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Xie O, Davies MR, Tong SYC. Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes. Clin Microbiol Rev 2024:e0017523. [PMID: 38856686 DOI: 10.1128/cmr.00175-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, 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
| | - 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 Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP, Tonkin-Hill G, Schrieber L, McIntyre L, Lacey JA, James TB, Sriprakash KS, Beatson SA, Hasegawa T, Giffard P, Steer AC, Batzloff MR, Beall BW, Pinho MD, Ramirez M, Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nat Commun 2024; 15:2286. [PMID: 38480728 PMCID: PMC10937727 DOI: 10.1038/s41467-024-46530-2] [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: 01/12/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
| | - Jacqueline M Morris
- 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
| | - Rebecca J Towers
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, Cambridgeshire, UK
| | - Nouri L Ben Zakour
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Olga Berking
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen P Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Layla Schrieber
- Faculty of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Taylah B James
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Kadaba S Sriprakash
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Science & Technology, University of New England, Armidale, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Tadao Hasegawa
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Phil Giffard
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Andrew C Steer
- Tropical Diseases, Murdoch Children's Research Institute, Parkville, Australia
| | - Michael R Batzloff
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute for Glycomics, Griffith University, Southport, Australia
| | - Bernard W Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marcos D Pinho
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Debra E Bessen
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, 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 Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David J McMillan
- School of Science, Technology and Engineering, and Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, 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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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Toyoshima H, Tanigawa M, Ishiguro C, Tanaka H, Nakanishi Y, Sakabe S. Group A Streptococcus dysgalactiae subspecies equisimilis vertebral osteomyelitis accompanied by progressive atlantoaxial subluxation: A case report and literature review. Medicine (Baltimore) 2023; 102:e34968. [PMID: 37653834 PMCID: PMC10470678 DOI: 10.1097/md.0000000000034968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023] Open
Abstract
RATIONALE Clinically, vertebral osteomyelitis commonly occurs in immunocompromised individuals, such as people with diabetes, immunosuppression, chronic liver disease, and malignancy. Microbiologically, vertebral osteomyelitis is commonly caused by Staphylococcus aureus; however, Streptococcus dysgalactiae subspecies equisimilis (SDSE) may also potentially cause vertebral osteomyelitis, albeit rarely. Since no case reports have documented the occurrence of SDSE cervical osteomyelitis accompanied by progressive atlantoaxial subluxation, its clinical characteristics remain uncertain. Herein, we report the first case of progressive atlantoaxial subluxation in addition to cervical osteomyelitis due to septic atlantoaxial arthritis caused by SDSE in an immunocompetent individual, and provide a review of the relevant literature. PATIENT CONCERNS A 63-year-old man with hypertension but no history of trauma or musculoskeletal disorders presented with worsening neck pain for 1 month without fever. Physical examination revealed neck pain due to neck retroflexion and tenderness with swelling of the upper cervical spine. No neurological deficit was observed. Magnetic resonance imaging revealed low-intensity areas on a T1-weighted image and high-intensity areas on a short tau inversion recovery image at the C2, C5, and C6 vertebral bodies with atlantoaxial subluxation. Two sets of blood culture tests (aerobic and anaerobic) were performed. DIAGNOSES The anaerobic blood culture bottle showed the presence of beta-hemolytic pyrrolidonyl arylamidase-negative SDSE expressing Lancefield group A antiserum. Hence, the patient was diagnosed with SDSE cervical osteomyelitis with atlantoaxial subluxation; intensive intravenous ampicillin (2 g every 6 hours) - which is effective against SDSE - was administered. INTERVENTIONS Posterior fusion (occipital bone, C4) was performed on day 33 because a follow-up magnetic resonance imaging on day 31 revealed progression of atlantoaxial subluxation with thickened atlantodental soft tissue. OUTCOMES The patient's neck pain was completely relieved after treatment with intravenous ampicillin for 6 weeks, followed by oral amoxicillin (1500 mg) daily for an additional 4 weeks. The patient did not experience recurrence or sequelae during the 2-year follow-up period. LESSONS SDSE expressing Lancefield group A antiserum can cause afebrile vertebral osteomyelitis and progressive atlantoaxial subluxation due to the occurrence of septic atlantoaxial arthritis in immunocompetent individuals. Spinal instrumentation for vertebral osteomyelitis may be acceptable after 6 weeks of antimicrobial therapy.
