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Jespersen MG, Hayes AJ, Tong SYC, Davies MR. Pangenome evaluation of gene essentiality in Streptococcus pyogenes. Microbiol Spectr 2024:e0324023. [PMID: 39012116 DOI: 10.1128/spectrum.03240-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 06/23/2024] [Indexed: 07/17/2024] Open
Abstract
Bacterial species often consist of strains with variable gene content, collectively referred to as the pangenome. Variations in the genetic makeup of strains can alter bacterial physiology and fitness. To define biologically relevant genes of a genome, genome-wide transposon mutant libraries have been used to identify genes essential for survival or virulence in a given strain. Such phenotypic studies have been conducted in four different genotypes of the human pathogen Streptococcus pyogenes, yet challenges exist in comparing results across studies conducted in different genetic backgrounds and conditions. To advance genotype to phenotype inferences across different S. pyogenes strains, we built a pangenome database of 249 S. pyogenes reference genomes. We systematically re-analyzed publicly available transposon sequencing datasets from S. pyogenes using a transposon sequencing-specific analysis pipeline, Transit. Across four genetic backgrounds and nine phenotypic conditions, 355 genes were essential for survival, corresponding to ~24% of the core genome. Clusters of Orthologous Genes (COG) categories related to coenzyme and lipid transport and growth functions were overrepresented as essential. Finally, essential operons across S. pyogenes genotypes were defined, with an increased number of essential operons detected under in vivo conditions. This study provides an extendible database to which new studies can be added, and a searchable html-based resource to direct future investigations into S. pyogenes biology.IMPORTANCEStreptococcus pyogenes is a human-adapted pathogen occupying restricted ecological niches. Understanding the essentiality of genes across different strains and experimental conditions is important to direct research questions and efforts to prevent the large burden of disease caused by S. pyogenes. To this end we systematically reanalyzed transposon sequencing studies in S. pyogenes using transposon sequencing-specific methods, integrating them into an extendible meta-analysis framework. This provides a repository of gene essentiality in S. pyogenes which was used to highlight specific genes of interest and for the community to guide future phenotypic studies.
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Affiliation(s)
- Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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2
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Odo CM, Vega LA, Mukherjee P, DebRoy S, Flores AR, Shelburne SA. Emergent emm4 group A Streptococcus evidences a survival strategy during interaction with immune effector cells. Infect Immun 2024; 92:e0015224. [PMID: 38888310 PMCID: PMC11238559 DOI: 10.1128/iai.00152-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence among emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. By creating and analyzing isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates than the historic strains. Via the creation of isogenic mutant strains, we linked the emergent strain "survival" phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found a high ratio of mucosal (i.e., pharyngeal) relative to invasive infections among emm4 GAS. Since ever-increasing virulence is unlikely to be evolutionarily advantageous for a microbial pathogen, our data further understanding of the well-described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a "survival" strategy to outcompete previously circulating isolates.
