyogenes and effect on gene transcript levels and pathogenesis. PLoS One 2020; 15:e0229064. [PMID: 32214338 PMCID: PMC7098570 DOI: 10.1371/journal.pone.0229064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pyogenes is a strict human pathogen responsible for more than 700 million infections annually worldwide. Strains of serotype M28 S. pyogenes are typically among the five more abundant types causing invasive infections and pharyngitis in adults and children. Type M28 strains also have an unusual propensity to cause puerperal sepsis and neonatal disease. We recently discovered that a one-nucleotide indel in an intergenic homopolymeric tract located between genes Spy1336/R28 and Spy1337 altered virulence in a mouse model of infection. In the present study, we analyzed size variation in this homopolymeric tract and determined the extent of heterogeneity in the number of tandemly-repeated 79-amino acid domains in the coding region of Spy1336/R28 in large samples of strains recovered from humans with invasive infections. Both repeat sequence elements are highly polymorphic in natural populations of M28 strains. Variation in the homopolymeric tract results in (i) changes in transcript levels of Spy1336/R28 and Spy1337 in vitro, (ii) differences in virulence in a mouse model of necrotizing myositis, and (iii) global transcriptome changes as shown by RNAseq analysis of isogenic mutant strains. Variation in the number of tandem repeats in the coding sequence of Spy1336/R28 is responsible for size variation of R28 protein in natural populations. Isogenic mutant strains in which genes encoding R28 or transcriptional regulator Spy1337 are inactivated are significantly less virulent in a nonhuman primate model of necrotizing myositis. Our findings provide impetus for additional studies addressing the role of R28 and Spy1337 variation in pathogen-host interactions.
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Affiliation(s)
- Jesus M. Eraso
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Priyanka Kachroo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - 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, Texas, United States of America
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - 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, Texas, United States of America
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Traci Badu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Sydney Shannon
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Concepcion C. Cantu
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - 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, Texas, United States of America
| | - Samantha L. Kubiak
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, United States of America
| | - Adeline R. Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Frank R. DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - 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, Texas, United States of America
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
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13
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Abstract
Streptococcus pyogenes encodes multiple virulence factors and their presence is often related to the severity of the disease. We designed the system of four low-volume multiplex PCR reactions to detect genes encoding 20 virulence factors: spd3, sdc, sdaB, sdaD, speB, spyCEP, scpA, mac, sic, speL, speK, speM, speC, speI, speA, speH, speG, speJ, smeZ, and ssa. Classification of strains based on the virulence factors absence or presence correlates with PFGE MLST and emm typing results. The typing/detection system is fast and cost-effective, can be used to detect GAS virulence factors and as a rapid tool to effectively differentiate between strains.
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14
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Sanson MA, Macias OR, Shah BJ, Hanson B, Vega LA, Alamarat Z, Flores AR. Unexpected relationships between frequency of antimicrobial resistance, disease phenotype and emm type in group A Streptococcus. Microb Genom 2019; 5:e000316. [PMID: 31755853 PMCID: PMC6927302 DOI: 10.1099/mgen.0.000316] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Despite universal susceptibility to β-lactams, resistance to second-line antimicrobials (e.g. erythromycin) is increasingly common among group A Streptococcus (GAS). To better understand the frequency of regional GAS antimicrobial resistance, we screened a previously described GAS strain collection from Houston, TX, USA, for resistance to commonly used antimicrobials. A total of 100/929 (10.8 %) showed resistance to at least one antimicrobial. Tetracycline resistance was identified in 52 (5.6 %) GAS strains. The cumulative frequency of erythromycin and clindamycin resistance [macrolide (M) and macrolide-lincosamide-streptogramin (MLS) phenotypes] was greatest among invasive GAS strains (9.9 %) compared to that of strains derived from any other infection type (5.9 %, P=0.045). We identified emm types 11, 75, 77 and 92 as the only emm types with high (e.g. >50 %) within-emm type resistance and contributing to the majority (24/26; 92 %) of erythromycin/clindamycin resistance in invasive GAS. High-frequency resistance emm types were also significantly overrepresented in invasive GAS strains as indicated by invasive index. We performed whole-genome sequencing to define genetic elements associated with resistance among emm types 11, 75, 77 and 92. Diverse mobile elements contributed to GAS resistance including transposons, integrative conjugative elements, prophage and a plasmid. Phylogenetic analysis suggests recent clonal emergence of emm92 GAS strains. Our findings indicate that less frequently encountered GAS emm types disproportionately contribute to resistance phenotypes, are defined by diverse mobile genetic elements and may favour invasive disease.
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Affiliation(s)
- Misu A. Sanson
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | - Olga R. Macias
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | - Brittany J. Shah
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Luis Alberto Vega
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | - Zain Alamarat
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, Houston, TX, USA,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Sciences Center at Houston, Houston, TX, USA,*Correspondence: Anthony R. Flores,
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15
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Azuar A, Jin W, Mukaida S, Hussein WM, Toth I, Skwarczynski M. Recent Advances in the Development of Peptide Vaccines and Their Delivery Systems Against Group A Streptococcus. Vaccines (Basel) 2019; 7:E58. [PMID: 31266253 PMCID: PMC6789462 DOI: 10.3390/vaccines7030058] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023] Open
Abstract
Group A Streptococcus (GAS) infection can cause a variety of diseases in humans, ranging from common sore throats and skin infections, to more invasive diseases and life-threatening post-infectious diseases, such as rheumatic fever and rheumatic heart disease. Although research has been ongoing since 1923, vaccines against GAS are still not available to the public. Traditional approaches taken to develop vaccines for GAS failed due to poor efficacy and safety. Fortunately, headway has been made and modern subunit vaccines that administer minimal bacterial components provide an opportunity to finally overcome previous hurdles in GAS vaccine development. This review details the major antigens and strategies used for GAS vaccine development. The combination of antigen selection, peptide epitope modification and delivery systems have resulted in the discovery of promising peptide vaccines against GAS; these are currently in preclinical and clinical studies.
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Affiliation(s)
- Armira Azuar
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Wanli Jin
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Saori Mukaida
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo 11795, Egypt
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Pharmacy, Woolloongabba, The University of Queensland, QLD 4072, Australia
- Institute of Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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16
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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17
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Abstract
The clinico-epidemiological features of diseases caused by group A streptococci (GAS) is presented through the lens of the ecology, population genetics, and evolution of the organism. The serological targets of three typing schemes (M, T, SOF) are themselves GAS cell surface proteins that have a myriad of virulence functions and a diverse array of structural forms. Horizontal gene transfer expands the GAS antigenic cell surface repertoire by generating numerous combinations of M, T, and SOF antigens. However, horizontal gene transfer of the serotype determinant genes is not unconstrained, and therein lies a genetic organization that may signify adaptations to a narrow ecological niche, such as the primary tissue reservoirs of the human host. Adaptations may be further shaped by selection pressures such as herd immunity. Understanding the molecular evolution of GAS on multiple levels-short, intermediate, and long term-sheds insight on mechanisms of host-pathogen interactions, the emergence and spread of new clones, rational vaccine design, and public health interventions.