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Affiliation(s)
- Hirokazu Toyoshima
- Department of Infectious Diseases, Japanese Red Cross Ise Hospital, Mie, Japan
- Infection Prevention and Control Office, Japanese Red Cross Ise Hospital, Mie, Japan
| | - Motoaki Tanigawa
- Department of Respiratory Medicine, Japanese Red Cross Ise Hospital, Mie, Japan
| | - Chiaki Ishiguro
- Infection Prevention and Control Office, Japanese Red Cross Ise Hospital, Mie, Japan
- Department of Medical Technology, Japanese Red Cross Ise Hospital, Mie, Japan
| | - Hiroyuki Tanaka
- Department of Infectious Diseases, Japanese Red Cross Ise Hospital, Mie, Japan
| | - Yuki Nakanishi
- Department of Infectious Diseases, Japanese Red Cross Ise Hospital, Mie, Japan
| | - Shigetoshi Sakabe
- Department of Infectious Diseases, Japanese Red Cross Ise Hospital, Mie, Japan
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Beres SB, Olsen RJ, Long SW, Eraso JM, Boukthir S, Faili A, Kayal S, Musser JM. Analysis of the Genomics and Mouse Virulence of an Emergent Clone of Streptococcus dysgalactiae Subspecies equisimilis. Microbiol Spectr 2023; 11:e0455022. [PMID: 36971562 PMCID: PMC10100674 DOI: 10.1128/spectrum.04550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis is a bacterial pathogen that is increasingly recognized as a cause of severe human infections. Much less is known about the genomics and infection pathogenesis of S. dysgalactiae subsp. equisimilis strains compared to the closely related bacterium Streptococcus pyogenes. To address these knowledge deficits, we sequenced to closure the genomes of seven S. dysgalactiae subsp. equisimilis human isolates, including six that were emm type stG62647. Recently, for unknown reasons, strains of this emm type have emerged and caused an increasing number of severe human infections in several countries. The genomes of these seven strains vary between 2.15 and 2.21 Mbp. The core chromosomes of these six S. dysgalactiae subsp. equisimilis stG62647 strains are closely related, differing on average by only 495 single-nucleotide polymorphisms, consistent with a recent descent from a common progenitor. The largest source of genetic diversity among these seven isolates is differences in putative mobile genetic elements, both chromosomal and extrachromosomal. Consistent with the epidemiological observations of increased frequency and severity of infections, both stG62647 strains studied were significantly more virulent than a strain of emm type stC74a in a mouse model of necrotizing myositis, as assessed by bacterial CFU burden, lesion size, and survival curves. Taken together, our genomic and pathogenesis data show the strains of emm type stG62647 we studied are closely genetically related and have enhanced virulence in a mouse model of severe invasive disease. Our findings underscore the need for expanded study of the genomics and molecular pathogenesis of S. dysgalactiae subsp. equisimilis strains causing human infections. IMPORTANCE Our studies addressed a critical knowledge gap in understanding the genomics and virulence of the bacterial pathogen Streptococcus dysgalactiae subsp. equisimilis. S. dysgalactiae subsp. equisimilis strains are responsible for a recent increase in severe human infections in some countries. We determined that certain S. dysgalactiae subsp. equisimilis strains are genetically descended from a common ancestor and that these strains can cause severe infections in a mouse model of necrotizing myositis. Our findings highlight the need for expanded studies on the genomics and pathogenic mechanisms of this understudied subspecies of the Streptococcus family.