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Affiliation(s)
- Chioma M. Odo
- Microbiology and Infectious Disease, MD Anderson UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Luis A. Vega
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Piyali Mukherjee
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sruti DebRoy
- Department of Infectious Disease, MD Anderson Cancer Center, Houston, Texas, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Sciences Center Houston, Houston, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Disease, MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
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3
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Bertram R, Itzek A, Marr L, Manzke J, Voigt S, Chapot V, van der Linden M, Rath PM, Hitzl W, Steinmann J. Divergent effects of emm types 1 and 12 on invasive group A streptococcal infections-results of a retrospective cohort study, Germany 2023. J Clin Microbiol 2024:e0063724. [PMID: 38990040 DOI: 10.1128/jcm.00637-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
As a potential side effect of the severe acute respiratory syndrome coronavirus type 2 pandemic, invasive group A Streptococcus (iGAS) infections in Europe have increased dramatically in both children and adults in the end of 2022. This epidemiological and molecular study describes the distributions of streptococcal genes encoding the M antigen (emm types) and superantigens in patients with invasive and non-invasive GAS infections. From December 2022 to December 2023, a total of 163 GAS isolates were collected from sterile and non-sterile sites of patients at five hospitals in Germany including two tertiary care centers. Genes encoding M protein and superantigens were determined following the guidelines of CDC Streptococcus laboratory. Patients' characteristics were reviewed retrospectively. Correlations of clinical factors, emm types, and superantigens with rates of invasive infections were analyzed. Of the 163 included GAS cases, 112 (69%) were considered as invasive. In total, 33 different emm types were observed, of which emm1.0 (n = 49; 30%), emm89.0 (n = 15; 9%), and emm12.0 (n = 14; 9%) were most prevalent. In total, 70% of emm1.0 isolates belonged to M1UK lineage. No difference in invasive infections was observed for the M1UK lineage compared with other emm1.0 isolates. However, the emm1.0 type, presence of speA1-3, speG, or speJ, as well as adulthood were significantly associated with invasive infections. In contrast, emm12.0 isolates were significantly less associated with invasive infections. Multivariable analysis confirmed a significant influence of speJ and adulthood on iGAS infections. This study underlines the importance of continuous monitoring of genomic trends and identification of emerging GAS variants. This may aid in delineating pathogenicity factors of Streptococcus pyogenes that propel invasive infections.
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Affiliation(s)
- Ralph Bertram
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
| | - Andreas Itzek
- Reference Laboratory for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Lisa Marr
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
| | - Jana Manzke
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
| | - Sebastian Voigt
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Valérie Chapot
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mark van der Linden
- Reference Laboratory for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Wolfgang Hitzl
- Department of Research and Innovation Management, Biostatistics and publication of clinical trial studies, Paracelsus Medical University, Salzburg, Austria
- Department of Ophthalmology and Optometry, Paracelsus Medical University, Salzburg, Austria
- Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University, Salzburg, Austria
| | - Joerg Steinmann
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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4
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Vieira A, Wan Y, Ryan Y, Li HK, Guy RL, Papangeli M, Huse KK, Reeves LC, Soo VWC, Daniel R, Harley A, Broughton K, Dhami C, Ganner M, Ganner MA, Mumin Z, Razaei M, Rundberg E, Mammadov R, Mills EA, Sgro V, Mok KY, Didelot X, Croucher NJ, Jauneikaite E, Lamagni T, Brown CS, Coelho J, Sriskandan S. Rapid expansion and international spread of M1 UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nat Commun 2024; 15:3916. [PMID: 38729927 PMCID: PMC11087535 DOI: 10.1038/s41467-024-47929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The UK observed a marked increase in scarlet fever and invasive group A streptococcal infection in 2022 with severe outcomes in children and similar trends worldwide. Here we report lineage M1UK to be the dominant source of invasive infections in this upsurge. Compared with ancestral M1global strains, invasive M1UK strains exhibit reduced genomic diversity and fewer mutations in two-component regulator genes covRS. The emergence of M1UK is dated to 2008. Following a bottleneck coinciding with the COVID-19 pandemic, three emergent M1UK clades underwent rapid nationwide expansion, despite lack of detection in previous years. All M1UK isolates thus-far sequenced globally have a phylogenetic origin in the UK, with dispersal of the new clades in Europe. While waning immunity may promote streptococcal epidemics, the genetic features of M1UK point to a fitness advantage in pathogenicity, and a striking ability to persist through population bottlenecks.