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18
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Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis. Nat Genet 2019; 51:548-559. [PMID: 30778225 DOI: 10.1038/s41588-018-0343-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022]
Abstract
Streptococcus pyogenes causes 700 million human infections annually worldwide, yet, despite a century of intensive effort, there is no licensed vaccine against this bacterium. Although a number of large-scale genomic studies of bacterial pathogens have been published, the relationships among the genome, transcriptome, and virulence in large bacterial populations remain poorly understood. We sequenced the genomes of 2,101 emm28 S. pyogenes invasive strains, from which we selected 492 phylogenetically diverse strains for transcriptome analysis and 50 strains for virulence assessment. Data integration provided a novel understanding of the virulence mechanisms of this model organism. Genome-wide association study, expression quantitative trait loci analysis, machine learning, and isogenic mutant strains identified and confirmed a one-nucleotide indel in an intergenic region that significantly alters global transcript profiles and ultimately virulence. The integrative strategy that we used is generally applicable to any microbe and may lead to new therapeutics for many human pathogens.
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19
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Abstract
ABSTRACT
Streptococcus pyogenes
(i.e., the group A
Streptococcus
) is a human-restricted and versatile bacterial pathogen that produces an impressive arsenal of both surface-expressed and secreted virulence factors. Although surface-expressed virulence factors are clearly vital for colonization, establishing infection, and the development of disease, the secreted virulence factors are likely the major mediators of tissue damage and toxicity seen during active infection. The collective exotoxin arsenal of
S. pyogenes
is rivaled by few bacterial pathogens and includes extracellular enzymes, membrane active proteins, and a variety of toxins that specifically target both the innate and adaptive arms of the immune system, including the superantigens; however, despite their role in
S. pyogenes
disease, each of these virulence factors has likely evolved with humans in the context of asymptomatic colonization and transmission. In this article, we focus on the biology of the true secreted exotoxins of the group A
Streptococcus
, as well as their roles in the pathogenesis of human disease.
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20
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Galloway-Peña J, DebRoy S, Brumlow C, Li X, Tran TT, Horstmann N, Yao H, Chen K, Wang F, Pan BF, Hawke DH, Thompson EJ, Arias CA, Fowler VG, Bhatti MM, Kalia A, Flores AR, Shelburne SA. Hypervirulent group A Streptococcus emergence in an acaspular background is associated with marked remodeling of the bacterial cell surface. PLoS One 2018; 13:e0207897. [PMID: 30517150 PMCID: PMC6281247 DOI: 10.1371/journal.pone.0207897] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/06/2018] [Indexed: 12/28/2022] Open
Abstract
Inactivating mutations in the control of virulence two-component regulatory system (covRS) often account for the hypervirulent phenotype in severe, invasive group A streptococcal (GAS) infections. As CovR represses production of the anti-phagocytic hyaluronic acid capsule, high level capsule production is generally considered critical to the hypervirulent phenotype induced by CovRS inactivation. There have recently been large outbreaks of GAS strains lacking capsule, but there are currently no data on the virulence of covRS-mutated, acapsular strains in vivo. We investigated the impact of CovRS inactivation in acapsular serotype M4 strains using a wild-type (M4-SC-1) and a naturally-occurring CovS-inactivated strain (M4-LC-1) that contains an 11bp covS insertion. M4-LC-1 was significantly more virulent in a mouse bacteremia model but caused smaller lesions in a subcutaneous mouse model. Over 10% of the genome showed significantly different transcript levels in M4-LC-1 vs. M4-SC-1 strain. Notably, the Mga regulon and multiple cell surface protein-encoding genes were strongly upregulated–a finding not observed for CovS-inactivated, encapsulated M1 or M3 GAS strains. Consistent with the transcriptomic data, transmission electron microscopy revealed markedly altered cell surface morphology of M4-LC-1 compared to M4-SC-1. Insertional inactivation of covS in M4-SC-1 recapitulated the transcriptome and cell surface morphology. Analysis of the cell surface following CovS-inactivation revealed that the upregulated proteins were part of the Mga regulon. Inactivation of mga in M4-LC-1 reduced transcript levels of multiple cell surface proteins and reversed the cell surface alterations consistent with the effect of CovS inactivation on cell surface composition being mediated by Mga. CovRS-inactivating mutations were detected in 20% of current invasive serotype M4 strains in the United States. Thus, we discovered that hypervirulent M4 GAS strains with covRS mutations can arise in an acapsular background and that such hypervirulence is associated with profound alteration of the cell surface.
