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Bacon RL, Norman KN, Nickodem CA, Vinasco JA, Gray SB, Hodo CL, Lawhon SD. Whole-genome sequences of Campylobacter coli and Campylobacter jejuni isolates from rhesus macaques ( Macaca mulatta) with and without intestinal disease. Microbiol Resour Announc 2024; 13:e0001824. [PMID: 38446060 PMCID: PMC11008214 DOI: 10.1128/mra.00018-24] [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: 01/12/2024] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
Campylobacter jejuni or Campylobacter coli infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (Macaca mulatta). We report the complete genomes of 8 C. jejuni isolates and 103 C. coli isolates obtained from rhesus macaques with and without intestinal disease.
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Affiliation(s)
- Rebecca L. Bacon
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Keri N. Norman
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Colette A. Nickodem
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Javier A. Vinasco
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Stanton B. Gray
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Carolyn L. Hodo
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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2
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Shen Z, Zhang CY, Gull T, Zhang S. Comparison of genotypic and phenotypic antimicrobial resistance profiles of Salmonella enterica isolates from poultry diagnostic specimens. J Vet Diagn Invest 2024:10406387241242118. [PMID: 38571400 DOI: 10.1177/10406387241242118] [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: 04/05/2024] Open
Abstract
The spread of antimicrobial-resistant bacteria is a significant concern, as it can lead to increased morbidity and mortality in both humans and animals. Whole-genome sequencing (WGS) is a powerful tool that can be used to conduct a comprehensive analysis of the genetic basis of antimicrobial resistance (AMR). We compared the phenotypic and genotypic AMR profiles of 97 Salmonella isolates derived from chicken and turkey diagnostic samples. We focused AMR analysis on 5 antimicrobial classes: aminoglycoside, beta-lactam, phenicol, tetracycline, and trimethoprim. The overall sensitivity and specificity of WGS in predicting phenotypic antimicrobial resistance in the Salmonella isolates were 93.4% and 99.8%, respectively. There were 16 disagreement instances, including 15 that were phenotypically resistant but genotypically susceptible; the other instance involved phenotypic susceptibility but genotypic resistance. Of the isolates examined, 67 of 97 (69%) carried at least 1 resistance gene, with 1 isolate carrying as many as 12 resistance genes. Of the 31 AMR genes analyzed, 16 were identified as aminoglycoside-resistance genes, followed by 4 beta-lactam-resistance, 3 tetracycline-resistance, 2 sulfonamide-resistance, and 1 each of fosfomycin-, quinolone-, phenicol-, trimethoprim-, bleomycin-, and colistin-resistance genes. Most of the resistance genes found were located on plasmids.
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Affiliation(s)
- Zhenyu Shen
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri-Columbia, Columbia, MO, USA
| | - C Y Zhang
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri-Columbia, Columbia, MO, USA
| | - Tamara Gull
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri-Columbia, Columbia, MO, USA
| | - Shuping Zhang
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri-Columbia, Columbia, MO, USA
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3
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Sawhney SS, Vargas RC, Wallace MA, Muenks CE, Lubbers BV, Fritz SA, Burnham CAD, Dantas G. Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms. Nat Commun 2023; 14:7065. [PMID: 37923729 PMCID: PMC10624692 DOI: 10.1038/s41467-023-42694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Staphylococcus pseudintermedius is historically understood as a prevalent commensal and pathogen of dogs, though modern clinical diagnostics reveal an expanded host-range that includes humans. It remains unclear whether differentiation across S. pseudintermedius populations is driven primarily by niche-type or host-species. We sequenced 501 diagnostic and commensal isolates from a hospital, veterinary diagnostic laboratory, and within households in the American Midwest, and performed a comparative genomics investigation contrasting human diagnostic, animal diagnostic, human colonizing, pet colonizing, and household-surface S. pseudintermedius isolates. Though indistinguishable by core and accessory gene architecture, diagnostic isolates harbor more encoded and phenotypic resistance, whereas colonizing and surface isolates harbor similar CRISPR defense systems likely reflective of common household phage exposures. Furthermore, household isolates that persist through anti-staphylococcal decolonization report elevated rates of base-changing mutations in - and parallel evolution of - defense genes, as well as reductions in oxacillin and trimethoprim-sulfamethoxazole susceptibility. Together we report parallel niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation.