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Affiliation(s)
- Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
| | - Yu Wan
- Department of Infectious Disease, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Yan Ryan
- Reference Services Division, UK Health Security Agency, London, UK
| | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca L Guy
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Maria Papangeli
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Lucy C Reeves
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Valerie W C Soo
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Roger Daniel
- Reference Services Division, UK Health Security Agency, London, UK
| | | | - Karen Broughton
- Reference Services Division, UK Health Security Agency, London, UK
| | - Chenchal Dhami
- Reference Services Division, UK Health Security Agency, London, UK
| | - Mark Ganner
- Reference Services Division, UK Health Security Agency, London, UK
| | | | - Zaynab Mumin
- Reference Services Division, UK Health Security Agency, London, UK
| | - Maryam Razaei
- Reference Services Division, UK Health Security Agency, London, UK
| | - Emma Rundberg
- Reference Services Division, UK Health Security Agency, London, UK
| | - Rufat Mammadov
- Reference Services Division, UK Health Security Agency, London, UK
| | - Ewurabena A Mills
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Vincenzo Sgro
- Department of Infectious Disease, Imperial College London, London, UK
| | - Kai Yi Mok
- Department of Infectious Disease, Imperial College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Nicholas J Croucher
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Theresa Lamagni
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Colin S Brown
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK.
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK.
- Reference Services Division, UK Health Security Agency, London, UK.
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK.
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK.
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5
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Odo CM, Vega LA, Mukherjee P, DebRoy S, Flores AR, Shelburne SA. Emergent emm4 group A Streptococcus evidences a survival strategy during interaction with immune effector cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588776. [PMID: 38645060 PMCID: PMC11030381 DOI: 10.1101/2024.04.09.588776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence amongst emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. Through the creation and analysis of isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates relative to the historic strains. Via creation of isogenic mutant strains, we linked the emergent strain "survival" phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found high ratio of mucosal (i.e., pharyngeal) relative to invasive infections amongst emm4 GAS. Inasmuch as ever-increasing virulence is unlikely to be evolutionary advantageous for a microbial pathogen, our data furthers understanding of the well described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a "survival" strategy to outcompete previously circulating isolates.
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6
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Beres SB, Olsen RJ, Long SW, Langley R, Williams T, Erlendsdottir H, Smith A, Kristinsson KG, Musser JM. Increase in invasive Streptococcus pyogenes M1 infections with close evolutionary genetic relationship, Iceland and Scotland, 2022 to 2023. Euro Surveill 2024; 29:2400129. [PMID: 38551096 PMCID: PMC10979525 DOI: 10.2807/1560-7917.es.2024.29.13.2400129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024] Open
Abstract
Group A Streptococcus isolates of the recently described M1UK clade have emerged to cause human infections in several European countries and elsewhere. Full-genome sequence analysis of M1 isolates discovered a close genomic relationship between some isolates from Scotland and the majority of isolates from Iceland causing serious infections in 2022 and 2023. Phylogenetic analysis strongly suggests that an isolate from or related to Scotland was the precursor to an M1UK variant responsible for almost all recent M1 infections in Iceland.
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Affiliation(s)