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Affiliation(s)
- Jessica Galloway-Peña
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chelcy Brumlow
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Xiqi Li
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Truc T. Tran
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, UTHealth McGovern Medical School, Houston, Texas, United States of America
| | - Nicola Horstmann
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Bih-Fang Pan
- The Proteomics and Metabolomics Facility, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - David H. Hawke
- The Proteomics and Metabolomics Facility, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Erika J. Thompson
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Cesar A. Arias
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, UTHealth McGovern Medical School, Houston, Texas, United States of America
- Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, United States of America
- Molecular Genetics and Antimicrobial Resistance Unit-International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Micah M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Anthony R. Flores
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, UTHealth McGovern Medical School, Houston, Texas, United States of America
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, Texas, United States of America
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- The Proteomics and Metabolomics Facility, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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21
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DebRoy S, Li X, Kalia A, Galloway-Pena J, Shah BJ, Fowler VG, Flores AR, Shelburne SA. Identification of a chimeric emm gene and novel emm pattern in currently circulating strains of emm4 Group A Streptococcus. Microb Genom 2018; 4. [PMID: 30412460 PMCID: PMC6321872 DOI: 10.1099/mgen.0.000235] [Citation(s) in RCA: 6] [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] [Indexed: 11/24/2022] Open
Abstract
Group A Streptococcus (GAS) is classified on the basis of the sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm–enn fusion event in 51 out of 52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm–enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013–2017). The novel emm–enn gene fusion and new emm pattern has potential vaccine implications.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiqi Li
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jessica Galloway-Pena
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brittany J. Shah
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
- *Correspondence: Samuel A. Shelburne,
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22
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Phenotypic Variation in the Group A Streptococcus Due to Natural Mutation of the Accessory Protein-Encoding Gene rocA. mSphere 2018; 3:3/5/e00519-18. [PMID: 30333182 PMCID: PMC6193603 DOI: 10.1128/msphere.00519-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Populations of a bacterial pathogen, whether recovered from a single patient or from a worldwide study, are often a heterogeneous mix of genetically and phenotypically divergent strains. Such heterogeneity is of value in changing environments and arises via mechanisms such as gene gain or gene mutation. Here, we identify an isolate of serotype M12 group A Streptococcus (GAS) (Streptococcus pyogenes) that has a natural mutation in rocA, which encodes an accessory protein to the virulence-regulating two-component system CovR/CovS (CovR/S). Disruption of RocA activity results in the differential expression of multiple GAS virulence factors, including the anti-phagocytic hyaluronic acid capsule and the chemokine protease SpyCEP. While some of our data regarding RocA-regulated genes overlaps with previous studies, which were performed with isolates of alternate GAS serotypes, some variability was also observed. Perhaps as a consequence of this alternate regulatory activity, we discovered that the contribution of RocA to the ability of the M12 isolate to survive and proliferate in human blood ex vivo is opposite that previously observed in M1, M3, and M18 GAS strains. Specifically, rocA mutation reduced, rather than enhanced, survival of the isolate. Finally, we also present data from an analysis of rocA transcription and show that rocA is transcribed in both mono- and polycistronic mRNAs. In aggregate, our data provide insight into the important regulatory role of RocA and into the mechanisms and consequences of GAS phenotypic heterogeneity.IMPORTANCE This study investigates the regulatory and phenotypic consequences of a naturally occurring mutation in a strain of the bacterial pathogen the group A Streptococcus (Streptococcus pyogenes). We show that this mutation, which occurs in a regulator-encoding gene, rocA, leads to altered virulence factor expression and reduces the ability of this isolate to survive in human blood. Critically, the blood survival phenotype and the assortment of genes regulated by RocA differ compared to previous studies into RocA activity. The data are consistent with there being strain- or serotype-specific variability in RocA function. Given that phenotypic variants can lead to treatment failures and escape from preventative regimes, our data provide information with regard to a mechanism of phenotypic variation in a prevalent Gram-positive pathogen.
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23
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Weckel A, Ahamada D, Bellais S, Méhats C, Plainvert C, Longo M, Poyart C, Fouet A. The N-terminal domain of the R28 protein promotes emm28 group A Streptococcus adhesion to host cells via direct binding to three integrins. J Biol Chem 2018; 293:16006-16018. [PMID: 30150299 DOI: 10.1074/jbc.ra118.004134] [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: 05/23/2018] [Revised: 08/20/2018] [Indexed: 01/07/2023] Open
Abstract
Group A Streptococcus (GAS) is a human-specific pathogen responsible for a wide range of diseases, ranging from superficial to life-threatening invasive infections, including endometritis, and autoimmune sequelae. GAS strains express a vast repertoire of virulence factors that varies depending on the strain genotype, and many adhesin proteins that enable GAS to adhere to host cells are restricted to some genotypes. GAS emm28 is the third most prevalent genotype in invasive infections in France and is associated with gyneco-obstetrical infections. emm28 strains harbor R28, a cell wall-anchored surface protein that has previously been reported to promote adhesion to cervical epithelial cells. Here, using cellular and biochemical approaches, we sought to determine whether R28 supports adhesion also to other cells and to characterize its cognate receptor. We show that through its N-terminal domain, R28Nt, R28 promotes bacterial adhesion to both endometrial-epithelial and endometrial-stromal cells. R28Nt was further subdivided into two domains, and we found that both are involved in cell binding. R28Nt and both subdomains interacted directly with the laminin-binding α3β1, α6β1, and α6β4 integrins; interestingly, these bindings events did not require divalent cations. R28 is the first GAS adhesin reported to bind directly to integrins that are expressed in most epithelial cells. Finally, R28Nt also promoted binding to keratinocytes and pulmonary epithelial cells, suggesting that it may be involved in supporting the prevalence in invasive infections of the emm28 genotype.
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Affiliation(s)
- Antonin Weckel
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and
| | - Dorian Ahamada
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and
| | - Samuel Bellais
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and
| | - Céline Méhats
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and
| | - Céline Plainvert
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and.,the Centre National de Référence des Streptocoques and.,the Hôpitaux Universitaires Paris Centre, Institut Cochin, Assistance Publique Hôpitaux de Paris, 75014 Paris, France
| | - Magalie Longo
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and
| | - Claire Poyart
- From the INSERM U1016, Institut Cochin.,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and.,the Centre National de Référence des Streptocoques and.,the Hôpitaux Universitaires Paris Centre, Institut Cochin, Assistance Publique Hôpitaux de Paris, 75014 Paris, France
| | - Agnès Fouet
- From the INSERM U1016, Institut Cochin, .,CNRS UMR 8104, and.,Université Paris Descartes, UMR-S1016 Paris, France and.,the Centre National de Référence des Streptocoques and
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24
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Deutsch DR, Utter B, Verratti KJ, Sichtig H, Tallon LJ, Fischetti VA. Extra-Chromosomal DNA Sequencing Reveals Episomal Prophages Capable of Impacting Virulence Factor Expression in Staphylococcus aureus. Front Microbiol 2018; 9:1406. [PMID: 30013526 PMCID: PMC6036120 DOI: 10.3389/fmicb.2018.01406] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/07/2018] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus is a major human pathogen with well-characterized bacteriophage contributions to its virulence potential. Recently, we identified plasmidial and episomal prophages in S. aureus strains using an extra-chromosomal DNA (exDNA) isolation and sequencing approach, uncovering the plasmidial phage ϕBU01, which was found to encode important virulence determinants. Here, we expanded our extra-chromosomal sequencing of S. aureus, selecting 15 diverse clinical isolates with known chromosomal sequences for exDNA isolation and next-generation sequencing. We uncovered the presence of additional episomal prophages in 5 of 15 samples, but did not identify any plasmidial prophages. exDNA isolation was found to enrich for circular prophage elements, and qPCR characterization of the strains revealed that such prophage enrichment is detectable only in exDNA samples and would likely be missed in whole-genome DNA preparations (e.g., detection of episomal prophages did not correlate with higher prophage excision rates nor higher excised prophage copy numbers in qPCR experiments using whole-genome DNA). In S. aureus MSSA476, we found that enrichment and excision of the prophage ϕSa4ms into the cytoplasm was temporal and that episomal prophage localization did not appear to be a precursor to lytic cycle replication, suggesting ϕSa4ms excision into the cytoplasm may be part of a novel lysogenic switch. For example, we show that ϕSa4ms excision alters the promoter and transcription of htrA2 , encoding a stress-response serine protease, and that alternative promotion of htrA2 confers increased heat-stress survival in S. aureus COL. Overall, exDNA isolation and focused sequencing may offer a more complete genomic picture for bacterial pathogens, offering insights into important chromosomal dynamics likely missed with whole-genome DNA-based approaches.