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Affiliation(s)
- Sanjam S Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meghan A Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol E Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Lubbers
- Department of Clinical Sciences, Kansas State University, Manhattan, KS, USA
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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4
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Chung HC, Foxx CL, Hicks JA, Stuber TP, Friedberg I, Dorman KS, Harris B. An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species. PLoS One 2023; 18:e0290473. [PMID: 37616210 PMCID: PMC10449230 DOI: 10.1371/journal.pone.0290473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.
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Affiliation(s)
- Henri C. Chung
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Christine L. Foxx
- Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Jessica A. Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Tod P. Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Karin S. Dorman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States of America
- Department of Statistics, Iowa State University, Ames, IA, United States of America
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
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5
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Srednik ME, Perea CA, Giacoboni GI, Hicks JA, Foxx CL, Harris B, Schlater LK. Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study. Int J Mol Sci 2023; 24:11361. [PMID: 37511121 PMCID: PMC10379401 DOI: 10.3390/ijms241411361] [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: 06/07/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.
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Affiliation(s)
- Mariela E Srednik
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Claudia A Perea
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Gabriela I Giacoboni
- Departamento de Microbiología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1427, Argentina
| | - Jessica A Hicks
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Christine L Foxx
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Transboundary Disease Analytics, Center for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO 80526, USA
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Linda K Schlater
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
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6
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Lake KM, Rankin SC, Rosenkrantz WS, Sastry L, Jacob M, Campos DD, Maddock K, Cole SD. In vitro efficacy of 0.2% and 0.4% sodium oxychlorosene against meticillin-resistant Staphylococcus pseudintermedius. Vet Dermatol 2023; 34:33-39. [PMID: 36097719 DOI: 10.1111/vde.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/14/2022] [Accepted: 05/20/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND There is a need for alternative topical therapies as a consequence of the increased prevalence of meticillin-resistant Staphylococcus pseudintermedius (MRSP) skin infections in dogs. Sodium oxychlorosene has been used as a topical antibacterial agent in human medicine since 1955. OBJECTIVES To determine whether 0.2% and 0.4% sodium oxychlorosene solutions have a bactericidal effect (>3-log reduction) on MRSP strains isolated from canine skin infections. METHODS AND MATERIALS A genetically heterogeneous collection of MRSP isolates from dogs was assembled from laboratories across the United States. Time-kill assays were performed with 0.2% and 0.4% sodium oxychlorosene on a 0.5 McFarland standard [approximately 108 colony-forming units (cfu/ml)] suspension of each strain. The average bacterial counts (cfu/ml) of each MRSP strain then were determined at 5, 10, 20 and 60 s after exposure to sodium oxychlorosene; cfu/ml data were converted to log10 scale to calculate microbial reduction. RESULTS The average bacterial counts following exposure to the 0.2% solution at 5, 10, 20 and 60 s were 6.94 × 104 , 5.63 × 103 , 2.96 × 102 and 1.48 × 102 cfu/ml, respectively. For the 0.4% solution, the average bacterial count at 5 s was 2.12 × 103 cfu/ml. No bacterial growth was observed for any MRSP strain by 10 s. The greatest reduction in cfu/ml occurred within 5 s following exposure to each solution 3.4-log and 4.9-log reduction for 0.2% and 0.4%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE 0.2% and 0.4% sodium oxychlorosene solutions have a bactericidal effect (>99.9% reduction) against MRSP in vitro. Further in vivo studies are necessary to determine whether it is an appropriate alternative therapy for canine pyoderma.