- Stephen B Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - S Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross Langley
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow, Scotland
| | - Thomas Williams
- Department of Child Life and Health, University of Edinburgh, Edinburgh, Scotland
| | - Helga Erlendsdottir
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Andrew Smith
- College of Medical, Veterinary and Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, Glasgow, Scotland
- Scottish Microbiology Reference Laboratory, New Lister Building, Glasgow, Scotland
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
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7
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Orieux A, Prevel R, Dumery M, Lascarrou JB, Zucman N, Reizine F, Fillatre P, Detollenaere C, Darreau C, Antier N, Saint-Léger M, Schnell G, La Combe B, Guesdon C, Bruna F, Guillon A, Varillon C, Lesieur O, Grand H, Bertrand B, Siami S, Oudeville P, Besnard C, Persichini R, Bauduin P, Thyrault M, Evrard M, Schnell D, Auchabie J, Auvet A, Rigaud JP, Beuret P, Leclerc M, Berger A, Ben Hadj Salem O, Lorber J, Stoclin A, Guisset O, Bientz L, Khan P, Guillotin V, Lacherade JC, Boyer A, Orieux A, Prevel R, Dumery M, Lascarrou JB, Zucman N, Reizine F, Fillatre P, Detollenaere C, Darreau C, Antier N, Saint-Léger M, Schnell G, La Combe B, Guesdon C, Bruna F, Guillon A, Varillon C, Lesieur O, Grand H, Bertrand B, Siami S, Oudeville P, Besnard C, Persichini R, Bauduin P, Thyrault M, Evrard M, Schnell D, Auchabie J, Auvet A, Rigaud JP, Beuret P, Leclerc M, Berger A, Ben Hadj Salem O, Lorber J, Stoclin A, Guisset O, Bientz L, Khan P, Guillotin V, Lacherade JC, Boyer A. Invasive group A streptococcal infections requiring admission to ICU: a nationwide, multicenter, retrospective study (ISTRE study). Crit Care 2024; 28:4. [PMID: 38167516 PMCID: PMC10759709 DOI: 10.1186/s13054-023-04774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Group A Streptococcus is responsible for severe and potentially lethal invasive conditions requiring intensive care unit (ICU) admission, such as streptococcal toxic shock-like syndrome (STSS). A rebound of invasive group A streptococcal (iGAS) infection after COVID-19-associated barrier measures has been observed in children. Several intensivists of French adult ICUs have reported similar bedside impressions without objective data. We aimed to compare the incidence of iGAS infection before and after the COVID-19 pandemic, describe iGAS patients' characteristics, and determine ICU mortality associated factors. METHODS We performed a retrospective multicenter cohort study in 37 French ICUs, including all patients admitted for iGAS infections for two periods: two years before period (October 2018 to March 2019 and October 2019 to March 2020) and a one-year after period (October 2022 to March 2023) COVID-19 pandemic. iGAS infection was defined by Group A Streptococcus isolation from a normally sterile site. iGAS infections were identified using the International Classification of Diseases and confirmed with each center's microbiology laboratory databases. The incidence of iGAS infections was expressed in case rate. RESULTS Two hundred and twenty-two patients were admitted to ICU for iGAS infections: 73 before and 149 after COVID-19 pandemic. Their case rate during the period before and after COVID-19 pandemic was 205 and 949/100,000 ICU admissions, respectively (p < 0.001), with more frequent STSS after the COVID-19 pandemic (61% vs. 45%, p = 0.015). iGAS patients (n = 222) had a median SOFA score of 8 (5-13), invasive mechanical ventilation and norepinephrine in 61% and 74% of patients. ICU mortality in iGAS patients was 19% (14% before and 22% after COVID-19 pandemic; p = 0.135). In multivariate analysis, invasive mechanical ventilation (OR = 6.08 (1.71-21.60), p = 0.005), STSS (OR = 5.75 (1.71-19.22), p = 0.005), acute kidney injury (OR = 4.85 (1.05-22.42), p = 0.043), immunosuppression (OR = 4.02 (1.03-15.59), p = 0.044), and diabetes (OR = 3.92 (1.42-10.79), p = 0.008) were significantly associated with ICU mortality. CONCLUSION The incidence of iGAS infections requiring ICU admission increased by 4 to 5 after the COVID-19 pandemic. After the COVID-19 pandemic, the rate of STSS was higher, with no significant increase in ICU mortality rate.
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Affiliation(s)
- Arthur Orieux
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France.