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Affiliation(s)
- Douglas R Deutsch
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, United States
| | - Bryan Utter
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, United States
| | - Kathleen J Verratti
- Applied Physics Laboratory, National Security Systems Biology Center, Johns Hopkins University, Laurel, MD, United States
| | - Heike Sichtig
- Center for Devices and Radiological Health, Office of In Vitro Diagnostics, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Luke J Tallon
- Genomics Resource Center, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, United States
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25
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Buckley SJ, Timms P, Davies MR, McMillan DJ. In silico characterisation of the two-component system regulators of Streptococcus pyogenes. PLoS One 2018; 13:e0199163. [PMID: 29927994 PMCID: PMC6013163 DOI: 10.1371/journal.pone.0199163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/02/2018] [Indexed: 12/14/2022] Open
Abstract
Bacteria respond to environmental changes through the co-ordinated regulation of gene expression, often mediated by two-component regulatory systems (TCS). Group A Streptococcus (GAS), a bacterium which infects multiple human body sites and causes multiple diseases, possesses up to 14 TCS. In this study we examined genetic variation in the coding sequences and non-coding DNA upstream of these TCS as a method for evaluating relationships between different GAS emm-types, and potential associations with GAS disease. Twelve of the 14 TCS were present in 90% of the genomes examined. The length of the intergenic regions (IGRs) upstream of TCS coding regions varied from 39 to 345 nucleotides, with an average nucleotide diversity of 0.0064. Overall, IGR allelic variation was generally conserved with an emm-type. Subsequent phylogenetic analysis of concatenated sequences based on all TCS IGR sequences grouped genomes of the same emm-type together. However grouping with emm-pattern and emm-cluster-types was much weaker, suggesting epidemiological and functional properties associated with the latter are not due to evolutionary relatedness of emm-types. All emm5, emm6 and most of the emm18 genomes, all historically considered rheumatogenic emm-types clustered together, suggesting a shared evolutionary history. However emm1, emm3 and several emm18 genomes did not cluster within this group. These latter emm18 isolates were epidemiologically distinct from other emm18 genomes in study, providing evidence for local variation. emm-types associated with invasive disease or nephritogenicity also did not cluster together. Considering the TCS coding sequences (cds), correlation with emm-type was weaker than for the IGRs, and no strong correlation with disease was observed. Deletion of the malate transporter, maeP, was identified that serves as a putative marker for the emm89.0 subtype, which has been implicated in invasive outbreaks. A recombination-related, subclade-forming DNA motif was identified in the putative receiver domain of the Spy1556 response regulator that correlated with throat-associated emm-pattern-type A-C strains.
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Affiliation(s)
- Sean J. Buckley
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Peter Timms
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mark R. Davies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David J. McMillan
- Inflammation and Healing Biomedical Research Cluster, and School of Health and Sports Sciences, Faculty of Science, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Rößler S, Berner R, Jacobs E, Toepfner N. Prevalence and molecular diversity of invasive Streptococcus dysgalactiae and Streptococcus pyogenes in a German tertiary care medical centre. Eur J Clin Microbiol Infect Dis 2018; 37:1325-1332. [PMID: 29725958 DOI: 10.1007/s10096-018-3254-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022]
Abstract
Prevalence of invasive ß-haemolytic streptococci (BHS) at a tertiary care hospital and molecular diversity of S. pyogenes and S. dysgalactiae was studied. Between 2012 and 2016, all blood culture sets (n = 55,839), CSF (n = 8413) and soft tissue (n = 20,926) samples were analysed for BHS positivity using HYBASE software. Molecular profiles of 99 S. pyogenes and S. dysgalactiae were identified by sequencing of M protein genes (emm types) and multiplex PCR typing of 20 other virulence determinants. Streptococci contributed to 6.2% of blood, 10.7% of CSF and 14.5% of soft tissue isolates, being among the most common invasive isolates. The overall rates of invasive S. pyogenes, S. agalactiae, S. dysgalactiae and S. pneumoniae were 2.4, 4.4, 2.1, and 5.3%. Whereas S. pneumoniae was 1.5% more common in CSF samples, BHS isolates were 2-fold and 11-fold higher in bacteraemia and invasive soft tissue infections. Genetic BHS typing revealed wide molecular diversity of invasive and noninvasive group A and group G BHS, whereas one emm-type (stG62647.0) and no other virulence determinants except scpA were detected in invasive group C BHS. BHS were important invasive pathogens, outpacing S. pneumoniae in bacteraemia and invasive soft tissue infections. The incidence of S. dysgalactiae infections was comparable to that of S. pyogenes even with less diversity of molecular virulence. The results of this study emphasise the need for awareness of BHS invasiveness in humans and the need to develop BHS prevention strategies.
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Affiliation(s)
- S Rößler
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - R Berner
- Department of Paediatrics, Carl Gustav Carus University Hospital, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - E Jacobs
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - N Toepfner
- Department of Paediatrics, Carl Gustav Carus University Hospital, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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27
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Makthal N, Do H, VanderWal AR, Olsen RJ, Musser JM, Kumaraswami M. Signaling by a Conserved Quorum Sensing Pathway Contributes to Growth Ex Vivo and Oropharyngeal Colonization of Human Pathogen Group A Streptococcus. Infect Immun 2018; 86:e00169-18. [PMID: 29531135 PMCID: PMC5913841 DOI: 10.1128/iai.00169-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 02/06/2023] Open
Abstract
Bacterial virulence factor production is a highly coordinated process. The temporal pattern of bacterial gene expression varies in different host anatomic sites to overcome niche-specific challenges. The human pathogen group A streptococcus (GAS) produces a potent secreted protease, SpeB, that is crucial for pathogenesis. Recently, we discovered that a quorum sensing pathway comprised of a leaderless short peptide, SpeB-inducing peptide (SIP), and a cytosolic global regulator, RopB, controls speB expression in concert with bacterial population density. The SIP signaling pathway is active in vivo and contributes significantly to GAS invasive infections. In the current study, we investigated the role of the SIP signaling pathway in GAS-host interactions during oropharyngeal colonization. The SIP signaling pathway is functional during growth ex vivo in human saliva. SIP-mediated speB expression plays a crucial role in GAS colonization of the mouse oropharynx. GAS employs a distinct pattern of SpeB production during growth ex vivo in saliva that includes a transient burst of speB expression during early stages of growth coupled with sustained levels of secreted SpeB protein. SpeB production aids GAS survival by degrading LL37, an abundant human antimicrobial peptide. We found that SIP signaling occurs during growth in human blood ex vivo. Moreover, the SIP signaling pathway is critical for GAS survival in blood. SIP-dependent speB regulation is functional in strains of diverse emm types, indicating that SIP signaling is a conserved virulence regulatory mechanism. Our discoveries have implications for future translational studies.