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Affiliation(s)
| | - Shelley C Rankin
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lakshmi Sastry
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Megan Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Dubra Diaz Campos
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Kelli Maddock
- AES Veterinary Diagnostic Services, North Dakota State University, Fargo, North Dakota, USA
| | - Stephen D Cole
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Viñes J, Fàbregas N, Pérez D, Cuscó A, Fonticoba R, Francino O, Ferrer L, Migura-Garcia L. Concordance between Antimicrobial Resistance Phenotype and Genotype of Staphylococcus pseudintermedius from Healthy Dogs. Antibiotics (Basel) 2022; 11:antibiotics11111625. [PMID: 36421269 PMCID: PMC9686559 DOI: 10.3390/antibiotics11111625] [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: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus pseudintermedius, a common commensal canine bacterium, is the main cause of skin infections in dogs and is a potential zoonotic pathogen. The emergence of methicillin-resistant S. pseudintermedius (MRSP) has compromised the treatment of infections caused by these bacteria. In this study, we compared the phenotypic results obtained by minimum inhibitory concentration (MICs) for 67 S. pseudintermedius isolates from the skin of nine healthy dogs versus the genotypic data obtained with Nanopore sequencing. A total of 17 antibiotic resistance genes (ARGs) were detected among the isolates. A good correlation between phenotype and genotype was observed for some antimicrobial classes, such as ciprofloxacin (fluoroquinolone), macrolides, or tetracycline. However, for oxacillin (beta-lactam) or aminoglycosides the correlation was low. Two antibiotic resistance genes were located on plasmids integrated in the chromosome, and a third one was in a circular plasmid. To our knowledge, this is the first study assessing the correlation between phenotype and genotype regarding antimicrobial resistance of S. pseudintermedius from healthy dogs using Nanopore sequencing technology.
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Affiliation(s)
- Joaquim Viñes
- Vetgenomics, Edifici EUREKA, PRUAB, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Molecular Genetics Veterinary Service (SVGM), Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Correspondence:
| | - Norma Fàbregas
- Vetgenomics, Edifici EUREKA, PRUAB, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
| | - Daniel Pérez
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, Edifici EUREKA, PRUAB, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Rocío Fonticoba
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
| | - Lluís Ferrer
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
| | - Lourdes Migura-Garcia
- Unitat mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
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8
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Bruce SA, Smith JT, Mydosh JL, Ball J, Needle DB, Gibson R, Andam CP. Accessory Genome Dynamics of Local and Global Staphylococcus pseudintermedius Populations. Front Microbiol 2022; 13:798175. [PMID: 35222331 PMCID: PMC8867027 DOI: 10.3389/fmicb.2022.798175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/06/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus pseudintermedius is a major bacterial colonizer and opportunistic pathogen in dogs. Methicillin-resistant S. pseudintermedius (MRSP) continues to emerge as a significant challenge to maintaining canine health. We sought to determine the phylogenetic relationships of S. pseudintermedius across five states in the New England region of the United States and place them in a global context. The New England dataset consisted of 125 previously published S. pseudintermedius genomes supplemented with 45 newly sequenced isolates. The core genome phylogenetic tree revealed many deep branching lineages consisting of 142 multi-locus sequence types (STs). In silico detection of the mecA gene revealed 40 MRSP and 130 methicillin-susceptible S. pseudintermedius (MSSP) isolates. MRSP were derived from five structural types of SCCmec, the mobile genetic element that carries the mecA gene conferring methicillin resistance. Although many genomes were MSSP, they nevertheless harbored genes conferring resistance to many other antibiotic classes, including aminoglycosides, macrolides, tetracyclines and penams. We compared the New England genomes to 297 previously published genomes sampled from five other states in the United States and 13 other countries. Despite the prevalence of the clonally expanding ST71 found worldwide and in other parts of the United States, we did not detect it in New England. We next sought to interrogate the combined New England and global datasets for the presence of coincident gene pairs linked to antibiotic resistance. Analysis revealed a large co-circulating accessory gene cluster, which included mecA as well as eight other resistance genes [aac (6′)-Ie-aph (2″)-Ia, aad (6), aph (3′)-IIIa, sat4, ermB, cat, blaZ, and tetM]. Furthermore, MRSP isolates carried significantly more accessory genes than their MSSP counterparts. Our results provide important insights to the evolution and geographic spread of high-risk clones that can threaten the health of our canine companions.
