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Ramos B, Cunha MV. Genomic epidemiology of Staphylococcus aureus from the Iberian Peninsula highlights the expansion of livestock associated-CC398 towards wildlife. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173027. [PMID: 38729368 DOI: 10.1016/j.scitotenv.2024.173027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990-2022 period and a subset of CC398 strains representing the 2008-2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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Barber MF, Fitzgerald JR. Mechanisms of host adaptation by bacterial pathogens. FEMS Microbiol Rev 2024; 48:fuae019. [PMID: 39003250 PMCID: PMC11308195 DOI: 10.1093/femsre/fuae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 07/15/2024] Open
Abstract
The emergence of new infectious diseases poses a major threat to humans, animals, and broader ecosystems. Defining factors that govern the ability of pathogens to adapt to new host species is therefore a crucial research imperative. Pathogenic bacteria are of particular concern, given dwindling treatment options amid the continued expansion of antimicrobial resistance. In this review, we summarize recent advancements in the understanding of bacterial host species adaptation, with an emphasis on pathogens of humans and related mammals. We focus particularly on molecular mechanisms underlying key steps of bacterial host adaptation including colonization, nutrient acquisition, and immune evasion, as well as suggest key areas for future investigation. By developing a greater understanding of the mechanisms of host adaptation in pathogenic bacteria, we may uncover new strategies to target these microbes for the treatment and prevention of infectious diseases in humans, animals, and the broader environment.
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Affiliation(s)
- Matthew F Barber
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, United States
- Department of Biology, University of Oregon, Eugene, OR 97403, United States
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
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Alves J, Vrieling M, Ring N, Yebra G, Pickering A, Prajsnar TK, Renshaw SA, Fitzgerald JR. Experimental evolution of Staphylococcus aureus in macrophages: dissection of a conditional adaptive trait promoting intracellular survival. mBio 2024; 15:e0034624. [PMID: 38682911 PMCID: PMC11237485 DOI: 10.1128/mbio.00346-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Staphylococcus aureus is a major pathogen associated with important diseases in humans and animals. Macrophages are a key component of the innate immune response to S. aureus infection and play a major role in disease outcomes. To investigate the adaptive evolution of S. aureus in response to macrophages, we developed an experimental infection assay. S. aureus strains representing major human epidemic clones were passaged many times in a macrophage cell line, accumulating mutations in an array of genomic loci. Phenotypic analysis revealed the emergence of a lineage exhibiting increased survival in macrophages and human blood, and resistance to vancomycin. The evolved lineage exhibited a previously undescribed small colony variant (SCV) phenotype characterized by hyper-pigmentation, which resulted from a missense mutation in rsbW. Notably, the novel SCV was a conditional adaptive trait that was unstable in nutrient-replete conditions in vitro, rapidly converting from hyper-pigmented SCV to a non-pigmented large colony variant via spontaneous sigB deletion events. Importantly, we identified similar deletions in the genome sequences of a limited number of clinical S. aureus isolates from public databases, indicating that related events may occur during clinical infection. Experimental infection of zebrafish did not reveal a difference in virulence between parent and novel SCV but demonstrated an in vivo fitness cost for the compensatory sigB deletion events. Taken together, we report an experimental evolutionary approach for investigating bacterial innate immune cell interactions, revealing a conditional adaptation that promotes S. aureus survival in macrophages and resistance to vancomycin. IMPORTANCE Staphylococcus aureus is an important human bacterial pathogen. The host response to S. aureus involves the production of innate immune cells such as macrophages which are important for fighting infection. Here we report a new model of experimental evolution for studying how S. aureus can evade killing by macrophages. We identified a novel adaptive phenotype that promotes survival in macrophages and blood and resistance to antibiotics. The phenotype is lost rapidly upon growth in nutrient-rich conditions via disruption of the alternative sigma factor sigB, revealing a conditional niche-specific fitness advantage. Genomic analysis of clinical isolates suggests similar adaptations may occur during human infections. Our model may be used broadly to identify adaptations of S. aureus to the innate immune response.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Manouk Vrieling
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Natalie Ring
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Amy Pickering
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Tomasz K. Prajsnar
- Florey Institute, Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, Sheffield, United Kingdom
| | - Stephen A. Renshaw
- Florey Institute, Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, Sheffield, United Kingdom
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
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Tuffs SW, Dufresne K, Rishi A, Walton NR, McCormick JK. Novel insights into the immune response to bacterial T cell superantigens. Nat Rev Immunol 2024; 24:417-434. [PMID: 38225276 DOI: 10.1038/s41577-023-00979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Bacterial T cell superantigens (SAgs) are a family of microbial exotoxins that function to activate large numbers of T cells simultaneously. SAgs activate T cells by direct binding and crosslinking of the lateral regions of MHC class II molecules on antigen-presenting cells with T cell receptors (TCRs) on T cells; these interactions alter the normal TCR-peptide-MHC class II architecture to activate T cells in a manner that is independent of the antigen specificity of the TCR. SAgs have well-recognized, central roles in human diseases such as toxic shock syndrome and scarlet fever through their quantitative effects on the T cell response; in addition, numerous other consequences of SAg-driven T cell activation are now being recognized, including direct roles in the pathogenesis of endocarditis, bloodstream infections, skin disease and pharyngitis. In this Review, we summarize the expanding family of bacterial SAgs and how these toxins can engage highly diverse adaptive immune receptors. We highlight recent findings regarding how SAg-driven manipulation of the adaptive immune response may operate in multiple human diseases, as well as contributing to the biology and life cycle of SAg-producing bacterial pathogens.
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Affiliation(s)
- Stephen W Tuffs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karine Dufresne
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Aanchal Rishi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Nicholas R Walton
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - John K McCormick
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada.
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Ramos B, Cunha MV. The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124241. [PMID: 38825220 DOI: 10.1016/j.envpol.2024.124241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/28/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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Souza SSR, Smith JT, Marcovici MM, Eckhardt EM, Hansel NB, Martin IW, Andam CP. Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:14. [PMID: 38725655 PMCID: PMC11076216 DOI: 10.1038/s44259-024-00032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Joshua T. Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Elissa M. Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Nicole B. Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
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Chakrawarti A, Eckstrom K, Laaguiby P, Barlow JW. Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies. Access Microbiol 2024; 6:000766.v3. [PMID: 38725589 PMCID: PMC11077346 DOI: 10.1099/acmi.0.000766.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/23/2024] [Indexed: 05/12/2024] Open
Abstract
Antimicrobial resistance (AMR) in Staphylococcus aureus is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of S. aureus, this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline. Our analyses showcased the hybrid-assembled genome's superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in S. aureus isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes blaZ, blaI, and blaR. In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of S. aureus isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.
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Affiliation(s)
- Ashma Chakrawarti
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pheobe Laaguiby
- Advanced Genome Technologies Core, Vermont Integrative Genomics Resource, The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - John W. Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
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Keinprecht H, Irimaso E, Rosel AC, Stessl B, Ntakirutimana C, Marek L, Fischer OW, Szostak MP, Zöchbauer J, Wittek T, Müller E, Desvars-Larrive A, Feßler AT, Braun SD, Schwarz S, Spergser J, Ehling-Schulz M, Monecke S, Ehricht R, Ruppitsch W, Grunert T, Loncaric I. Diversity of Staphylococcus aureus associated with mastitis from dairy cows in Rwanda. J Glob Antimicrob Resist 2024; 36:326-335. [PMID: 38307251 DOI: 10.1016/j.jgar.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVES The objective of the present study was to examine the diversity of Staphylococcus aureus from mastitis milk samples of cows in Rwanda. METHODS A total of 1080 quarter milk samples from 279 dairy cows were collected in 80 different farms from all five provinces of Rwanda. In total, 135 S. aureus isolates were obtained and subjected to genotyping (spa typing, DNA microarray, whole-genome sequencing (WGS)), antimicrobial susceptibility testing (AST) and phenotypic profiling by Fourier Transform Infrared (FTIR) spectroscopy (including capsular serotyping). RESULTS Resistance to penicillin and/or tetracycline was most frequently observed. Ten sequence types (STs) (ST1, ST151, ST152, ST5477, ST700, ST7110, ST7983, ST7984, ST8320, ST97) belonging to seven clonal complexes (CCs) (CC1, CC130, CC152, CC3591, CC3666, CC705, CC97) were detected. The Panton-Valentine leukocidin (PVL) genes (lukF-PV/lukS-PV), the bovine leukocidin genes (lukM/lukF-P83) and the human and bovine toxic shock syndrome toxin gene tst-1 variants were detected. FTIR-based capsular serotyping showed CC-specific differences. Most CC97 (cap5 allele) isolates were primarily nonencapsulated (82%), whereas isolates of CC3591 and CC3666 (cap8 allele) were mostly encapsulated (86.4% and 57.8%, respectively). Our results underline the widespread global distribution of cattle-adapted CC97. CONCLUSION The presence of CC3591 and CC3666 in bovine mastitis suggests an important role in cattle health and dairy production in Rwanda. The results of the present study support the need for a rigorous One-Health Surveillance program of the bovine-human interface.
