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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; 37:e0017523. [PMID: 38856686 PMCID: PMC11392527 DOI: 10.1128/cmr.00175-23] [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] [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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Glambek M, Skrede S, Sivertsen A, Kittang BR, Kaci A, Jonassen CM, Jørgensen HJ, Oppegaard O. Antimicrobial resistance patterns in Streptococcus dysgalactiae in a One Health perspective. Front Microbiol 2024; 15:1423762. [PMID: 39193432 PMCID: PMC11348040 DOI: 10.3389/fmicb.2024.1423762] [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: 04/26/2024] [Accepted: 05/15/2024] [Indexed: 08/29/2024] Open
Abstract
Background Streptococcus dysgalactiae (SD) is an important pathogen in humans as well as in a broad range of animal species. Escalating rates of antibiotic resistance in SD has been reported in both human and veterinary clinical practice, but the dissemination of resistance determinants has so far never been examined in a One Health Perspective. We wanted to explore the occurrence of zoonotic transmission of SD and the potential for exchange of resistance traits between SD from different host populations. Methods We compared whole genome sequences and phenotypical antimicrobial susceptibility of 407 SD isolates, comprising all isolates obtained from human bloodstream infections in 2018 (n = 274) and available isolates associated with animal infections from the years 2018 and 2019 (n = 133) in Norway. Results Antimicrobial resistance genes were detected in 70 (26%), 9 (25%) and 2 (2%) of the isolates derived from humans, companion animals and livestock, respectively. Notably, distinct host associated genotypic resistomes were observed. The erm(A) gene was the dominant cause of erythromycin resistance in human associated isolates, whereas only erm(B) and lsa(C) were identified in SD isolates from animals. Moreover, the tetracycline resistance gene tet(O) was located on different mobile genetic elements in SD from humans and animals. Evidence of niche specialization was also evident in the phylogenetic analysis, as the isolates could be almost perfectly delineated in accordance with host species. Nevertheless, near identical mobile genetic elements were observed in four isolates from different host species including one human, implying potential transmission of antibiotic resistance between different environments. Conclusion We found a phylogenetic delineation of SD strains in line with host adapted populations and niche specialization. Direct transmission of strains or genetic elements carrying resistance genes between SD from different ecological niches appears to be rare in our geographical region.
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Affiliation(s)
- Marte Glambek
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Steinar Skrede
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine 2, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Audun Sivertsen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Bård Reiakvam Kittang
- Department of Clinical Medicine 2, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Haraldsplass Deaconess Hospital (HDS), Bergen, Norway
| | - Alba Kaci
- Center for Laboratory Medicine, Østfold Hospital, Grålum, Norway
| | - Christine Monceyron Jonassen
- Center for Laboratory Medicine, Østfold Hospital, Grålum, Norway
- Department of Virology, Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Oddvar Oppegaard
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine 2, Department of Clinical Science, University of Bergen, Bergen, Norway
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Kaci A, Jonassen CM, Skrede S, Sivertsen A, Steinbakk M, Oppegaard O. Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018. Front Microbiol 2023; 14:1171913. [PMID: 37485526 PMCID: PMC10361778 DOI: 10.3389/fmicb.2023.1171913] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/31/2023] [Indexed: 07/25/2023] Open
Abstract
Background Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized. Methods We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE. Results The phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling. Conclusion Recombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.
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Affiliation(s)
- Alba Kaci
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
| | - Christine M. Jonassen
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Steinar Skrede
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Audun Sivertsen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | - Martin Steinbakk
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
| | - Oddvar Oppegaard
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Itzek A, Weißbach V, Meintrup D, Rieß B, van der Linden M, Borgmann S. Epidemiological and Clinical Features of Streptococcus dysgalactiae ssp. equisimilis stG62647 and Other emm Types in Germany. Pathogens 2023; 12:pathogens12040589. [PMID: 37111475 PMCID: PMC10143538 DOI: 10.3390/pathogens12040589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
(1) Background: Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an important β-hemolytic pathogen historically described as mainly affecting animals. Studies epidemiologically assessing the pathogenicity in the human population in Germany are rare. (2) Methods: the present study combines national surveillance data from 2010 to 2022 with a single-center clinical study conducted from 2016 to 2022, focusing on emm type, Lancefield antigen, antimicrobial resistance, patient characteristics, disease severity, and clinical infection markers. (3) Results: The nationwide reported invasive SDSE infections suggest an increasing infection burden for the German population. One particular emm type, stG62647, increased over the study period, being the dominant type in both study cohorts, suggesting a mutation-driven outbreak of a virulent clone. The patient data show that men were more affected than women, although in the single-center cohort, this trend was reversed for patients with stG62647 SDSE. Men affected by stG62647 developed predominantly fascial infections, whereas women suffering from superficial and fascial non-stG62647 SDSE infections were significantly younger than other patients. Increasing age was a general risk factor for invasive SDSE infections. (4) Conclusions: further studies are needed to further elucidate the raised questions regarding outbreak origin, underlying molecular mechanisms as well as sex-dependent pathogen adaptation.