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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, Texas, USA
| | - 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, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - 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, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Jesus M. Eraso
- 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, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Sarrah Boukthir
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Ahmad Faili
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Pharmacie, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - Samer Kayal
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - 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, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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Shinohara K, Murase K, Tsuchido Y, Noguchi T, Yukawa S, Yamamoto M, Matsumura Y, Nakagawa I, Nagao M. Clonal Expansion of Multidrug-Resistant Streptococcus dysgalactiae Subspecies equisimilis Causing Bacteremia, Japan, 2005-2021. Emerg Infect Dis 2023; 29:528-539. [PMID: 36823027 PMCID: PMC9973691 DOI: 10.3201/eid2903.221060] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Incidence of Streptococcus dysgalactiae subspecies equisimilis (SDSE) bacteremia is increasing in the Kyoto-Shiga region of Japan. We retrospectively analyzed clinical features of SDSE bacteremia and conducted comparative genomic analyses of isolates collected from 146 bacteremia episodes among 133 patients during 2005-2021. Of those patients, 7.7% required vasopressor support, and 7.0% died while in the hospital. The prevalence of isolates resistant to erythromycin, minocycline, and clindamycin increased from 8.6% during 2005-2017 to 21.6% during 2018-2021. Our genomic analysis demonstrated that sequence type 525 and clonal complex 25 were predominant in SDSE isolates collected during 2018-2021. In addition, those isolates had acquired 2 antimicrobial-resistance genes, ermB and tetM, via Tn916-like integrative and conjugative elements (ICEs). Phylogenetic analysis revealed clonal distribution of Tn916-like ICEs in SDSE isolates. Our findings suggest that Tn916-like ICEs contributed to the emergence and recent increase of multidrug-resistant SDSE bacteremia in this region of Japan.
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Jagne I, Keeley AJ, Bojang A, Camara B, Jallow E, Senghore E, Oluwalana C, Bah SY, Turner CE, Sesay AK, D’Alessandro U, Bottomley C, de Silva TI, Roca A. Impact of intra-partum azithromycin on carriage of group A streptococcus in the Gambia: a posthoc analysis of a double-blind randomized placebo-controlled trial. BMC Infect Dis 2022; 22:103. [PMID: 35093029 PMCID: PMC8800276 DOI: 10.1186/s12879-022-07080-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/11/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Group A Streptococcus (GAS) is a major human pathogen and an important cause of maternal and neonatal sepsis. Asymptomatic bacterial colonization is considered a necessary step towards sepsis. Intra-partum azithromycin may reduce GAS carriage.
Methods
A posthoc analysis of a double-blind, placebo-controlled randomized-trial was performed to determine the impact of 2 g oral dose of intra-partum azithromycin on maternal and neonatal GAS carriage and antibiotic resistance. Following screening, 829 mothers were randomized who delivered 843 babies. GAS was determined by obtaining samples from the maternal and newborn nasopharynx, maternal vaginal tract and breastmilk. Whole Genome Sequencing (WGS) of GAS isolates was performed using the Illumina Miseq platform.
Results
GAS carriage was lower in the nasopharynx of both mothers and babies and breast milk among participants in the azithromycin arm. No differences in GAS carriage were found between groups in the vaginal tract. The occurrence of azithromycin-resistant GAS was similar in both arms, except for a higher prevalence in the vaginal tract among women in the azithromycin arm. WGS revealed all macrolide-resistant vaginal tract isolates from the azithromycin arm were Streptococcus dysgalactiae subspecies equisimilis expressing Lancefield group A carbohydrate (SDSE(A)) harbouring macrolide resistant genes msr(D) and mef(A). Ten of the 45 GAS isolates (22.2%) were SDSE(A).
Conclusions
Oral intra-partum azithromycin reduced GAS carriage among Gambian mothers and neonates however carriage in the maternal vaginal tract was not affected by the intervention due to azithromycin resistant SDSE(A). SDSE(A) resistance must be closely monitored to fully assess the public health impact of intrapartum azithromycin on GAS.