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Affiliation(s)
- Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
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28
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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: 2.3] [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.
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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
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29
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Streptococcal pharyngitis and rheumatic heart disease: the superantigen hypothesis revisited. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29530660 DOI: 10.1016/j.meegid.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Streptococcus pyogenes is a human-specific and globally prominent bacterial pathogen that despite causing numerous human infections, this bacterium is normally found in an asymptomatic carrier state. This review provides an overview of both bacterial and human factors that likely play an important role in nasopharyngeal colonization and pharyngitis, as well as the development of acute rheumatic fever and rheumatic heart disease. Here we highlight a recently described role for bacterial superantigens in promoting acute nasopharyngeal infection, and discuss how these immune system activating toxins could be crucial to initiate the autoimmune process in rheumatic heart disease.
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30
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Remmington A, Turner CE. The DNases of pathogenic Lancefield streptococci. MICROBIOLOGY (READING, ENGLAND) 2018; 164:242-250. [PMID: 29458565 DOI: 10.1099/mic.0.000612] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNases are abundant among the pathogenic streptococci, with most species harbouring genes for at least one. Despite their prevalence, however, the role for these extracellular enzymes is still relatively unclear. The DNases of the Lancefield group A Streptococcus, S. pyogenes are the best characterized, with a total of eight DNase genes identified so far. Six are known to be associated with integrated prophages. Two are chromosomally encoded, and one of these is cell-wall anchored. Homologues of both prophage-associated and chromosomally encoded S. pyogenes DNases have been identified in other streptococcal species, as well as other unique DNases. A major role identified for streptococcal DNases appears to be in the destruction of extracellular traps produced by immune cells, such as neutrophils, to ensnare bacteria and kill them. These traps are composed primarily of DNA which can be degraded by the secreted and cell-wall-anchored streptococcal DNases. DNases can also reduce TLR-9 signalling to dampen the immune response and produce cytotoxic deoxyadenosine to limit phagocytosis. Upper respiratory tract infection models of S. pyogenes have identified a role for DNases in potentiating infection and transmission, possibly by limiting the immune response or through some other unknown mechanism. Streptococcal DNases may also be involved in interacting with other microbial communities through communication, bacterial killing and disruption of competitive biofilms, or control of their own biofilm production. The contribution of DNases to pathogenesis may therefore be wide ranging and extend beyond direct interference with the host immune response.
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Affiliation(s)
- Alex Remmington
- Department of Molecular Biology and Biotechnology, The Florey Institute, University of Sheffield, Sheffield, UK
| | - Claire E Turner
- Department of Molecular Biology and Biotechnology, The Florey Institute, University of Sheffield, Sheffield, UK
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31
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Flórez AB, Mayo B. Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances. Front Microbiol 2017; 8:2608. [PMID: 29312272 PMCID: PMC5744436 DOI: 10.3389/fmicb.2017.02608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 12/26/2022] Open
Abstract
The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability.
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Affiliation(s)
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (CSIC), Paseo Río Linares s/n, Asturias, Spain
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32
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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: 15] [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.
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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
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33
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Sitkiewicz I. How to become a killer, or is it all accidental? Virulence strategies in oral streptococci. Mol Oral Microbiol 2017; 33:1-12. [PMID: 28727895 DOI: 10.1111/omi.12192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 01/03/2023]
Abstract
Streptococci are a diverse group of Gram-positive microorganisms sharing common virulence traits and similar strategies to escape the oral niche and establish an infection in other parts of the host organism. Invasive infection with oral streptococci is "a perfect storm" that requires the concerted action of multiple biotic and abiotic factors. Our understanding of streptococcal pathogenicity and infectivity should probably be less mechanistic and driven not only by the identification of novel virulence factors. The observed diversity of the genus, including the range of virulence and pathogenicity mechanisms, is most likely the result of interspecies interactions, a massive horizontal gene transfer between streptococci within a shared oral niche, recombination events, selection of specialized clones, and modification of regulatory circuits. Selective pressure by the host and bacterial communities is a driving force for the selection of virulence traits and shaping the streptococcal genome. Global regulatory events driving niche adaptation and interactions with bacterial communities and the host steer research interests towards attempts to define the oral interactome on the transcriptional level and define signal cross-feeding and co-expression and co-regulation of virulence genes.
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Affiliation(s)
- I Sitkiewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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34
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Oda M, Domon H, Kurosawa M, Isono T, Maekawa T, Yamaguchi M, Kawabata S, Terao Y. Streptococcus pyogenes Phospholipase A 2 Induces the Expression of Adhesion Molecules on Human Umbilical Vein Endothelial Cells and Aorta of Mice. Front Cell Infect Microbiol 2017; 7:300. [PMID: 28713783 PMCID: PMC5491884 DOI: 10.3389/fcimb.2017.00300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
The Streptococcus pyogenes phospholipase A2 (SlaA) gene is highly conserved in the M3 serotype of group A S. pyogenes, which often involves hypervirulent clones. However, the role of SlaA in S. pyogenes pathogenesis is unclear. Herein, we report that SlaA induces the expression of intercellular adhesion molecule 1 (ICAM1) and vascular cell adhesion molecule 1 (VCAM1) via the arachidonic acid signaling cascade. Notably, recombinant SlaA induced ICAM1 and VCAM1 expression in human umbilical vein endothelial cells (HUVECs), resulting in enhanced adhesion of human monocytic leukemia (THP-1) cells. However, C134A, a variant enzyme with no enzymatic activity, did not induce such events. In addition, culture supernatants from S. pyogenes SSI-1 enhanced the adhesion of THP-1 cells to HUVECs, but culture supernatants from the ΔslaA isogenic mutant strain had limited effects. Aspirin, a cyclooxygenase 2 inhibitor, prevented the adhesion of THP-1 cells to HUVECs and did not induce ICAM1 and VCAM1 expression in HUVECs treated with SlaA. However, zileuton, a 5-lipoxygenase inhibitor, did not exhibit such effects. Furthermore, pre-administration of aspirin in mice intravenously injected with SlaA attenuated the transcriptional abundance of ICAM1 and VCAM1 in the aorta. These results suggested that SlaA from S. pyogenes stimulates the expression of adhesion molecules in vascular endothelial cells. Thus, SlaA contributes to the inflammation of vascular endothelial cells upon S. pyogenes infection.