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Affiliation(s)
- Helga Keinprecht
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria; New Vision Veterinary Hospital (NVVH) Northern Province, Musanze District, Rwanda
| | - Emmanuel Irimaso
- School of Veterinary Medicine- CAVM, University of Rwanda, Nyagatare Campus, Nyagatare, Rwanda, Rwanda
| | - Adriana Cabal Rosel
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Beatrix Stessl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Lydia Marek
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria; New Vision Veterinary Hospital (NVVH) Northern Province, Musanze District, Rwanda
| | - Otto W Fischer
- New Vision Veterinary Hospital (NVVH) Northern Province, Musanze District, Rwanda
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jennifer Zöchbauer
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Wittek
- Clinical Unit of Ruminant Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany
| | - Amelie Desvars-Larrive
- Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria; Complexity Science Hub Vienna, Vienna, Austria
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Sascha D Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany; Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany; Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Tom Grunert
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria.
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Cuny C, Layer-Nicolaou F, Werner G, Witte W. A look at staphylococci from the one health perspective. Int J Med Microbiol 2024; 314:151604. [PMID: 38367509 DOI: 10.1016/j.ijmm.2024.151604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.
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Affiliation(s)
- Christiane Cuny
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.
| | - Franziska Layer-Nicolaou
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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Chakrawarti A, Casey CL, Burk A, Mugabi R, Ochoa A, Barlow JW. An observational study demonstrates human-adapted Staphylococcus aureus strains have a higher frequency of antibiotic resistance compared to cattle-adapted strains isolated from dairy farms making farmstead cheese. BMC Vet Res 2024; 20:75. [PMID: 38409123 PMCID: PMC10898128 DOI: 10.1186/s12917-024-03910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Staphylococcus aureus is a multi-host zoonotic pathogen causing human and livestock diseases. Dairy farms that make artisan cheese have distinctive concerns for S. aureus control. Antimicrobial-resistant (AMR) S. aureus is a public and animal health concern. There is a need to study the population structure of AMR S. aureus at the human-animal interface and understand the path of zoonotic transmission. This cross-sectional observational study aimed to assess the genetic diversity and AMR patterns of S. aureus isolated from cattle and humans on conventional and organic Vermont dairy farms that produce and sell farmstead cheese. RESULTS A convenience sample of 19 dairy farms in Vermont was enrolled, and 160 S. aureus isolates were collected from cow quarter milk (CQM), bulk tank milk (BTM), human-hand and -nasal swabs. After deduplication, 89 isolates were used for the analysis. Sequence types (STs) were determined by multilocus sequence typing and cataloged to the PubMLST database. Nine defined and five novel STs were identified. For BTM and CQM samples, six STs were identified within cow-adapted CC97 and CC151. Two human-adapted STs were isolated from BTM and CQM. Seven human-adapted clonal complexes with eight STs were identified from human samples. One cow-adapted ST was isolated from a human. Antimicrobial susceptibility of the isolates was tested using disc diffusion and broth microdilution methods. Approximately 27% of the isolates were beta-lactam resistant and blaZ gene-positive. S. aureus isolates from human swabs were more likely to carry blaZ compared to isolates from CQM or BTM. S. aureus isolated from cows and humans on the same farm belonged to different STs. CONCLUSION Humans were more likely to carry beta-lactam-resistant S. aureus compared to cows, and on organic farms only human-adapted blaZ positive STs were isolated from BTM. Moreover, we identified potential spillover events of S. aureus sequence types between host species. The presence of penicillin-resistant-human-adapted S. aureus on both organic and conventional dairy farms highlights a "One Health" concern at the junction of public and animal health requiring further surveillance.
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Affiliation(s)
- Ashma Chakrawarti
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Christine L Casey
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, USA
| | - Ariela Burk
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Robert Mugabi
- Department of Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, IA, USA
| | | | - John W Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA.
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Barcudi D, Blasko E, Gonzalez MJ, Gagetti P, Lamberghini R, Garnero A, Sarkis C, Faccone D, Lucero C, Tosoroni D, Bocco JL, Corso A, Sola C. Different evolution of S. aureus methicillin-resistant and methicillin-susceptible infections, Argentina. Heliyon 2024; 10:e22610. [PMID: 38163174 PMCID: PMC10755277 DOI: 10.1016/j.heliyon.2023.e22610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
Staphylococcus aureus-(SA) is widespread among healthcare-associated-(HA) and the community-associated-(CA) infections. However, the contributions of MRSA and MSSA to the SA overall burden remain unclear. In a nationally-representative-survey conducted in Argentina, 668 SA clinical isolates from 61 hospitals were examined in a prospective, cross-sectional, multicenter study in April 2015. The study aimed to analyze MRSA molecular epidemiology, estimate overall SA infection incidence (MSSA, MRSA, and genotypes) in community-onset (CO: HACO, Healthcare-Associated-CO and CACO, Community-Associated-CO) and healthcare-onset (HO: HAHO, Healthcare-associated-HO) infections, stratified by age groups. Additionally temporal evolution was estimated by comparing this study's (2015) incidence values with a previous study (2009) in the same region. Erythromycin-resistant-MSSA and all MRSA strains were genetically typed. The SA total-infections (TI) overall-incidence was 49.1/100,000 monthly-visits, 25.1 and 24.0 for MRSA and MSSA respectively (P = 0.5889), in April 2015. In adults with invasive-infections (INVI), MSSA was 15.7 and MRSA was 11.8 (P = 0.0288), 1.3-fold higher. HA SA infections, both MSSA and MRSA, surpassed CA infections by over threefold. During 2009-2015, there was a significant 23.4 % increase in the SA infections overall-incidence, mainly driven by MSSA, notably a 54.2 % increase in INVI among adults, while MRSA infection rates remained stable. The MSSA rise was accompanied by increased antimicrobial resistance, particularly to erythromycin, linked to MSSA-CC398-t1451-ermT + -IEC+-pvl- emergence. The SA-infections rise was primarily attributed to community-onset-infections (37.3 % and 62.4 % increase for TI and INVI, respectively), particularly HACO-MSSA and HACO-MRSA in adults, as well as CACO-MSSA. The main CA-MRSA-PFGE-typeN-ST30-SCCmecIVc-PVL+/- clone along with other clones (USA300-ST8-IV-LV-PVL+/-, PFGE-typeDD-ST97-IV- PVL-) added to rather than replaced CA-MRSA-PFGE-typeI-ST5-SCCmecIVa-PVL+/- clone in HA invasive-infections. They also displaced clone HA-MRSA-PFGE-typeA-ST5-SCCmecI, mainly in HAHO infections. The overall-burden of SA infections is rising in Argentina, driven primarily by community-onset MSSA, particularly in adults, linked to increased erythromycin-resistance and MSSA-CC398-t1451-ermT + -IEC+-pvl- emergence. Novel knowledge and transmission-control strategies are required for MSSA.
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Affiliation(s)
- Danilo Barcudi
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000, Córdoba, Argentina
| | - Enrique Blasko
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000, Córdoba, Argentina
| | - María José Gonzalez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000, Córdoba, Argentina
| | - Paula Gagetti
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ricardo Lamberghini
- Cátedra de Infectología I, Hospital Rawson, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Bajada Pucará 2025, X5000, Córdoba, Argentina
| | - Analía Garnero
- Servicio de Infectología, Hospital de Niños de la Santísima Trinidad de Córdoba, Córdoba, Bajada Pucará 787, X 5000, ANN, Argentina
| | - Claudia Sarkis
- Hospital de Pediatría S.A.M.I.C."Prof. Dr. Juan P. Garrahan”, Combate de los Pozos 1881, C1245, AAM, CABA, Argentina
| | - Diego Faccone
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Celeste Lucero
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Dario Tosoroni
- Informática Médica, Facultad de Medicina, Universidad Católica de Córdoba, Jacinto Ríos 555, X5004, ASK, Córdoba, Argentina
| | | | - José L. Bocco
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000, Córdoba, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudia Sola
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET and Universidad Nacional de Córdoba, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000, Córdoba, Argentina
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12
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Loncaric I, Keinprecht H, Irimaso E, Cabal-Rosel A, Stessl B, Ntakirutimana C, Marek L, Fischer OW, Szostak MP, Oberrauch C, Wittek T, Müller E, Desvars-Larrive A, Feßler AT, Braun SD, Schwarz S, Ehling-Schulz M, Monecke S, Ehricht R, Ruppitsch W, Grunert T, Spergser J. Diversity of Staphylococcus aureus isolated from nares of ruminants. J Appl Microbiol 2024; 135:lxad304. [PMID: 38159931 DOI: 10.1093/jambio/lxad304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/12/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
AIMS To examine the diversity of Staphylococcus aureus isolated from nasal swabs of ruminants in Rwanda. METHODS AND RESULTS A total of 454 nasal swabs from 203 cows, 170 goats, and 81 sheep were examined for the presence of S. aureus, and 30 S. aureus isolates were detected and characterized pheno- and genotypically. Resistance to penicillin and/or tetracycline was observed. The isolates were assigned to eight different spa types (t21057 (novel), t10103, t18853, t20842, t318, t355, t458, and t9432) belonging to six clonal complexes (CCs) (CC152, CC30, CC3591, CC3666, CC522, and CC97). Panton-Valentine leukocidin (PVL) genes (lukF-PV/lukS-PV), the bovine leukocidin genes (lukM/lukF-P83), and the human and bovine variants of the toxic shock syndrome toxin gene tst-1 variants were detected. CONCLUSION These findings demonstrate that the nares of ruminants in Rwanda are colonized with mastitis-associated S. aureus, including lineages that are also carried by humans, underscoring the zoonotic risk, especially for livestock keepers. These results highlight the crucial importance of hygiene measures when handling livestock.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Helga Keinprecht
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- New Vision Veterinary Hospital (NVVH) Northern Province, Musanze district, Rwaza sector, Rwanda
| | - Emmanuel Irimaso
- School of Veterinary Medicine-CAVM, University of Rwanda, Nyagatare Campus, P.O. Box 210, Nyagatare, Rwanda
| | - Adriana Cabal-Rosel
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna 1090, Austria
| | - Beatrix Stessl
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | | | - Lydia Marek
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- New Vision Veterinary Hospital (NVVH) Northern Province, Musanze district, Rwaza sector, Rwanda
| | - Otto W Fischer
- New Vision Veterinary Hospital (NVVH) Northern Province, Musanze district, Rwaza sector, Rwanda
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Celine Oberrauch