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Affiliation(s)
- Andreas Itzek
- German National Reference Center for Streptococci, Institute of Medical Microbiology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Victoria Weißbach
- Department of Infectious Diseases and Infection Control, Ingolstadt Hospital, 85049 Ingolstadt, Germany
| | - David Meintrup
- Faculty of Engineering and Management, University of Applied Sciences Ingolstadt, 85049 Ingolstadt, Germany
| | - Beate Rieß
- Department of Infectious Diseases and Infection Control, Ingolstadt Hospital, 85049 Ingolstadt, Germany
| | - Mark van der Linden
- German National Reference Center for Streptococci, Institute of Medical Microbiology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Stefan Borgmann
- Department of Infectious Diseases and Infection Control, Ingolstadt Hospital, 85049 Ingolstadt, Germany
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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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A New Integrative and Mobilizable Element Is a Major Contributor to Tetracycline Resistance in Streptococcus dysgalactiae subsp. equisimilis. Antibiotics (Basel) 2023; 12:antibiotics12030579. [PMID: 36978446 PMCID: PMC10044688 DOI: 10.3390/antibiotics12030579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the tet(M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn916-family. In this study, we analyzed the genes involved in tetracycline resistance and the associated mobile genetic elements (MGEs) in Streptococcus dysgalactiae subsp. equisimilis (SDSE) causing invasive disease. SDSE resistant to tetracycline collected from 2012 to 2019 in a single hospital and from 2018 in three other hospitals were analyzed by whole genome sequencing. Out of a total of 84 SDSE isolates, 24 (28.5%) were resistant to tetracycline due to the presence of tet(M) (n = 22), tet(W) (n = 1), or tet(L) plus tet(W) (n = 1). The tet(M) genes were found in the ICEs of the Tn916-family (n = 10) and in a new integrative and mobilizable element (IME; n = 12). Phylogenetic analysis showed a higher genetic diversity among the strains carrying Tn916 than those having the new IME, which were closely related, and all belonged to CC15. In conclusion, tetracycline resistance in SDSE is mostly due to the tet(M) gene associated with ICEs belonging to the Tn916-family and a new IME. This new IME is a major cause of tetracycline resistance in invasive Streptococcus dysgalactiae subsp. equisimilis in our settings.
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Berbel D, González-Díaz A, López de Egea G, Càmara J, Ardanuy C. An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics. Microorganisms 2022; 10:2316. [PMID: 36557569 PMCID: PMC9783990 DOI: 10.3390/microorganisms10122316] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.
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Affiliation(s)
- Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Guillem López de Egea
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08007 Barcelona, Spain
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Tetracycline, Macrolide and Lincosamide Resistance in Streptococcus canis Strains from Companion Animals and Its Genetic Determinants. Antibiotics (Basel) 2022; 11:antibiotics11081034. [PMID: 36009903 PMCID: PMC9405182 DOI: 10.3390/antibiotics11081034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Growing antimicrobial resistance (AMR) in companion-animal pathogens, including Streptococcus canis (S. canis), is a significant concern for pet treatment as well for public health. Despite the importance of S. canis in veterinary and human medicine, studies concerning the AMR of this bacterium are still scarce. A total of 65 S. canis strains, isolated from dogs and cats, were assessed to test for susceptibility to six clinically relevant antimicrobials via a microdilution method. The prevalence of the selected acquired-resistance genes was also investigated via PCR. High MIC50 and MIC90 values (≥128 μg/mL) were noted for tetracycline, erythromycin and clindamycin. Only a few strains were resistant to the tested beta-lactams (6.2%). Tetracycline resistance was found in 66.2% of the strains. Resistance to erythromycin and clindamycin (ML resistance) was found in 55.4% of the strains. Strains with a phenotype showing concurrent resistance to tetracycline and ML were predominant (53.8%). AMR in the tested S. canis strains was associated with a variety of acquired and potentially transferable genes. Tetracycline resistance was conferred by tet(O) (40.0%), tet(M) (9.2%), and tet(T) (1.5%), which is reported for the first time in S. canis. In most cases, the tet(M) gene was detected in relation to the conjugative transposon Tn916. The MLSB phenotype was confirmed in the strains harboring erm(B) (43.1%) and erm(TR) (7.7%). To conclude, a high rate of S. canis strains occurring in dogs and cats displayed resistance to antimicrobials important for treatment; moreover, they are a potential reservoirs of various resistance determinants. Therefore, AMR in these pathogens should be continuously monitored, especially regarding the One Health concept.
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