| | - Renaud Prevel
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France
- Unité INSERM U1045, Université de Bordeaux, Bordeaux, France
| | - Margot Dumery
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France
| | | | - Noémie Zucman
- Service de Réanimation Médico-Chirurgicale, CH Annecy Genevois, Epagny Metz-Tessy, France
| | - Florian Reizine
- Service de Réanimation Polyvalente, CH de Vannes, Vannes, France
| | - Pierre Fillatre
- Service de Réanimation Polyvalente, CH de Saint Brieuc, Saint Brieuc, France
| | - Charles Detollenaere
- Service de Réanimation - Unité de Soins Continus, CH de Boulogne Sur Mer, Boulogne, France
| | - Cédric Darreau
- Service de Réanimation Médico-Chirurgicale, CH Le Mans, Le Mans, France
| | | | | | - Guillaume Schnell
- Service de Réanimation Médico-Chirurgicale, Groupe Hospitalier du Havre, Le Havre, France
| | - Béatrice La Combe
- Service de Réanimation Polyvalente, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Charlotte Guesdon
- Service de Réanimation Polyvalente, Centre Hospitalier de Pau, Pau, France
| | - Franklin Bruna
- Service de Réanimation, CH Alpes Leman, Contamine Sur Arve, France
| | - Antoine Guillon
- Service de Médecine Intensive Réanimation, INSERM, Centre d'Étude des Pathologies Respiratoires (CEPR), UMR 1100, CHRU de Tours, Université de Tours, Tours, France
| | - Caroline Varillon
- Service de Médecine Intensive Réanimation, CH Dunkirk, Dunkirk, France
| | - Olivier Lesieur
- Service de Réanimation Médico-Chirurgical, CH La Rochelle, La Rochelle, France
| | - Hubert Grand
- Service de Réanimation Polyvalente, Hôpital Robert Boulin, Libourne, France
| | - Benjamin Bertrand
- Service de Réanimation Polyvalente, CH Intercommunal Toulon, La Seyne sur Mer (CHITS), Toulon, France
| | - Shidasp Siami
- Service de Réanimation Polyvalente, CH Sud Essonne, Étampes, France
| | - Pierre Oudeville
- Service de Réanimation Médicale, Groupe Hospitalier Régional Mulhouse Sud Alsace (GHRMSA), Mulhouse, France
| | - Céline Besnard
- Service de Médecine Intensive Réanimation, CH Régional de Orléans, Orléans, France
| | - Romain Persichini
- Service de Réanimation Et Soins Continus, CH de Saintonge, Saintes, France
| | - Pierrick Bauduin
- Service de Médecine Intensive Réanimation, CHU de Caen, Caen, France
| | - Martial Thyrault
- Service de Réanimation Polyvalente, Groupe Hospitalier Nord Essonne - site Longjumeau, Longjumeau, France
| | - Mathieu Evrard
- Service Réanimation Polyvalente et Surveillance Continue, CH de Lens, Lens, France
| | - David Schnell
- Service de Réanimation Polyvalente, CH d'Angoulême, Angoulême, France
| | - Johann Auchabie
- Service de Réanimation Polyvalente, CH de Cholet, Cholet, France
| | - Adrien Auvet
- Service de Réanimation Polyvalente, CH de Dax, Dax, France
| | | | - Pascal Beuret
- Service de Réanimation et Soins Continus, CH de Roanne, Roanne, France
| | - Maxime Leclerc
- Service de Réanimation et Soins Intensifs Polyvalents, CH Mémorial Saint-Lô, Saint-Lô, France
| | - Asaël Berger
- Service de Réanimation, CH de Haguenau, Haguenau, France
| | - Omar Ben Hadj Salem
- Service de Réanimation Médico-Chirurgicale, CHI Meulan - les Mureaux, Meulan en Yvelines, France
| | - Julien Lorber
- Service de Médecine Intensive Réanimation, CH de Saint Nazaire, Saint Nazaire, France
| | - Annabelle Stoclin
- Département Interdisciplinaire d'Organisation des Parcours Patients (DIOPP), Service de Réanimation, Gustave Roussy Cancer Campus, Villejuif, France
| | - Olivier Guisset
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France
| | - Léa Bientz
- Laboratoire de Bactériologie, CHU de Bordeaux; Microbiologie Fondamentale et Pathogénicité UMR5234, Université de Bordeaux, Bordeaux, France
| | - Pierre Khan
- Département d'Anesthésie Réanimation Sud, Centre Médico-Chirurgical Magellan, Hôpital Haut Lévêque, CHU de Bordeaux, Pessac, France
| | - Vivien Guillotin
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France
| | - Jean-Claude Lacherade
- Service de Médecine Intensive Réanimation, CH Départemental de la Vendée, La Roche-sur-Yon, France
| | - Alexandre Boyer
- Service de Médecine Intensive Réanimation, Hôpital Pellegrin et Hôpital Saint André, CHU de Bordeaux, Place Amélie Raba Léon, 33000, Bordeaux, France
- Unité INSERM U1045, Université de Bordeaux, Bordeaux, France
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8