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Wittek
- Clinical Unit of Ruminant Medicine, University of Veterinary Medicine, Vienna 1210, Austria
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- InfectoGnostics Research Campus, Jena 07743, Germany
| | - Amelie Desvars-Larrive
- Unit of Veterinary Public Health and Epidemiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Complexity Science Hub Vienna, Vienna 1080, Austria
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Sascha D Braun
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- InfectoGnostics Research Campus, Jena 07743, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Monika Ehling-Schulz
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- InfectoGnostics Research Campus, Jena 07743, Germany
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden 01307, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena 07745, Germany
- InfectoGnostics Research Campus, Jena 07743, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna 1090, Austria
| | - Tom Grunert
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
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13
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Rong D, Liu Z, Huang J, Zhang F, Wu Q, Dai J, Li Y, Zhao M, Li Q, Zhang J, Wu S. Prevalence and characterization of Staphylococcus aureus and Staphylococcus argenteus isolated from rice and flour products in Guangdong, China. Int J Food Microbiol 2023; 406:110348. [PMID: 37573713 DOI: 10.1016/j.ijfoodmicro.2023.110348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Staphylococcus aureus and Staphylococcus argenteus have been implicated in food poisoning outbreaks, and have been found in various types of food products according to our previous study. Rice and flour products are popular and widely consumed around the world. However, limited data are available on the microbial safety of S. aureus in rice and flour products, and S. argenteus has never been reported. Thus, this study aimed to investigate the contamination of S. aureus and S. argenteus in 250 fresh rice and flour product samples from five cities in Guangdong, China. According to qualitative and quantitative analyses, 68 (27.2 %) and 11 (4.4 %) samples were positive for S. aureus and S. argenteus, including 9 samples that exceeded 100 MPN/g. For antibiotics susceptibility tests in 16 antibiotics, the S. aureus isolates exhibited higher rates of resistance and multidrug resistance than S. argenteus. The S. aureus and S. argenteus isolates were mainly resistant to penicillin (70.21 %; 79.17 %), tetracycline (20.21 %; 58.33 %) and azithromycin (19.68 %, 8.33 %). However, the other antibiotic resistance rates were <10 %. Furthermore, the genetic background of the isolates was analyzed by whole-genome sequencing (WGS). As a result, the S. aureus isolates were divided into 18 known sequence types (STs) and 4 novel STs (ST7675, ST7679, ST7680 and ST7682), which mainly belonged to ST188 (20.6 %) and ST6 (14.7 %). The S. argenteus isolates mainly belonged to ST2250 (90.9 %), with a novel type (ST7683). In total, 36 and 16 antibiotic resistance genes (ARGs) were found in S. aureus and S. argenteus isolates, respectively. In addition, 91 virulence genes (VFs) were detected in S. aureus isolates as well as 90 % of core VFs were similar to S. argenteus. More than 20 % of the S. aureus isolates carried the classic enterotoxin gene (sea-sec), but chp, cna and map were free in all S. argenteus isolates. Importantly, 33.8 % of S. aureus isolates belonged to the immune evasion cluster (IEC) type B, whereas most of S. argenteus isolates (90.9 %) belong to IEC type E. According to the phylogenetic analysis, the S. aureus and S. argenteus isolates in fresh rice and flour products may indicate loss or acquisition of ARGs and VFs to survive and adapt to the environment. Our study confirmed the presence of S. argenteus in rice and flour products at first and focused on the multi-dimensional systematic comparative analysis of S. aureus and S. argenteus to reveal their ubiquity and similarities or differences, and provide more accurate and effective basic information for follow-up monitoring and tracking.
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Affiliation(s)
- Dongli Rong
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Zhenjie Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jiahui Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Feng Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jingsha Dai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yuanyu Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Miao Zhao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qi Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
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14
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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15
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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16
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Pan Y, Chen L, Zhang L, Li G, Zeng J, Hu J, Liu W, Li Y, Zeng Z. One health genomic insights into the host-specific evolution and cross-host transmission of Staphylococcus aureus in animal farm environments, food of animal origin, and humans. Int J Antimicrob Agents 2023; 62:106932. [PMID: 37495058 DOI: 10.1016/j.ijantimicag.2023.106932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/23/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
OBJECTIVES Staphylococcus aureus is an opportunistic pathogen that is considered a high priority for research. However, comparative studies of S. aureus strains from different environments and hosts are still lacking. METHODS Here, we performed a high-resolution bioinformatics analysis of 576 S. aureus genomes isolated from livestock, farm environments, farm workers, animal-origin food, and humans. RESULTS The S. aureus isolates showed high diversity in genetic lineages and demonstrated host specialization and multi-host range in the population phylogeny. Recent transmission events, historical divergences, and frequent host switching in specific sequence types (STs) and through the food chain and animal farm mediums were observed. Frequent gene transfer may quickly give rise to new fitness to colonize their host or switch to other hosts, even in isolates with the closest vertical evolutionary history. The large multi-host-shared antibiotic resistance gene (ARG) pool was the major factor shaping antibiotic resistance in S. aureus isolates. We revealed the genetic backgrounds of mec, cfr, and optrA, which could be spread among isolates from different species, hosts, and environments. CONCLUSION Overall, our findings provide One Health genomic insights into the evolution, transmission, gene content characteristics, and antibiotic resistance profiles of S. aureus from different hosts, suggesting that, despite well-formed host specificity during the evolution of S. aureus, the ever-expanding host range and the cross-hosts/niches transmission (at both the strain and genetic level) may be facilitated by diverse bacterial vehicles (e.g., food chain, farm environments, and workers), which will lead to emerging antibiotic resistance consequences and threaten public health and food safety.
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Affiliation(s)
- Yu Pan
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lin Chen
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lingxuan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Guihua Li
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jiaxiong Zeng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jianxin Hu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Weiqi Liu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Yafei Li
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Zhenling Zeng
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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17
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Banaszkiewicz S, Tabiś A, Wałecki B, Łyżwińska K, Bystroń J, Bania J. spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar. MICROBIAL ECOLOGY 2023; 86:2184-2191. [PMID: 37156959 PMCID: PMC10497643 DOI: 10.1007/s00248-023-02236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.
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Affiliation(s)
- Sylwia Banaszkiewicz
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Tabiś
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Wałecki
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Łyżwińska
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jarosław Bystroń
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
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Zhu Z, Wu S, Chen X, Tan W, Zou G, Huang Q, Meng X, Hu DL, Li S. Heterogeneity and transmission of food safety-related enterotoxigenic Staphylococcus aureus in pig abattoirs in Hubei, China. Microbiol Spectr 2023; 11:e0191323. [PMID: 37772855 PMCID: PMC10581196 DOI: 10.1128/spectrum.01913-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
The dissemination of Staphylococcus aureus in the pork production chain is a major food safety concern. Abattoirs can serve both as disruptor and transmitter for S. aureus. In this study, we conducted a systematic genomic epidemiology research on the prevalence, heterogeneity, and transmission of S. aureus in 3,638 samples collected from four pig abattoirs in Hubei province, China. Our findings revealed substantial heterogeneity between S. aureus recovered from samples collected at upstream (from stunning step to head-removal step) and downstream (from splitting step to chilling step) locations within the slaughter process. Overall, 966 (26.6%) samples were positive for S. aureus, with significantly higher overall prevalence for upstream samples (29.0%, 488/1,681) compared to downstream samples (24.4%, 478/1,957). Antimicrobial susceptibility testing demonstrated that the isolates from the upstream exhibited significantly higher resistance proportions to different antimicrobials than those from the downstream. Whole-genome sequencing of 126 isolates revealed that ST398 (32.9%, 23/70) and ST9 (22.9%, 16/70) were more common among upstream isolates, while ST7 (35.7%, 20/56) and ST97 (28.6%, 16/56) were most frequently observed among downstream isolates. Additionally, molecular characterization analysis demonstrated that upstream isolates possessed significantly higher enterotoxigenic potential, more antimicrobial resistance genes, and S. aureus pathogenicity islands than downstream isolates. Notably, we discovered that enterotoxigenic S. aureus could be transmitted across different slaughter stages, with knives, water, and air serving as vectors. Although slaughtering processes had a substantial effect on reducing the food safety risk posed by enterotoxigenic S. aureus, the possibility of its widespread transmission should not be disregarded. IMPORTANCE Staphylococcus aureus (S. aureus) is one of the most important foodborne pathogens, and can cause foodborne poisoning by producing enterotoxins. Pork is a preferable reservoir and its contamination often occurs during the slaughter process. Our findings revealed significant differences in the prevalence, antimicrobial resistance, and enterotoxigenic potential between the upstream and downstream isolates within the slaughter process. Also, it is imperative not to overlook enterotoxigenic S. aureus transmitted across all stages of the slaughter process, with notable vectors being knives, water, and air. These findings hold significant implications for policy-makers to reassess their surveillance projects, and underscore the importance of implementing effective control measures to minimize the risk of S. aureus contamination in pork production. Moreover, we provide a more compelling method of characterizing pathogen transmission based on core-SNPs of bacterial genomes.