Trial registration ClinicalTrials.gov Identifier NCT01800942
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Glajzner P, Szewczyk EM, Szemraj M. Pathogenicity and drug resistance of animal streptococci responsible for human infections. J Med Microbiol 2021; 70. [PMID: 33750514 DOI: 10.1099/jmm.0.001339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacteria of the genus Streptococcus, earlier considered typically animal, currently have also been causing infections in humans. It is necessary to make clinicians aware of the emergence of new species that may cause the development of human diseases. There is an increasing frequency of isolation of streptococci such as S. suis, S. dysgalactiae, S. iniae and S. equi from people. Isolation of Streptococcus bovis/Streptococcus equinus complex bacteria has also been reported. The streptococcal species described in this review are gaining new properties and virulence factors by which they can thrive in new environments. It shows the potential of these bacteria to changes in the genome and the settlement of new hosts. Information is presented on clinical cases that concern streptococcus species belonging to the groups Bovis, Pyogenic and Suis. We also present the antibiotic resistance profiles of these bacteria. The emerging resistance to β-lactams has been reported. In this review, the classification, clinical characteristics and antibiotic resistance of groups and species of streptococci considered as animal pathogens are summarized.
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Affiliation(s)
- Paulina Glajzner
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Lodz, Lodz, Poland
| | - Eligia Maria Szewczyk
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Lodz, Lodz, Poland
| | - Magdalena Szemraj
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Lodz, Lodz, Poland
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Ishihara H, Ogura K, Nguyen VA, Miyohi-Akiyama T, Okamoto S, Takemoto N. Comparative genome analysis of three Group A Streptococcus dysgalactiae subsp. equisimilis strains isolated in Japan. J Med Microbiol 2021; 70. [PMID: 33533709 DOI: 10.1099/jmm.0.001322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction . Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a β-hemolytic streptococcus that causes severe invasive streptococcal infections, especially in the elderly and people with underlying diseases. SDSE strains are primarily characterized by Lancefield group G or C antigens.Hypothesis/Gap Statement. We have previously reported the prevalence of Lancefield group A SDSE (GA-SDSE) strains in Japan and have analysed the draft genome sequences of these strains. As GA-SDSE is a rare type of SDSE, only one complete genome has been sequenced to date.Aim. The present study is focused on genetic characteristics of GA-SDSE strains. In order to examine molecular characteristics, we also tested growth inhibition of other streptococci by GA-SDSE.Methodology. We determined the complete genome sequences of three GA-SDSE strains by two new generation sequencing systems (short-read and long-read sequencing data). Using the sequences, we also conducted a comparative analysis of GA-SDSE and group C/G SDSE strains. In addition, we tested multiplex and quantitative PCRs targeting the GA-SDSE, group G SDSE, and S. pyogenes.Results. We found a group-specific conserved region in GA-SDSE strains that is composed of genes encoding predicted anti-bacteriocin and streptococcal lantibiotic (Sal) proteins. Multiplex and quantitative PCRs targeting the GA-SDSE-specific region were able to distinguish between GA-SDSE, other SDSE, and S. pyogenes strains. The growth of GA-SDSE was suppressed in the presence of group G SDSE, indicating a possible explanation for the low frequency of isolation of GA-SDSE.Conclusion. The comparative genome analysis shows that the genome of GA-SDSE has a distinct arrangement, enabling the differentiation between S. pyogenes, GA-SDSE, and other SDSE strains using our PCR methods.