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Affiliation(s)
- Masataka Oda
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan.,Department of Microbiology and Infection Control Sciences, Kyoto Pharmaceutical UniversityKyoto, Japan
| | - Hisanori Domon
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan.,Research Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan
| | - Mie Kurosawa
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan
| | - Toshihito Isono
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan
| | - Tomoki Maekawa
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan.,Research Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan
| | - Masaya Yamaguchi
- Department of Oral and Molecular Microbiology, Osaka University, Graduate School of DentistryOsaka, Japan
| | - Shigetada Kawabata
- Department of Oral and Molecular Microbiology, Osaka University, Graduate School of DentistryOsaka, Japan
| | - Yutaka Terao
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan.,Research Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata UniversityNiigata, Japan
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35
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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. 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: 6.1] [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.
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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
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Ibrahim J, Eisen JA, Jospin G, Coil DA, Khazen G, Tokajian S. Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections. PLoS One 2016; 11:e0168177. [PMID: 27977735 PMCID: PMC5158041 DOI: 10.1371/journal.pone.0168177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/25/2016] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pyogenes is a very important human pathogen, commonly associated with skin or throat infections but can also cause life-threatening situations including sepsis, streptococcal toxic shock syndrome, and necrotizing fasciitis. Various studies involving typing and molecular characterization of S. pyogenes have been published to date; however next-generation sequencing (NGS) studies provide a comprehensive collection of an organism’s genetic variation. In this study, the genomes of nine S. pyogenes isolates associated with pharyngitis and skin infection were sequenced and studied for the presence of virulence genes, resistance elements, prophages, genomic recombination, and other genomic features. Additionally, a comparative phylogenetic analysis of the isolates with global clones highlighted their possible evolutionary lineage and their site of infection. The genomes were found to also house a multitude of features including gene regulation systems, virulence factors and antimicrobial resistance mechanisms.
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Affiliation(s)
- Joe Ibrahim
- Department of Natural Sciences, Lebanese American University, School of Arts and Sciences, Byblos, Lebanon
| | - Jonathan A. Eisen
- University of California Davis Genome Center, Davis, California, United States of America
| | - Guillaume Jospin
- University of California Davis Genome Center, Davis, California, United States of America
| | - David A. Coil
- University of California Davis Genome Center, Davis, California, United States of America
| | - Georges Khazen
- Department of Computer Science and Mathematics, Lebanese American University, School of Arts and Sciences, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, School of Arts and Sciences, Byblos, Lebanon
- * E-mail:
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Huang J, Ma J, Shang K, Hu X, Liang Y, Li D, Wu Z, Dai L, Chen L, Wang L. Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci. Front Cell Infect Microbiol 2016; 6:118. [PMID: 27774436 PMCID: PMC5053989 DOI: 10.3389/fcimb.2016.00118] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 02/04/2023] Open
Abstract
Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.
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Affiliation(s)
- Jinhu Huang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jiale Ma
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Yuan Liang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Daiwei Li
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State UniversityAmes, IA, USA; Department of Pharmacy, The Second Hospital of Dalian Medical UniversityDalian, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Li Chen
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Liping Wang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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Guérin F, Isnard C, Bucquet F, Fines-Guyon M, Giard JC, Burrus V, Cattoir V. Novel chromosome-encoded erm(47) determinant responsible for constitutive MLSB resistance in Helcococcus kunzii. J Antimicrob Chemother 2016; 71:3046-3049. [PMID: 27494920 DOI: 10.1093/jac/dkw290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The aim of the study was to identify the determinant responsible for erythromycin resistance in Helcococcus kunzii clinical isolate UCN99 and to characterize the genetic support and environment of this novel gene. METHODS MICs were determined using the broth microdilution method according to EUCAST guidelines. The entire genome sequence of H. kunzii UCN99 was determined using a 454/Roche GS Junior sequencer. The fragment encompassing the new resistance gene and its own promoter was cloned into the pAT29 shuttle vector and the recombinant plasmid pAT29Ωerm(47) was expressed in both Staphylococcus aureus and Streptococcus agalactiae. The transcription start site (TSS) was experimentally determined by 5' RACE-PCR. RESULTS UCN99 exhibited a constitutive macrolide/lincosamide/streptogramin B (MLSB) resistance phenotype, suggesting the presence of an Erm protein. WGS allowed the identification of a novel gene, named erm(47), encoding a protein sharing 44%-48% amino acid identity with known Erm methylases. In both S. aureus and S. agalactiae, the introduction of pAT29Ωerm(47) conferred a significant increase (≥16-fold) in MICs of all macrolides and lincosamides tested, as well as a 4-fold increase in MICs of quinupristin (streptogramin B), confirming the MLSB resistance. The TSS identification revealed the presence of a short leader peptide, potentially implicated in a translational attenuation mechanism. It was also demonstrated that erm(47) was harboured by a 81 kb genomic island integrated into a chromosomal gene. CONCLUSIONS This is the first description of a novel MLSB resistance determinant, named erm(47). The prevalence of this gene among Gram-positive cocci must be further investigated to determine its clinical significance.
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Affiliation(s)
- François Guérin
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Caen, France
| | - Christophe Isnard
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France
| | - Fiona Bucquet
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France
| | - Marguerite Fines-Guyon
- CHU de Caen, Service de Microbiologie, Caen, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Caen, France
| | - Jean-Christophe Giard
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France
| | - Vincent Burrus
- Université Sherbrooke, Département de Biologie, Faculté des Sciences, Sherbrooke, Québec, Canada
| | - Vincent Cattoir
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France .,CHU de Caen, Service de Microbiologie, Caen, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Caen, France
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Al-Shahib A, Underwood A, Afshar B, Turner CE, Lamagni T, Sriskandan S, Efstratiou A. Emergence of a novel lineage containing a prophage in emm/M3 group A Streptococcus associated with upsurge in invasive disease in the UK. Microb Genom 2016; 2:e000059. [PMID: 28348855 PMCID: PMC5320645 DOI: 10.1099/mgen.0.000059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/23/2022] Open
Abstract
A sudden increase in invasive Group A Streptococcus (iGAS) infections associated with emm/M3 isolates during the winter of 2008/09 prompted the initiation of enhanced surveillance in England. In order to characterise the population of emm/M3 GAS within the UK and determine bacterial factors that might be responsible for this upsurge, 442 emm/M3 isolates from cases of invasive and non-invasive infections during the period 2001-2013 were subjected to whole genome sequencing. MLST analysis differentiated emm/M3 isolates into three sequence types (STs): ST15, ST315 and ST406. Analysis of the whole genome SNP-based phylogeny showed that the majority of isolates from the 2008-2009 upsurge period belonged to a distinct lineage characterized by the presence of a prophage carrying the speC exotoxin and spd1 DNAase genes but loss of two other prophages considered typical of the emm/M3 lineage. This lineage was significantly associated with the upsurge in iGAS cases and we postulate that the upsurge could be attributed in part to expansion of this novel prophage-containing lineage within the population. The study underlines the importance of prompt genomic analysis of changes in the GAS population, providing an advanced public health warning system for newly emergent, pathogenic strains.