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Affiliation(s)
- Zhihao Zhu
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Simin Wu
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xingyu Chen
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Tan
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Geng Zou
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qi Huang
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xianrong Meng
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dong-Liang Hu
- Department of Zoonoses, Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Shaowen Li
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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19
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Liu H, Ji X, Wang H, Hou X, Sun H, Billington C, Zhang L, Wang X, Wang R. Genomic epidemiology and characterization of Staphylococcus aureus isolates from raw milk in Jiangsu, China: emerging broader host tropism strain clones ST59 and ST398. Front Microbiol 2023; 14:1266715. [PMID: 37808296 PMCID: PMC10556526 DOI: 10.3389/fmicb.2023.1266715] [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: 07/25/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Staphylococcus aureus is highly pathogenic and can cause disease in both humans and domestic animals. The aim of this study was to investigate the genomic epidemiology of S. aureus isolates from raw milk in Jiangsu Province, China, to identify predominant lineages and their associated genomic and phenotypic characteristics. In this study, we identified 117 S. aureus isolates collected from 1,062 samples in Jiangsu Province between 2021 and 2022. Based on whole-genome sequencing (WGS) data from 117 S. aureus isolates, molecular analyses indicated CC1-ST1 (26.50%, 31/117), CC97-ST97 (18.80%, 22/117), CC398-ST398 (10.26%, 12/117), CC8-ST630 (7.69%, 9/117) and CC59-ST59 (2.56%, 3/117) were the major lineages. The prevalence of mecA-positive strains was 11.11%. Four methicillin-resistant S. aureus (MRSA) lineages were found, including MRSA-ST59-t172 (n = 3), OS-MRSA-ST398-t011 (n = 1), MRSA-ST630-t2196 (n = 2) and OS-MRSA-ST630-t2196 (n = 7). Phenotypic resistance to penicillin (30.77%, 36/117), ciprofloxacin (17.09%, 20/117) and erythromycin (15.38%, 18/117) was observed which corresponded with resistance genotypes. All of the isolates could produce biofilms, and 38.46% (45/117) of isolates had invasion rates in mammary epithelial cells (MAC-T) of greater than 1%. Interestingly, most biofilm-producing and invading isolates harbored ebp-icaA-icaB-icaC-icaR-clfA-clfB-fnbA-fnbB-sdrC-sdrD-sdrE-map-can (27.35%, 32/117) and ebp-icaA-icaB-icaC-icaD-icaR-clfA-clfB-fnbA-fnbB-sdrC-sdrD-sdrE-map (33.33%, 39/117) adherence-associated gene patterns and belonged to lineages CC1 and CC97, respectively. Virulence factor assays showed that 47.01% of the isolates contained at least enterotoxin genes. Isolates harboring the immune evasion cluster (IEC) genes (sea, sak, chp, and scn) were predominantly categorized as STs 464, 398, and 59. IEC-positive ST398 and ST59 isolates contained a very high proportion of virulence genes located on prophages, whereas most IEC-negative ST398 clade isolates carried broad-spectrum drug resistance genes. Meanwhile, the IEC-positive ST398 clade showed a close genetic relationship with isolates from the pork supply chain and hospital surgical site infections. MRSA-ST59 strains showed the closest genetic relationship with an isolate from quick-frozen products. High-risk livestock-associated strains ST398 and MRSA-ST59 were detected in raw milk, indicating a potential public health risk of S. aureus transmission between livestock and humans. Our study highlights the necessity for S. aureus surveillance in the dairy industry.
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Affiliation(s)
- Hui Liu
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xing Ji
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Heye Wang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiang Hou
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Haichang Sun
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Craig Billington
- Institute of Environmental Science and Research, Ilam, Christchurch, New Zealand
| | - Lili Zhang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoye Wang
- College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ran Wang
- Key Laboratory of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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20
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Yu S, Zhou Y, Feng D, Jiang Q, Li T, Jiang G, Zhou Z, Li H. Whole genome sequence-based characterization of virulence and antimicrobial resistance gene profiles of Staphylococcus aureus isolated from food poisoning incidents in eastern China. Front Microbiol 2023; 14:1225472. [PMID: 37795294 PMCID: PMC10546991 DOI: 10.3389/fmicb.2023.1225472] [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: 05/19/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Staphylococcus aureus is an opportunistic foodborne pathogen occasionally isolated from diarrhea patients. In recent years, increasing studies have reported the detection of S. aureus in food poisoning incidents due to food contamination in the North and South of China. However, the epidemiology and genetic characteristics of S. aureus from food poisoning incidents in Eastern China remain unknown. The present study examined the genetic characteristics, antimicrobial resistance, and virulent factors of multidrug-resistant S. aureus isolated from 22 food poisoning incidents reported by the hospitals and health centers in Eastern China from 2011 to 2021. A total of 117 resistant and enterotoxigenic S. aureus isolates were collected and sequenced, among which 20 isolates were identified as methicillin resistant. Genetic analysis revealed 19 distinct CC/ST types, with CC6, CC22, CC59, CC88, and CC398 being the most frequent variants in methicillin-resistant S. aureus (MRSA). A considerable shift in CC types from CC1 to CC398 between 2011 and 2021 was observed in this study, indicating that CC398 may be the main epidemic strain circulating in the current food poisoning incidents. Additionally, genes for enterotoxins were detected in 55 isolates, with a prevalence of 27.8% (27/97) for methicillin-sensitive variants and 35.0% (7/20) for MRSA. The scn gene was detected in 59.0% of the isolates, demonstrating diverse contaminations of S. aureus among livestock-to-human transmission. Of the 117 isolates, only ten isolates displayed multi-drug resistance (MDR) to penicillin, tetracycline, and macrolides. None of the 117 foodborne S. aureus isolates tested positive for vanA in this study. Together, the present study provided phylogenetic characteristics of S. aureus from food poisoning incidents that emerged in Eastern China from 2011 to 2021. Our results suggested that these diarrhea episodes were hypotonic and merely transient low-MDR infections, however, further research for continued surveillance given the detection of virulence and antimicrobial resistance determinants is required to elucidate the genomic characteristics of pathogenic S. aureus in food poisoning incidents in the context of public health.
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21
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Souza SSR, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Multi-host infection and phylogenetically diverse lineages shape the recombination and gene pool dynamics of Staphylococcus aureus. BMC Microbiol 2023; 23:235. [PMID: 37626313 PMCID: PMC10463932 DOI: 10.1186/s12866-023-02985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States. RESULTS Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages. CONCLUSIONS Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S. aureus colonization, infection, and transmission across the One Health continuum.
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Affiliation(s)
- Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Spencer A Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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22
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Youngblom MA, Imhoff MR, Smyth LM, Mohamed MA, Pepperell CS. Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553882. [PMID: 37645846 PMCID: PMC10462137 DOI: 10.1101/2023.08.18.553882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists. Data summary Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics . Impact statement It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.
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23
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Postiglione U, Batisti Biffignandi G, Corbella M, Merla C, Olivieri E, Petazzoni G, Feil EJ, Bandi C, Cambieri P, Gaiarsa S, Brilli M, Sassera D. Combining Genome Surveillance and Metadata To Characterize the Diversity of Staphylococcus aureus Circulating in an Italian Hospital over a 9-Year Period. Microbiol Spectr 2023; 11:e0101023. [PMID: 37458594 PMCID: PMC10433831 DOI: 10.1128/spectrum.01010-23] [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] [Received: 03/15/2023] [Accepted: 06/18/2023] [Indexed: 08/19/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen and a leading cause of morbidity and mortality worldwide. Genomic-based surveillance has greatly improved our ability to track the emergence and spread of high-risk clones, but the full potential of genomic data is only reached when used in conjunction with detailed metadata. Here, we demonstrate the utility of an integrated approach by leveraging a curated collection of clinical and epidemiological metadata of S. aureus in the San Matteo Hospital (Italy) through a semisupervised clustering strategy. We sequenced 226 sepsis S. aureus samples, recovered over a period of 9 years. By using existing antibiotic profiling data, we selected strains that capture the full diversity of the population. Genome analysis revealed 49 sequence types, 16 of which are novel. Comparative genomic analyses of hospital- and community-acquired infection ruled out the existence of genomic features differentiating them, while evolutionary analyses of genes and traits of interest highlighted different dynamics of acquisition and loss between antibiotic resistance and virulence genes. Finally, highly resistant clones belonging to clonal complexes (CC) 8 and 22 were found to be responsible for abundant infections and deaths, while the highly virulent CC30 was responsible for rare but deadly episodes of infections. IMPORTANCE Genome sequencing is an important tool in clinical microbiology, as it allows in-depth characterization of isolates of interest and can propel genome-based surveillance studies. Such studies can benefit from ad hoc methods of sample selection to capture the genomic diversity present in a data set. Here, we present an approach based on clustering of antibiotic resistance profiles that allows optimal sample selection for bacterial genomic surveillance. We apply the method to a 9-year collection of Staphylococcus aureus from a large hospital in northern Italy. Our method allows us to sequence the genomes of a large variety of strains of this important pathogen, which we then leverage to characterize the epidemiology in the hospital and to perform evolutionary analyses on genes and traits of interest. These analyses highlight different dynamics of acquisition and loss between antibiotic resistance and virulence genes.