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Affiliation(s)
- Spencer A Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Jennifer L Mydosh
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - John Ball
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - David B Needle
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, United States.,New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, United States
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, United States
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
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9
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Absence of Host-Specific Genes in Canine and Human Staphylococcus pseudintermedius as Inferred from Comparative Genomics. Antibiotics (Basel) 2021; 10:antibiotics10070854. [PMID: 34356775 PMCID: PMC8300826 DOI: 10.3390/antibiotics10070854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus pseudintermedius is an important pathogen in dogs that occasionally causes infections in humans as an opportunistic pathogen of elderly and immunocompromised people. This study compared the genomic relatedness and antimicrobial resistance genes using genome-wide association study (GWAS) to examine host association of canine and human S. pseudintermedius isolates. Canine (n = 25) and human (n = 32) methicillin-susceptible S. pseudintermedius (MSSP) isolates showed a high level of genetic diversity with an overrepresentation of clonal complex CC241 in human isolates. This clonal complex was associated with carriage of a plasmid containing a bacteriocin with cytotoxic properties, a CRISPR-cas domain and a pRE25-like mobile element containing five antimicrobial resistance genes. Multi-drug resistance (MDR) was predicted in 13 (41%) of human isolates and 14 (56%) of canine isolates. CC241 represented 54% of predicted MDR isolates from humans and 21% of predicted MDR canine isolates. While it had previously been suggested that certain host-specific genes were present the current GWAS analysis did not identify any genes that were significantly associated with human or canine isolates. In conclusion, this is the first genomic study showing that MSSP is genetically diverse in both hosts and that multidrug resistance is important in dog and human-associated S. pseudintermedius isolates.
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10
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Kizerwetter-Świda M, Chrobak-Chmiel D, Kwiecień E, Rzewuska M, Binek M. Molecular characterization of high-level mupirocin resistance in methicillin-resistant staphylococci isolated from companion animals. Vet Microbiol 2021; 259:109160. [PMID: 34197979 DOI: 10.1016/j.vetmic.2021.109160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
High-level mupirocin resistance (HLMR) is determined by the plasmid-located ileS2 gene flanked by two copies of the insertion sequence 257 (IS257). The molecular epidemiology of high-level mupirocin-resistant isolates could be assessed by the determination of their IS257-ileS2 spacer regions conformation. In this study, 188 isolates of methicillin-resistant staphylococci were subjected to the detection of HLMR, and analysis of the conformation of the IS257-ileS2 spacer regions. Mupirocin resistance was detected in five (2,6%) isolates, among which two were recognized as Staphylococcus pseudintermedius, two as Staphylococcus haemolyticus, and one as Staphylococcus aureus. High-level mupirocin resistance was revealed by the agar disk diffusion method, and MIC values, and was confirmed by the detection of the ileS2 gene. The conformations of the IS257-ileS2 spacer regions were homologous in two S. haemolyticus strains tested. The remaining three isolates showed diverse IS257-ileS2 conformations. The results of this study indicate that HLMR occasionally occurs in staphylococci isolated from companion animals. The heterogeneity and the homogeneity of the IS257-ileS2 spacer regions confirm that the ileS2 gene spread among staphylococci of animal origin by the transfer of different as well as the same plasmids. Surveillance of the occurrence of mupirocin resistance and molecular characterization of resistant isolates are strongly recommended due to the possibility of plasmid-located resistance gene transfer between staphylococci.
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Affiliation(s)
- Magdalena Kizerwetter-Świda
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786, Warsaw, Poland.
| | - Dorota Chrobak-Chmiel
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786, Warsaw, Poland
| | - Ewelina Kwiecień
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786, Warsaw, Poland
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786, Warsaw, Poland
| | - Marian Binek
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego Str. 8, 02-786, Warsaw, Poland
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