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Zhi X, Vieira A, Huse KK, Martel PJ, Lobkowicz L, Li HK, Croucher N, Andrew I, Game L, Sriskandan S. Characterization of the RofA regulon in the pandemic M1 global and emergent M1 UK lineages of Streptococcus pyogenes. Microb Genom 2023; 9:001159. [PMID: 38117674 PMCID: PMC10763501 DOI: 10.1099/mgen.0.001159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023] Open
Abstract
The standalone regulator RofA is a positive regulator of the pilus locus in Streptococcus pyogenes. Found in only certain emm genotypes, RofA has been reported to regulate other virulence factors, although its role in the globally dominant emm1 S. pyogenes is unclear. Given the recent emergence of a new emm1 (M1UK) toxigenic lineage that is distinguished by three non-synonymous SNPs in rofA, we characterized the rofA regulon in six emm1 strains that are representative of the two contemporary major emm1 lineages (M1global and M1UK) using RNAseq analysis, and then determined the specific role of the M1UK-specific rofA SNPs. Deletion of rofA in three M1global strains led to altered expression of 14 genes, including six non-pilus locus genes. In M1UK strains, deletion of rofA led to altered expression of 16 genes, including nine genes that were unique to M1UK. Only the pilus locus genes were common to the RofA regulons of both lineages, while transcriptomic changes varied between strains even within the same lineage. Although introduction of the three SNPs into rofA did not impact gene expression in an M1global strain, reversal of three SNPs in an M1UK strain led to an unexpected number of transcriptomic changes that in part recapitulated transcriptomic changes seen when deleting RofA in the same strain. Computational analysis predicted that interactions with a key histidine residue in the PRD domain of RofA would differ between M1UK and M1global. RofA is a positive regulator of the pilus locus in all emm1 strains but effects on other genes are strain- and lineage-specific, with no clear, common DNA binding motif. The SNPs in rofA that characterize M1UK may impact regulation of RofA; whether they alter phosphorylation of the RofA PRD domain requires further investigation.
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Affiliation(s)
- Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
| | - Kristin K. Huse
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Ludmila Lobkowicz
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nick Croucher
- MRC Centre for Global Infectious Disease Analysis, Sir Michael Uren Hub, White City Campus, Imperial College London, London,, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
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9
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Rodriguez-Ruiz JP, Lin Q, Lammens C, Smeesters PR, van Kleef-van Koeveringe S, Matheeussen V, Malhotra-Kumar S. Increase in bloodstream infections caused by emm1 group A Streptococcus correlates with emergence of toxigenic M1 UK, Belgium, May 2022 to August 2023. Euro Surveill 2023; 28:2300422. [PMID: 37676145 PMCID: PMC10486196 DOI: 10.2807/1560-7917.es.2023.28.36.2300422] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023] Open
Abstract
Many European countries have recently reported upsurges in invasive group A Streptococcus (iGAS) infections, mainly caused by emm1 Streptococcus pyogenes, specifically the toxigenic M1UK lineage. We present the epidemiology of emm1 causing iGAS in Belgium during 2018-August 2023, and describe an emergence of the toxigenic M1UK lineage in Belgium in mid-2022 that was observed as an increase in bloodstream infections caused by emm1 S. pyogenes that continued into 2023.
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Affiliation(s)
- Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
| | - Pierre R Smeesters
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Department of Paediatrics, Brussels University Hospital, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Stefanie van Kleef-van Koeveringe
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Laboratory of Microbiology, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
- Laboratory of Microbiology, University Hospital Antwerp, Edegem, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Antwerp, Belgium
- National Reference Centre for invasive β-haemolytic streptococci, Belgium
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