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Affiliation(s)
- U. Postiglione
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - M. Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - C. Merla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - E. Olivieri
- Istituto Zooproflattico Sperimentale della Lombardia e dell’Emilia Romagna, Pavia, Italy
| | - G. Petazzoni
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - E. J. Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - C. Bandi
- Department of Bioscience, University of Milan, Milan, Italy
| | - P. Cambieri
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - S. Gaiarsa
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - M. Brilli
- Department of Bioscience, University of Milan, Milan, Italy
| | - D. Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Leinweber H, Sieber RN, Bojer MS, Larsen J, Ingmer H. Fluoroquinolone resistance does not facilitate phage Φ13 integration or excision in Staphylococcus aureus. Access Microbiol 2023; 5:acmi000583.v4. [PMID: 37424547 PMCID: PMC10323784 DOI: 10.1099/acmi.0.000583.v4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 07/11/2023] Open
Abstract
Prophages of the ΦSa3int family are commonly found in human-associated strains of Staphylococcus aureus where they encode factors for evading the human innate immune system. In contrast, they are usually absent in livestock-associated methicillin-resistant S. aureus (LA-MRSA) strains where the phage attachment site is mutated compared to the human strains. However, ΦSa3int phages have been found in a subset of LA-MRSA strains belonging to clonal complex 398 (CC398), including a lineage that is widespread in pig farms in Northern Jutland, Denmark. This lineage contains amino acid changes in the DNA topoisomerase IV and the DNA gyrase encoded by grlA and gyrA, respectively, which have been associated with fluoroquinolone (FQ) resistance. As both of these enzymes are involved in DNA supercoiling, we speculated that the mutations might impact recombination between the ΦSa3int phage and the bacterial chromosome. To examine this, we introduced the FQ resistance mutations into S. aureus 8325-4attBLA that carry the mutated CC398-like bacterial attachment site for ΦSa3int phages. When monitoring phage integration and release of Φ13, a well-described representative of the ΦSa3int phage family, we did not observe any significant differences between the FQ-resistant mutant and the wild-type strain. Thus our results suggest that mutations in grlA and gyrA do not contribute to the presence of the ΦSa3int phages in LA-MRSA CC398.
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Affiliation(s)
- Helena Leinweber
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
| | - Raphael N. Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Martin S. Bojer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
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25
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Park JM, Ko DS, Kim HS, Kim NH, Kim EK, Roh YH, Kim D, Kim JH, Choi KS, Kwon HJ. Rapid Screening and Comparison of Chimeric Lysins for Antibacterial Activity against Staphylococcus aureus Strains. Antibiotics (Basel) 2023; 12:antibiotics12040667. [PMID: 37107029 PMCID: PMC10135017 DOI: 10.3390/antibiotics12040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Chimeric lysins composed of various combinations of cell wall-lysing (enzymatic) and cell-wall-binding (CWB) domains of endolysins, autolysins, and bacteriocins have been developed as alternatives to or adjuvants of conventional antibiotics. The screening of multiple chimeric lysin candidates for activity via E. coli expression is not cost effective, and we previously reported on a simple cell-free expression system as an alternative. In this study, we sufficiently improved upon this cell-free expression system for use in screening activity via a turbidity reduction test, which is more appropriate than a colony reduction test when applied in multiple screening. Using the improved protocol, we screened and compared the antibacterial activity of chimeric lysin candidates and verified the relatively strong activity associated with the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain of secretory antigen SsaA-like protein (ALS2). ALS2 expressed in E. coli showed two major bands, and the smaller one (subprotein) was shown to be expressed by an innate downstream promoter and start codon (ATG). The introduction of synonymous mutations in the promoter resulted in clearly reduced expression of the subprotein, whereas missense mutations in the start codon abolished antibacterial activity as well as subprotein production. Interestingly, most of the S. aureus strains responsible for bovine mastitis were susceptible to ALS2, but those from human and chicken were less susceptible. Thus, the simple and rapid screening method can be applied to select functional chimeric lysins and define mutations affecting antibacterial activity, and ALS2 may be useful in itself and as a lead molecule to control bovine mastitis.
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Affiliation(s)
- Jin-Mi Park
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Dae-Sung Ko
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Hee-Soo Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Nam-Hyung Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Eun-Kyoung Kim
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Young-Hye Roh
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Kang-Seuk Choi
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.)
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.)
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Rehman MNU, Dawar FU, Zeng J, Fan L, Feng W, Wang M, Yang N, Guo G, Zheng J. Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile. Front Vet Sci 2023; 10:1140655. [PMID: 36968469 PMCID: PMC10034365 DOI: 10.3389/fvets.2023.1140655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.
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Affiliation(s)
- Muhammad Nafees Ur Rehman
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Farman Ullah Dawar
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Jifeng Zeng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Lixia Fan
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Wei Feng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Mengqi Wang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Nuo Yang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Guiying Guo
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Jiping Zheng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
- *Correspondence: Jiping Zheng
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Torres G, Vargas K, Reyes-Vélez J, Jiménez N, Blanchard A, Olivera-Angel M. High genetic diversity and zoonotic potential of Staphylococcus aureus strains recovered from bovine intramammary infections in Colombians dairy herds. Comp Immunol Microbiol Infect Dis 2023; 93:101940. [PMID: 36603241 DOI: 10.1016/j.cimid.2022.101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
Genotyping of Staphylococcus aureus isolated from mastitis has become a fundamental tool to understand its complex epidemiology and to evaluate spillover events. The aim of this study was to describe the frequency of genotypes of the S. aureus strains isolated from intramammary infections by spa typing technique, and to evaluate the association between genotypes and the ability to form biofilm under in vitro conditions. Sixty-six strains of S. aureus recovered from bovines intramammary infections on 56 dairy herds located in 14 municipalities of the department of Antioquia were characterized. The majority of strains (65/66) were isolated from milk samples collected from dairy cows with subclinical intramammary infections. Nineteen different spa types were found in this study, t521 (19.70%), t267 (15.15%), and t605 (12.12%) being the most frequent. The strains from the t605 spa type showed the highest biofilm production. The high frequency of spa types with zoonotic potential found in this study, identified cattle as an important reservoir of theses clones for people in close proximity, such as milkers and consumers of unpasteurized dairy products.
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Affiliation(s)
- G Torres
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia; Instituto Colombiano de Medicina Tropical - Universidad CES, Cra. 43A No. 52 sur-99, Sabaneta, Antioquia, Colombia.
| | - K Vargas
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia
| | - J Reyes-Vélez
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia; Instituto Colombiano de Medicina Tropical - Universidad CES, Cra. 43A No. 52 sur-99, Sabaneta, Antioquia, Colombia
| | - N Jiménez
- Basic and Applied Microbiology Research Group, School of Microbiology, University of Antioquia, Cl. 67 No. 53-108, Medellín, Antioquia, Colombia
| | - A Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - M Olivera-Angel
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia
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28
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Howden BP, Giulieri SG, Wong Fok Lung T, Baines SL, Sharkey LK, Lee JYH, Hachani A, Monk IR, Stinear TP. Staphylococcus aureus host interactions and adaptation. Nat Rev Microbiol 2023; 21:380-395. [PMID: 36707725 PMCID: PMC9882747 DOI: 10.1038/s41579-023-00852-y] [Citation(s) in RCA: 114] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to develop drug resistance. S. aureus is an excellent case study of the potential for a bacterium to be commensal, colonizing, latent or disease-causing; these states defined by the interplay between S. aureus and host. This interplay is multidimensional and evolving, exemplified by the spread of S. aureus between humans and other animal reservoirs and the lack of success in vaccine development. In this Review, we examine recent advances in understanding the S. aureus-host interactions that lead to infections. We revisit the primary role of neutrophils in controlling infection, summarizing the discovery of new immune evasion molecules and the discovery of new functions ascribed to well-known virulence factors. We explore the intriguing intersection of bacterial and host metabolism, where crosstalk in both directions can influence immune responses and infection outcomes. This Review also assesses the surprising genomic plasticity of S. aureus, its dualism as a multi-mammalian species commensal and opportunistic pathogen and our developing understanding of the roles of other bacteria in shaping S. aureus colonization.