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Affiliation(s)
- Ali Al-Shahib
- Disease and Informatics, 61 Colindale Avenue, Public Health England, Colindale, UK
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Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes. mBio 2016; 7:mBio.00403-16. [PMID: 27247229 PMCID: PMC4895104 DOI: 10.1128/mbio.00403-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects. The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.
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42
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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: 2.9] [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.
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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
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Mingoia M, Morici E, Marini E, Brenciani A, Giovanetti E, Varaldo PE. Macrolide resistance gene erm(TR) and erm(TR)-carrying genetic elements in Streptococcus agalactiae: characterization of ICESagTR7, a new composite element containing IMESp2907. J Antimicrob Chemother 2015; 71:593-600. [PMID: 26679245 DOI: 10.1093/jac/dkv408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/03/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The objective of this study was to investigate macrolide-resistant Streptococcus agalactiae isolates harbouring erm(TR), an erm(A) gene subclass, with emphasis on their erm(TR)-carrying genetic elements. Four erm(TR)-carrying elements have been described to date: three closely related (ICE10750-RD.2, Tn1806 and ICESp1108) in Streptococcus pyogenes, Streptococcus pneumoniae and S. pyogenes, respectively; and one completely different (IMESp2907, embedded in ICESp2906 to form ICESp2905) in S. pyogenes. METHODS Seventeen macrolide-resistant erm(TR)-positive S. agalactiae isolates were phenotypically and genotypically characterized. Their erm(TR)-carrying elements were explored by analysing the distinctive recombination genes of known erm(TR)-carrying integrative and conjugative elements (ICEs) and by PCR mapping. The new genetic context and organization of IMESp2907 in S. agalactiae were explored using several experimental procedures and in silico analyses. RESULTS Five isolates harboured ICE10750-RD.2/Tn1806, five isolates harboured ICESp1108 and five isolates bore unknown erm(TR)-carrying elements. The remaining two isolates, exhibiting identical serotypes and pulsotypes, harboured IMESp2907 in a new genetic environment, which was further investigated in one of the two isolates, SagTR7. IMESp2907 was circularizable in S. agalactiae, as described in S. pyogenes. The new IMESp2907 junctions were identified based on its site-specific integration; the att sites were almost identical to those in S. pyogenes. In strain SagTR7, erm(TR)-carrying IMESp2907 was embedded in an erm(TR)-less internal element related to ICE10750-RD.2/Tn1806, which, in turn, was embedded in an ICESde3396-like element. The resulting whole ICE, ICESagTR7 (∼129 kb), was integrated into the chromosome downstream of the rplL gene, and was excisable in circular form and transferable by conjugation. CONCLUSIONS This is the first study exploring erm(TR)-carrying genetic elements in S. agalactiae.
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Affiliation(s)
- Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Morici
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Emanuela Marini
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
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Reglinski M, Gierula M, Lynskey NN, Edwards RJ, Sriskandan S. Identification of the Streptococcus pyogenes surface antigens recognised by pooled human immunoglobulin. Sci Rep 2015; 5:15825. [PMID: 26508447 PMCID: PMC4623672 DOI: 10.1038/srep15825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/01/2015] [Indexed: 11/30/2022] Open
Abstract
Immunity to common bacteria requires the generation of antibodies that promote opsonophagocytosis and neutralise toxins. Pooled human immunoglobulin is widely advocated as an adjunctive treatment for clinical Streptococcus pyogenes infection however, the protein targets of the reagent remain ill defined. Affinity purification of the anti-streptococcal antibodies present within pooled immunoglobulin resulted in the generation of an IgG preparation that promoted opsonophagocytic killing of S. pyogenes in vitro and provided passive immunity in vivo. Isolation of the streptococcal surface proteins recognised by pooled human immunoglobulin permitted identification and ranking of 94 protein antigens, ten of which were reproducibly identified across four contemporary invasive S. pyogenes serotypes (M1, M3, M12 and M89). The data provide novel insight into the action of pooled human immunoglobulin during invasive S. pyogenes infection, and demonstrate a potential route to enhance the efficacy of antibody based therapies.
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Affiliation(s)
- Mark Reglinski
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, United Kingdom
| | - Magdalena Gierula
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, United Kingdom
| | - Nicola N Lynskey
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, United Kingdom
| | - Robert J Edwards
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, United Kingdom
| | - Shiranee Sriskandan
- Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, United Kingdom
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45
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Miller EW, Danger JL, Ramalinga AB, Horstmann N, Shelburne SA, Sumby P. Regulatory rewiring confers serotype-specific hyper-virulence in the human pathogen group A Streptococcus. Mol Microbiol 2015; 98:473-89. [PMID: 26192205 DOI: 10.1111/mmi.13136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2015] [Indexed: 12/18/2022]
Abstract
Phenotypic heterogeneity is commonly observed between isolates of a given pathogen. Epidemiological analyses have identified that some serotypes of the group A Streptococcus (GAS) are non-randomly associated with particular disease manifestations. Here, we present evidence that a contributing factor to the association of serotype M3 GAS isolates with severe invasive infections is the presence of a null mutant allele for the orphan kinase RocA. Through use of RNAseq analysis, we identified that the natural rocA mutation present within M3 isolates leads to the enhanced expression of more than a dozen immunomodulatory virulence factors, enhancing phenotypes such as hemolysis and NAD(+) hydrolysis. Consequently, an M3 GAS isolate survived human phagocytic killing at a level 13-fold higher than a rocA complemented derivative, and was significantly more virulent in a murine bacteremia model of infection. Finally, we identified that RocA functions through the CovR/S two-component system as levels of phosphorylated CovR increase in the presence of functional RocA, and RocA has no regulatory activity following covR or covS mutation. Our data are consistent with RocA interfacing with the CovR/S two-component system, and that the absence of this activity in M3 GAS potentiates the severity of invasive infections caused by isolates of this serotype.