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Affiliation(s)
- Haruka Ishihara
- Clinical Laboratory, Dental Hospital, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan.,Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Van An Nguyen
- Department of Viral Infection and International Health, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8640, Japan
| | - Tohru Miyohi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Shigefumi Okamoto
- Medical, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Norihiko Takemoto
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
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Brouwer S, Barnett TC, Ly D, Kasper KJ, De Oliveira DMP, Rivera-Hernandez T, Cork AJ, McIntyre L, Jespersen MG, Richter J, Schulz BL, Dougan G, Nizet V, Yuen KY, You Y, McCormick JK, Sanderson-Smith ML, Davies MR, Walker MJ. Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes. Nat Commun 2020; 11:5018. [PMID: 33024089 PMCID: PMC7538557 DOI: 10.1038/s41467-020-18700-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 09/01/2020] [Indexed: 02/03/2023] Open
Abstract
The re-emergence of scarlet fever poses a new global public health threat. The capacity of North-East Asian serotype M12 (emm12) Streptococcus pyogenes (group A Streptococcus, GAS) to cause scarlet fever has been linked epidemiologically to the presence of novel prophages, including prophage ΦHKU.vir encoding the secreted superantigens SSA and SpeC and the DNase Spd1. Here, we report the molecular characterization of ΦHKU.vir-encoded exotoxins. We demonstrate that streptolysin O (SLO)-induced glutathione efflux from host cellular stores is a previously unappreciated GAS virulence mechanism that promotes SSA release and activity, representing the first description of a thiol-activated bacterial superantigen. Spd1 is required for resistance to neutrophil killing. Investigating single, double and triple isogenic knockout mutants of the ΦHKU.vir-encoded exotoxins, we find that SpeC and Spd1 act synergistically to facilitate nasopharyngeal colonization in a mouse model. These results offer insight into the pathogenesis of scarlet fever-causing GAS mediated by prophage ΦHKU.vir exotoxins. The pathogenesis of Streptococcus pyogenes (GAS) causing scarlet fever has been associated with the presence of prophages, such as ΦHKU.vir, and their products. Here, the authors characterize the exotoxins SpeC and Spd1 of ΦHKU.vir and show these to act synergistically to facilitate nasopharyngeal colonization in mice.
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Affiliation(s)
- Stephan Brouwer
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Timothy C Barnett
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Diane Ly
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Katherine J Kasper
- Department of Microbiology and Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David M P De Oliveira
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Tania Rivera-Hernandez
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Amanda J Cork
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Magnus G Jespersen
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Johanna Richter
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Benjamin L Schulz
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, Hong Kong, China
| | - Yuanhai You
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - John K McCormick
- Department of Microbiology and Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Lawson Health Research Institute, London, ON, Canada
| | - Martina L Sanderson-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Mark R Davies
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.,Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Mark J Walker
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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11
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Li Y, Rivers J, Mathis S, Li Z, Velusamy S, Nanduri SA, Van Beneden CA, Snippes-Vagnone P, Lynfield R, McGee L, Chochua S, Metcalf BJ, Beall B. Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016-2017. Front Microbiol 2020; 11:1547. [PMID: 32849323 PMCID: PMC7396493 DOI: 10.3389/fmicb.2020.01547] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Streptococcus pyogenes is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of S. pyogenes lineages could inform vaccine development and disease control strategies. METHODS We used whole-genome sequencing (WGS) to characterize all invasive S. pyogenes isolates obtained through the United States Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, including emm type, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages within emm type. RESULTS Seventy-one emm types were identified from 3873 isolates characterized. The emm types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of emm types collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of the erm-positive emm types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three emm types (emm 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (P-values < 0.0001). Specific genomic sequence changes were associated with these expanded lineages. CONCLUSIONS While the overall population structure of invasive S. pyogenes isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Joy Rivers
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Saundra Mathis
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivasan Velusamy
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivas A. Nanduri
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Chris A. Van Beneden
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | | | - Ruth Lynfield
- Minnesota Department of Health, St Paul, MN, United States
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Benjamin J. Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
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12
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Ishihara H, Ogura K, Miyoshi‐Akiyama T, Nakamura M, Kaya H, Okamoto S. Prevalence and genomic characterization of Group A
Streptococcus dysgalactiae
subsp.
equisimilis
isolated from patients with invasive infections in Toyama prefecture, Japan. Microbiol Immunol 2019; 64:113-122. [DOI: 10.1111/1348-0421.12760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/19/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Haruka Ishihara
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health SciencesKanazawa UniversityKanazawa Ishikawa Japan
| | - Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science InitiativeKanazawa UniversityKanazawa Ishikawa Japan
| | - Tohru Miyoshi‐Akiyama
- Pathogenic Microbe Laboratory, Research InstituteNational Center for Global Health and MedicineShinjuku‐ku Tokyo Japan
| | - Masahiko Nakamura
- Department of Medical LaboratoryToyama Prefectural Central HospitalToyama Toyama Japan
| | - Hiroyasu Kaya
- Department of Internal MedicineToyama Prefectural Central HospitalToyama Toyama Japan
| | - Shigefumi Okamoto
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health SciencesKanazawa UniversityKanazawa Ishikawa Japan
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