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Affiliation(s)
- Benjamin P. Howden
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.410678.c0000 0000 9374 3516Department of Infectious Diseases, Austin Health, Heidelberg, Victoria Australia ,grid.416153.40000 0004 0624 1200Microbiology Department, Royal Melbourne Hospital, Melbourne, Victoria Australia
| | - Stefano G. Giulieri
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.416153.40000 0004 0624 1200Victorian Infectious Diseases Service, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Tania Wong Fok Lung
- grid.21729.3f0000000419368729Department of Paediatrics, Columbia University, New York, NY USA
| | - Sarah L. Baines
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Liam K. Sharkey
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Jean Y. H. Lee
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.419789.a0000 0000 9295 3933Department of Infectious Diseases, Monash Health, Clayton, Victoria Australia
| | - Abderrahman Hachani
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Ian R. Monk
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
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29
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Liu A, Wan Q, Li J, Li Q, Hu K, Ao X, Chen S, He L, Hu X, Hu B, Yang Y, Zou L, Liu S. Rose bud extract as a natural antimicrobial agent against Staphylococcus aureus: Mechanisms and application in maintaining pork safety. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Konstantinovski MM, Schouls LM, Witteveen S, Claas ECJ, Kraakman ME, Kalpoe J, Mattson E, Hetem DJ, van Elzakker EPM, Kerremans J, Hira V, Bosch T, Gooskens J. Livestock-associated methicillin-resistant Staphylococcus aureus epidemiology, genetic diversity, and clinical characteristics in an urban region. Front Microbiol 2022; 13:875775. [PMID: 36590396 PMCID: PMC9795226 DOI: 10.3389/fmicb.2022.875775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
Objectives While Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), defined as CC398, is a well-known pathogen among those working with livestock, there are indications that LA-MRSA prevalence among the general population is increasing. However, the clinical impact in urban areas remains unknown. The aim of this study was to assess the genetic epidemiology and clinical characteristics of LA-MRSA in an urban area with a limited livestock population. Methods In this retrospective study, we evaluated LA-MRSA strains that were collected between 2014 and 2018 from patients who received clinical care in a single urban area in Netherlands. Patient files were assessed for livestock exposure data, clinical findings, and contact tracing information. Next-generation sequencing (NGS) analysis in combination with wgMLST was conducted to assess genetic diversity and relatedness and to detect virulence and resistance genes. Results LA-MRSA strains were cultured from 81 patients, comprising 12% of all the MRSA strains found in seven study laboratories between 2014 and 2018. No livestock link was found in 76% of patients (n = 61), and 28% of patients (n = 23) had an infection, mostly of the skin or soft tissue. Contact tracing had been initiated in 14 cases, leading to the identification of two hospital transmissions: a cluster of 9 cases and one of 2 cases. NGS data were available for 91% (n = 75) of the patients. wgMLST confirmed the clusters detected via contact tracing (n = 2) and identified 5 additional clusters without a known epidemiological link. Relevant resistance and virulence findings included the PVL virulence gene (3 isolates) and tetracycline resistance (79 isolates). Conclusion LA-MRSA may cause a relevant burden of disease in urban areas. Surprisingly, most infections in the present study occurred in the absence of a livestock link, suggesting inter-human transmission. These findings and the presence of PVL and other immune evasive complex virulence genes warrant future surveillance and preventative measures.
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Affiliation(s)
- Maria M. Konstantinovski
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands,Department of Microbiology, Medical Laboratories, Reinier de Graaf Groep, Delft, Netherlands,*Correspondence: Maria M. Konstantinovski,
| | - Leo M. Schouls
- Center for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sandra Witteveen
- Center for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Margriet E. Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jayant Kalpoe
- Department of Medical Microbiology, Regional Laboratory of Public Health Kennemerland, Haarlem, Netherlands
| | - Eva Mattson
- Department of Microbiology, Medical Laboratories, Reinier de Graaf Groep, Delft, Netherlands
| | - David J. Hetem
- Department of Medical Microbiology, Haaglanden Medical Center, The Hague, Netherlands
| | | | - Jos Kerremans
- Department of Medical Microbiology, Alrijne Hospital, Leiderdorp, Netherlands
| | - Vishal Hira
- Department of Medical Microbiology and Infection Prevention, Groene Hart Ziekenhuis, Gouda, Netherlands
| | - Thijs Bosch
- Center for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Jairo Gooskens
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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31
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Zhang H, Qin L, Jin C, Ju H, Jiang R, Li L, Zhang H, Gao W, Wei X, Dong H, Lu F, Lv G. Molecular Characteristics and Antibiotic Resistance of Staphylococcus aureus Isolated from Patient and Food Samples in Shijiazhuang, China. Pathogens 2022; 11:1333. [PMID: 36422585 PMCID: PMC9695393 DOI: 10.3390/pathogens11111333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a common opportunistic and zoonotic pathogen in the world and could easily cause human infections and food contaminations. This study investigated the sequence typing and resistance profiles of S. aureus isolates from patient and food samples in Shijiazhuang, China. A total of 101 S. aureus isolates were distributed into six clonal complexes (CCs) and 16 singletons. A total of 86 patient isolates were distributed into six clonal CCs and 12 singletons, including a new ST. CC59, CC5, CC22, and CC398 were the predominant CCs of patient isolates. A total of 15 foodborne S. aureus isolates were distributed into 3 CCs and 4 STs, and CC1 was the most prevalent CC. Moreover, 101 S. aureus isolates had high resistance to penicillin and low resistance to chloramphenicol and rifampicin. A total of 39 strains of methicillin-resistant Staphylococcus aureus (MRSA) were detected in this study, including thirty-eight strains of patient isolates (44.2%, 38/86) and one strain of food isolates (6.7%, 1/15). MRSA-ST5, MRSA-ST59, and MRSA-ST239 were the predominant MRSA isolates in hospitals. The present study explained the relationship between S. aureus isolated from patient and food samples and indicated the risks of S. aureus in infectious diseases.
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Affiliation(s)
- Han Zhang
- Basic Medicine College, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Liyun Qin
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Caiping Jin
- Basic Medicine College, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Huidong Ju
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China
| | - Ruiping Jiang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Lijie Li
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Hong Zhang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Weili Gao
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Xiuping Wei
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
| | - Hongyan Dong
- Basic Medicine College, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Fei Lu
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050011, China
- Hebei Key Laboratory of Unidentifiable Bacteria, Shijiazhuang 050011, China
| | - Guoping Lv
- Basic Medicine College, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
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Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches. Viruses 2022; 14:v14112471. [PMID: 36366569 PMCID: PMC9694928 DOI: 10.3390/v14112471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the Sa3-phages are highly human-specific, and most animal strains are Sa3 negative. Thus, both insertion and excision of the prophage could potentially confer a fitness advantage to S. aureus. Here, we analyzed the phage life cycle of two Sa3 phages, Φ13 and ΦN315, in different phage-cured S. aureus strains. Based on phage transfer experiments, strains could be classified into low (8325-4, SH1000, and USA300c) and high (MW2c and Newman-c) transfer strains. High-transfer strains promoted the replication of phages, whereas phage adsorption, integration, excision, or recA transcription was not significantly different between strains. RNASeq analyses of replication-deficient lysogens revealed no strain-specific differences in the CI/Mor regulatory switch. However, lytic genes were significantly upregulated in the high transfer strain MW2c Φ13 compared to strain 8325-4 Φ13. By transcriptional start site prediction, new promoter regions within the lytic modules were identified, which are likely targeted by specific host factors. Such host-phage interaction probably accounts for the strain-specific differences in phage replication and transfer frequency. Thus, the genetic makeup of the host strains may determine the rate of phage mobilization, a feature that might impact the speed at which certain strains can achieve host adaptation.
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33
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Golob M, Pate M, Kušar D, Zajc U, Papić B, Ocepek M, Zdovc I, Avberšek J. Antimicrobial Resistance and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus from Two Pig Farms: Longitudinal Study of LA-MRSA. Antibiotics (Basel) 2022; 11:1532. [PMID: 36358187 PMCID: PMC9687068 DOI: 10.3390/antibiotics11111532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 10/29/2023] Open
Abstract
Pigs were identified as the most important reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), mostly belonging to the emergent zoonotic clonal complex (CC) 398. Here, we investigated the presence of MRSA in sows and piglets over a period of several months in two pig farms (intensive farm A and family-run farm B). Isolates underwent antimicrobial susceptibility testing, PCR characterization and spa typing. We collected 280 samples, namely 206 nasal swabs from pigs and 74 environmental samples from pig housings at 12 consecutive time points. A total of 120/161 (74.5%) and 75/119 (63.0%) samples were MRSA-positive in farms A and B, respectively. All isolates harbored mecA but lacked mecC and PVL-encoding genes. The identified spa types (t571, t034, t1250 and t898 in farm A, t1451 and t011 in farm B) were indicative of CC398. Antimicrobial resistance patterns (all multidrug resistant in farm A, 57.2% in farm B) depended on the farm, suggesting the impact of farm size and management practices on the prevalence and characteristics of MRSA. Due to the intermittent colonization of pigs and the high contamination of their immediate environment, MRSA status should be determined at the farm level when considering preventive measures or animal trade between farms.
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Affiliation(s)
- Majda Golob
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, SI-1000 Ljubljana, Slovenia
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34
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Chaguza C, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. CELL GENOMICS 2022; 2:100194. [PMID: 36465278 PMCID: PMC9718559 DOI: 10.1016/j.xgen.2022.100194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA,Corresponding author
| | | | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA,Corresponding author
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35
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Homenta H, Julyadharma J, Susianti H, Noorhamdani N, Santosaningsih D. Molecular Epidemiology of Clinical Carbapenem-Resistant Acinetobacter baumannii-calcoaceticus complex Isolates in Tertiary Care Hospitals in Java and Sulawesi Islands, Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7100277. [PMID: 36288018 PMCID: PMC9607243 DOI: 10.3390/tropicalmed7100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (A. baumannii)-calcoaceticus complex (CRAb-cc) is an important pathogen causing nosocomial infections worldwide; however, molecular epidemiology of the A. baumannii-calcoaceticus complex in Indonesian hospitals is scarce. This study aimed to determine the clonal relatedness of CRAb-cc in two tertiary care hospitals in Malang and Manado in Indonesia. The CRAb-cc isolates from routine clinical cultures in two tertiary care hospitals in Malang and Manado were identified using the Vitek2® system (bioMérieux, Lyon, France). Multi-locus variable-number tandem-repeat analysis (MLVA) typing, multi-locus sequence typing (MLST), clonal complex (CC), and phylogenetic tree analysis were conducted for a subset of isolates. Seventy-three CRAb-cc isolates were collected. The CRAb-cc isolates were frequently found among lower-respiratory-tract specimens. We detected the MLVA type (MT) 1, MT3, and MT4 CRAB-cc isolates belonging to the sequence type (ST) 642, and CC1 was the predominant clone in this study. In conclusion, we identified the clonal relatedness of A. baumannii-calcoaceticus complex isolates in two tertiary care hospitals in Malang and Manado in Indonesia. Further study is required to investigate the clinical importance and distribution of ST642 in Indonesian hospitals for developing prevention and control measures.