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Affiliation(s)
- Eric W Miller
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Jessica L Danger
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Anupama B Ramalinga
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Nicola Horstmann
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul Sumby
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
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46
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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: 54] [Impact Index Per Article: 6.0] [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.
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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.
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Marini E, Palmieri C, Magi G, Facinelli B. Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes. Vet Microbiol 2015; 178:99-104. [DOI: 10.1016/j.vetmic.2015.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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Bergmann R, Nitsche-Schmitz DP. Small plasmids in Streptococcus dysgalactiae subsp. equisimilis isolated from human infections in southern India and sequence analysis of two novel plasmids. Int J Med Microbiol 2015; 305:365-9. [PMID: 25769407 DOI: 10.1016/j.ijmm.2015.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/06/2015] [Accepted: 02/09/2015] [Indexed: 11/26/2022] Open
Abstract
Small plasmids are frequently found in S. pyogenes isolates from human infections in India. Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a streptococcal subspecies that is genetically similar to S. pyogenes and has a similar ecology. Therefore, we determined the distribution of small plasmids in a collection of 254 SDSE isolates, comprising 44 different emm-types and emm non-typable strains, from southern India, utilizing an established PCR based method. Briefly, 1.2% (n=3) of the isolates were positive for repA (encoding the replication initiation protein A) and 1.6% (n=4) were repB positive (encoding the replication initiation protein B). One isolate (G315) showed a co-detection of repB and dysA (encoding the bacteriocin dysgalacticin) which is characteristic for previously described pDN281/pW2580-like plasmids, observed in SDSE and S. pyogenes. The remaining plasmid bearing isolates showed no characteristic co-detection of known plasmid-associated genes. Thus, plasmids pG271 and pG279, representatives for repB and repA harboring plasmids, respectively, were analyzed. The plasmids pG271 and pG279 could be assigned to the pMV158 and the pC194/pUB110 family of rolling-circle plasmids, respectively. Like the characterized small native plasmids of S. pyogenes from India, the SDSE plasmids discovered and described in this study did not carry any of the known antibiotic resistance genes. SDSE bore less of the investigated small native plasmids that were distinct from the small native plasmids of S. pyogenes of the same geographic region. This indicates a low rate of lateral transfer of these genetic elements between these two related streptococcal species.
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Affiliation(s)
- René Bergmann
- Department of Medical Microbiology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
| | - D Patric Nitsche-Schmitz
- Department of Medical Microbiology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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Danger JL, Cao TN, Cao TH, Sarkar P, Treviño J, Pflughoeft KJ, Sumby P. The small regulatory RNA FasX enhances group A Streptococcus virulence and inhibits pilus expression via serotype-specific targets. Mol Microbiol 2015; 96:249-62. [PMID: 25586884 DOI: 10.1111/mmi.12935] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 12/31/2022]
Abstract
Bacterial pathogens commonly show intra-species variation in virulence factor expression and often this correlates with pathogenic potential. The group A Streptococcus (GAS) produces a small regulatory RNA (sRNA), FasX, which regulates the expression of pili and the thrombolytic agent streptokinase. As GAS serotypes are polymorphic regarding (a) FasX abundance, (b) the fibronectin, collagen, T-antigen (FCT) region of the genome, which contains the pilus genes (nine different FCT-types), and (c) the streptokinase-encoding gene (ska) sequence (two different alleles), we sought to test whether FasX regulates pilus and streptokinase expression in a serotype-specific manner. Parental, fasX mutant and complemented derivatives of serotype M1 (ska-2, FCT-2), M2 (ska-1, FCT-6), M6 (ska-2, FCT-1) and M28 (ska-1, FCT-4) isolates were compared. While FasX reduced pilus expression in each serotype, the molecular basis differed, as FasX bound, and inhibited the translation of, different FCT-region mRNAs. FasX enhanced streptokinase expression in each serotype, although the degree of regulation varied. Finally, we established that the regulation afforded by FasX enhances GAS virulence, assessed by a model of bacteremia using human plasminogen-expressing mice. Our data are the first to identify and characterize serotype-specific regulation by an sRNA in GAS, and to show an sRNA directly contributes to GAS virulence.
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Affiliation(s)
- Jessica L Danger
- Center for Molecular Medicine, Department of Microbiology & Immunology, University of Nevada, School of Medicine, Reno, Nevada, USA
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Giovanetti E, Brenciani A, Morroni G, Tiberi E, Pasquaroli S, Mingoia M, Varaldo PE. Transduction of the Streptococcus pyogenes bacteriophage Φm46.1, carrying resistance genes mef(A) and tet(O), to other Streptococcus species. Front Microbiol 2015; 5:746. [PMID: 25620959 PMCID: PMC4288039 DOI: 10.3389/fmicb.2014.00746] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/09/2014] [Indexed: 11/13/2022] Open
Abstract
Φm46.1 – Streptococcus pyogenes bacteriophage carrying mef(A) and tet(O), respectively, encoding resistance to macrolides (M phenotype) and tetracycline – is widespread in S. pyogenes but has not been reported outside this species. Φm46.1 is transferable in vitro among S. pyogenes isolates, but no information is available about its transferability to other Streptococcus species. We thus investigated Φm46.1 for its ability to be transduced in vitro to recipients of different Streptococcus species. Transductants were obtained from recipients of Streptococcus agalactiae, Streptococcus gordonii, and Streptococcus suis. Retransfer was always achieved, and from S. suis to S. pyogenes occurred at a much greater frequency than in the opposite direction. In transductants Φm46.1 retained its functional properties, such as inducibility with mitomycin C, presence both as a prophage and as a free circular form, and transferability. The transductants shared the same Φm46.1 chromosomal integration site as the donor, at the 3′ end of a conserved RNA uracil methyltransferase (rum) gene, which is an integration hotspot for a variety of genetic elements. No transfer occurred to recipients of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus salivarius, even though rum-like genes were also detected in the sequenced genomes of these species. A largely overlapping 18-bp critical sequence, where the site-specific recombination process presumably takes place, was identified in the rum genes of all recipients, including those of the species yielding no transductants. Growth assays to evaluate the fitness cost of Φm46.1 acquisition disclosed a negligible impact on S. pyogenes, S. agalactiae, and S. gordonii transductants and a noticeable fitness advantage in S. suis. The S. suis transductant also displayed marked overexpression of the autolysin-encoding gene atl.
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Affiliation(s)
- Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Erika Tiberi
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Sonia Pasquaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
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