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Affiliation(s)
- Heriyannis Homenta
- Doctoral Program in Medical Science, Faculty of Medicine, Universitas Brawijaya, Malang 65145, Indonesia
- Department of Clinical Microbiology, Faculty of Medicine, Sam Ratulangi University, Manado 95163, Indonesia
| | - Julyadharma Julyadharma
- Laboratory of Clinical Microbiology, Prof. Dr. R. D. Kandou Hospital, Manado 95163, Indonesia
| | - Hani Susianti
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
- Department of Clinical Pathology, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia
| | - Noorhamdani Noorhamdani
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
| | - Dewi Santosaningsih
- Department of Clinical Microbiology, Faculty of Medicine, Brawijaya University, Malang 65145, Indonesia
- Department of Clinical Microbiology, Dr. Saiful Anwar Hospital, Malang 65112, Indonesia
- Correspondence:
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Silva V, Monteiro A, Pereira JE, Maltez L, Igrejas G, Poeta P. MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going. Pathogens 2022; 11:1110. [PMID: 36297167 PMCID: PMC9608539 DOI: 10.3390/pathogens11101110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 09/10/2023] Open
Abstract
Over the years, molecular typing of methicillin-resistant S. aureus (MRSA) has allowed for the identification of endemic MRSA strains and pathogenic strains. After reaching a peak of predominance in a given geographic region, MRSA strains are usually replaced by a new strain. This process is called clonal replacement and is observed worldwide. The worldwide spread of hospital-associated MRSA (HA-MRSA), community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA) clones over the last few decades has allowed this microorganism to be currently considered a pandemic. In Portugal, most HA-MRSA infections are associated with EMRSA-15 (S22-IV), New York/Japan (ST5-II) and Iberian (ST247-I) clones. Regarding the strains found in the community, many of them are frequently associated with the hospital environment, namely the Pediatric, Brazilian and Iberian clones. On the other hand, a strain that is typically found in animals, MRSA clonal complex (CC) 398, has been described in humans as colonizing and causing infections. The ST398 clone is found across all animal species, particularly in farm animals where the economic impact of LA-MRSA infections can have disastrous consequences for industries. In contrast, the EMRSA-15 clone seems to be more related to companion animals. The objective of this review is to better understand the MRSA epidemiology because it is, undoubtedly, an important public health concern that requires more attention, in order to achieve an effective response in all sectors.
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Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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Anthroponotic-Based Transfer of Staphylococcus to Dog: A Case Study. Pathogens 2022; 11:pathogens11070802. [PMID: 35890046 PMCID: PMC9316149 DOI: 10.3390/pathogens11070802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
Although usually harmless, Staphylococcus spp. can cause nosocomial and community-onset skin and soft tissue infections in both humans and animals; thus, it is considered a significant burden for healthcare systems worldwide. Companion animals have been identified as potential reservoirs of pathogenic Staphylococcus with specific reference to Methicillin Resistant Staphylococcus aureus (MRSA). In this study, we investigated the circulation and the genetic relationships of a collection of Staphylococcus spp. isolates in a family composed of four adults (a mother, father, grandmother, and grandfather), one child, and a dog, which were sampled over three years. The routes of transmission among humans and between humans and the dog werelyzed. The results displayed the circulation of many Staphylococcus lineages, belonging to different species and sequence types (ST) and being related to both human and pet origins. However, among the observed host-switch events, one of them clearly underpinnthroponotic route from a human to a dog. This suggests that companion animals can potentially have a role as a carrier of Staphylococcus, thus posing a serious concern about MRSA spreading within human and animal microbial communities.
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Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches. mSystems 2022; 7:e0037822. [PMID: 35862809 PMCID: PMC9426533 DOI: 10.1128/msystems.00378-22] [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] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of sak and scn can discriminate strains based on their host specificity, while other genes such as mecA are often associated with virulent outcomes. Both GWAS and RF indicated the importance of intergenic regions (IGRs) and coding DNA sequence (CDS) but not sRNAs in forecasting an outcome. Additional transcriptomic analyses performed on the most prevalent clonal complex 8 (CC8) clonal types, in media mimicking nasal colonization or bacteremia, indicated three RNAs as potential RNA markers to forecast infection, followed by 30 others that could serve as infection severity predictors. Our report shows that genetic association and transcriptomics are complementary approaches that will be combined in a single analytical framework to improve our understanding of bacterial pathogenesis and ultimately identify potential predictive molecular markers. IMPORTANCE Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome. In addition, transcriptomic analyses performed on the most prevalent clonal types, in media mimicking either nasal colonization or bacteremia, revealed significant differences and therefore potent RNA markers. Overall, the use of both genomic and transcriptomic data in a single analytical framework can enhance our understanding of bacterial pathogenesis.
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Matuszewska M, Murray GGR, Ba X, Wood R, Holmes MA, Weinert LA. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA. eLife 2022; 11:74819. [PMID: 35762208 PMCID: PMC9239682 DOI: 10.7554/elife.74819] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/23/2022] [Indexed: 01/11/2023] Open
Abstract
Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised. Antibiotic-resistant infections are a growing threat to human health. In 2019, these hard-to-treat infections resulted in 4.95 million deaths making them the third leading cause of death that year. Excessive use of antibiotics in humans is likely driving the emergence of drug-resistant bacteria. But there is a concern that use of antibiotics on livestock farms is also contributing. A type of bacteria traced back to livestock is a growing cause of human infections that do not respond to treatment with the antibiotic methicillin in Europe. It is called livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA). Bacteria can share genes that make them drug resistant or more deadly. These genes are often carried on mobile genetic elements that promote their movement from one bacterial cell to another. The most common type of LA-MRSA in Europe is clonal-complex 398 (CC398). It has two mobile genetic elements carrying antibiotic-resistance genes, but generally lacks a mobile genetic element that helps the bacterium escape the human immune system. Learning more about how LA-MRSA acquired these genetic changes may help scientists develop better strategies to protect the public. Matuszewska, Murray et al. analyzed the genomes of more than 1,000 samples of CC398 collected from humans, pigs and 13 other animal species in 28 countries over 27 years. They used this data to reconstruct the bacteria’s evolutionary history. Matuszewska, Murray et al. show that two mobile elements containing antibiotic resistance genes in CC398 were gained decades ago. One is more than 50 years old and was likely acquired around the time antibiotic use in livestock became common. While most CC398 in livestock do not have a mobile element that helps LA-MRSA evade the human immune system, they often gain it when they infect humans. This leads to highly drug-resistant human MRSA infections. The results of this study suggest that LA-MRSA is a serious threat to human health. The resistance of this bacterium has persisted for decades, spreading across different livestock species and different countries. These drug-resistant bacteria in livestock readily infect humans. Current efforts to reduce antibiotic use in farms may take decades to mitigate these risks. Additionally, the ban on zinc-oxide use on livestock in the European Union (coming into force June 2022) may not help reduce LA-MRSA, because the genes conferring resistance to bacteria and zinc treatment are not always linked.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rhiannon Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Ramos B, Rosalino LM, Palmeira JD, Torres RT, Cunha MV. Antimicrobial resistance in commensal Staphylococcus aureus from wild ungulates is driven by agricultural land cover and livestock farming. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 303:119116. [PMID: 35276250 DOI: 10.1016/j.envpol.2022.119116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 05/25/2023]
Abstract
Staphylococcus aureus is a human pathobiont (i.e., a commensal microorganism that is potentially pathogenic under certain conditions), a nosocomial pathogen and a leading cause of morbidity and mortality in humans. S. aureus is also a commensal and pathogen of companion animals and livestock. The dissemination of antimicrobial resistant (AMR) S. aureus, particularly methicillin-resistant (MRSA), has been associated to its ability for establishing new reservoirs, but limited attention has been devoted to the role of the environment. To fill this gap, we aimed to characterize animal carrier status, AMR phenotypes, predominant clonal lineages and their relationship with clinical and food-chain settings, as well as to find predictors of AMR occurrence. Nasal swabs (n = 254) from wild boar (n = 177), red deer (n = 54) and fallow deer (n = 23) hunted in Portugal, during the season 2019/2020, yielded an overall carrier proportion of 35.8%, ranging from 53.7% for red deer and 32.2% for wild boar to 21.7% for fallow deer. MRSA from wild boar and phenotypically linezolid-resistant S. aureus from wild boar and red deer were isolated, indicating that resistance to antimicrobials restricted to clinical practice also occurs in wildlife. The most prevalent genotypes were t11502/ST2678 (29.6%) and t12939/ST2678 (9.4%), previously reported in wild boar from Spain. Clonal lineages reported in humans and livestock, like CC1, CC5 or CC8 (19.1%) and ST425, CC133 or CC398 (23.5%), respectively, were also found. The sequence type ST544, previously restricted to humans, is described in wildlife for the first time. We also identified that land use (agricultural land cover), human driven disturbance (swine abundance) and host-related factors (sex) determine resistance occurrence. These findings suggest that antibiotics used in clinical settings, agriculture and livestock farming, spill over to wildlife, leading to AMR emergence, with potential biological, ecological, and human health effects. This work is one of the most comprehensive surveys in Europe of S. aureus occurrence and determinants among widely distributed wild ungulates.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Luís Miguel Rosalino
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Josman D Palmeira
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Rita T Torres
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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Silva V, Correia E, Pereira JE, González-Machado C, Capita R, Alonso-Calleja C, Igrejas G, Poeta P. Biofilm Formation of Staphylococcus aureus from Pets, Livestock, and Wild Animals: Relationship with Clonal Lineages and Antimicrobial Resistance. Antibiotics (Basel) 2022; 11:antibiotics11060772. [PMID: 35740178 PMCID: PMC9219840 DOI: 10.3390/antibiotics11060772] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/14/2022] Open
Abstract
This study aimed to compare the biofilm formation ability of Staphylococcus aureus isolated from a wide range of animals and study the association between biofilm formation and antimicrobial resistance and genetic lineages. A total of 214 S. aureus strains isolated from pets, livestock, and wild animals were evaluated regarding their ability to form biofilms by the microtiter biofilm assay and their structure via confocal scanning laser microscopy. Statistical analysis was used to find an association between biofilm formation and antimicrobial resistance, multidrug resistance, sequence types (STs), spa and agr-types of the isolates. The antimicrobial susceptibility of 24 h-old biofilms was assessed against minimum inhibitory concentrations (MIC) and 10× MIC of amikacin and tetracycline, and the biomass reduction was measured. The metabolic activity of biofilms after antimicrobial treatment was evaluated by the XTT assay. All isolates were had the ability to form biofilms. Yet, significant differences in biofilm biomass production were detected among animal species. Multidrug resistance had a positive association with biofilm formation as well as methicillin-resistance. Significant differences were also detected among the clonal lineages of the isolates. Both tetracycline and amikacin were able to significantly reduce the biofilm mass. However, none of the antimicrobials were able to eradicate the biofilm at the maximum concentration used. Our results provide important information on the biofilm-forming capacity of animal-adapted S. aureus isolates, which may have potential implications for the development of new biofilm-targeted therapeutics.
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Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Elisete Correia
- Center for Computational and Stochastic Mathematics (CEMAT), Department of Mathematics, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal;
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Camino González-Machado
- Department of Food Hygiene and Technology, Veterinary Faculty, University of León, E-24071 León, Spain; (C.G.-M.); (R.C.); (C.A.-C.)
- Institute of Food Science and Technology, University of León, E-24071 León, Spain
| | - Rosa Capita
- Department of Food Hygiene and Technology, Veterinary Faculty, University of León, E-24071 León, Spain; (C.G.-M.); (R.C.); (C.A.-C.)
- Institute of Food Science and Technology, University of León, E-24071 León, Spain
| | - Carlos Alonso-Calleja
- Department of Food Hygiene and Technology, Veterinary Faculty, University of León, E-24071 León, Spain; (C.G.-M.); (R.C.); (C.A.-C.)
- Institute of Food Science and Technology, University of León, E-24071 León, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Correspondence:
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Shoaib M, Aqib AI, Ali MM, Ijaz M, Sattar H, Ghaffar A, Sajid Hasni M, Bhutta ZA, Ashfaq K, Kulyar MFEA, Pu W. Tracking Infection and Genetic Divergence of Methicillin-Resistant Staphylococcus aureus at Pets, Pet Owners, and Environment Interface. Front Vet Sci 2022; 9:900480. [PMID: 35720840 PMCID: PMC9201917 DOI: 10.3389/fvets.2022.900480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
Staphylococcus aureus (S. aureus) has become a leading animal and public health pathogen that keeps on transferring from one host to other, giving rise to newer strains by genetic shifts. The current study was designed to investigate the epidemiology and genetic relatedness of mecA gene in S. aureus isolated from pets, immediate individuals in contact with pets, and veterinary clinic environments. A total of n = 300 samples were collected from different veterinary hospitals in Pakistan using convenience sampling. The collected samples were subjected to microbiological and biochemical examination for the isolation of S. aureus. Methicillin resistance was investigated by both phenotypically using oxacillin disk diffusion assay and by genotypically targeting mecA gene by PCR. PCR amplicons were subjected for sequencing by Sanger method of sequencing, which were subsequently submitted to NCBI GenBank under the accession numbers MT874770, MT874771, and MT874772. Sequence evolutionary analysis and mecA gene characterization was done using various bioinformatics tools. Overall, 33.66% mecA genes harboring S. aureus strains were isolated from all sources (33.33% from pets, 46.0% from surrounding, and 28.0% from immediate contact individuals). The bioinformatics analysis noted that one SNP was identified at position c.253C>A (Transvertion). The phylogenetic tree (two clades) of S. aureus mecA revealed a possibility of inter-transmission of disease between the environment and pets. Frequency of adenine and thymine nucleotide in motifs were found to be the same (0.334). Cytosine and guanine frequency were also the same (0.166). Threonine was replaced by asparagine (p.T84D) in each sample of cat, environment, and human. On the other hand, protein structures ofcat-1 and cat-2 proteins were found identical while cat-3, environmental, and human proteins shared identical structures. The study thus concludes rising circulation of methicillin-resistant S. aureus (MRSA) strains in animal-human-environment interfaces, forecasting the development of novel strains withmodified range of resistance.
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Affiliation(s)
- Muhammad Shoaib
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
- Institute of Microbiology, Faculty of Veterinary Science, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Muddassir Ali
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Ijaz
- Department of Veterinary Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Huma Sattar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Awais Ghaffar
- Department of Clinical Sciences, KBCMA, College of Veterinary and Animal Sciences, Narowal, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Sajid Hasni
- Directorate General Farms and Feed Resources, Livestock and Dairy Development Department, Quetta, Pakistan
| | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, South Korea
| | - Khurram Ashfaq
- Department of Clinical Medicine and Surgery, University of Agriculture, Faisalabad, Pakistan
| | | | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province, Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou, China
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Silva V, Correia S, Rocha J, Manaia CM, Silva A, García-Díez J, Pereira JE, Semedo-Lemsaddek T, Igrejas G, Poeta P. Antimicrobial Resistance and Clonal Lineages of Staphylococcus aureus from Cattle, Their Handlers, and Their Surroundings: A Cross-Sectional Study from the One Health Perspective. Microorganisms 2022; 10:microorganisms10050941. [PMID: 35630384 PMCID: PMC9144820 DOI: 10.3390/microorganisms10050941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Staphylococcus aureus have been progressively identified in farm animals and in humans with direct contact with these animals showing that S. aureus may be a major zoonotic pathogen. Therefore, we aimed to isolate S. aureus from cows, their handlers, and their immediate surroundings, and to investigate the antimicrobial resistance and genetic lineages of the isolates. Mouth and nose swabs of 244 healthy cows (195 Maronesa, 11 Holstein-Friesians, and 28 crossbreeds), 82 farm workers, 53 water and 63 soil samples were collected. Identification of species was carried out by MALDI-TOF MS Biotyper. The presence of antimicrobial resistance genes and virulence factors was assessed based on gene search by PCR. All isolates were typed by multilocus sequence typing and spa-typing. From 442 samples, 33 (13.9%), 24 (29.3%), 1 (2%), and 1 (2%) S. aureus were recovered from cows, farm workers, water, and soil samples, respectively. Most of the isolates showed resistance only to penicillin. S. aureus isolates were ascribed to 17 sequence types (STs) and 26 spa-types. Some clonal lineages were common to both cows and farm workers such as ST30-t9413, ST72-t148, and ST45-t350. Through a One Health approach, this study revealed that there is a great diversity of clonal lineages of S. aureus in cows and their handlers. Furthermore, some S. aureus lineages are common to cows and handlers, which may suggest a possible transmission.
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Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (V.S.); (S.C.); (A.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
| | - Susana Correia
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (V.S.); (S.C.); (A.S.)
| | - Jaqueline Rocha
- Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal; (J.R.); (C.M.M.)
| | - Célia M. Manaia
- Centro de Biotecnologia e Química Fina (CBQF), Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal; (J.R.); (C.M.M.)
| | - Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (V.S.); (S.C.); (A.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
| | - Juan García-Díez
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.G.-D.); (J.E.P.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.G.-D.); (J.E.P.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Teresa Semedo-Lemsaddek
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Avenida da Universidade Técnica, Universidade de Lisboa, 1300-477 Lisboa, Portugal
- Correspondence: (T.S.-L.); (P.P.)
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (V.S.); (S.C.); (A.S.)
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.G.-D.); (J.E.P.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Correspondence: (T.S.-L.); (P.P.)
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Shared antibiotic resistance and virulence genes in Staphylococcus aureus from diverse animal hosts. Sci Rep 2022; 12:4413. [PMID: 35292708 PMCID: PMC8924228 DOI: 10.1038/s41598-022-08230-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses an important threat in human and animal health. In this study, we ask whether resistance and virulence genes in S. aureus are homogeneously distributed or constrained by different animal hosts. We carried out whole genome sequencing of 114 S. aureus isolates from ten species of animals sampled from four New England states (USA) in 2017-2019. The majority of the isolates came from cats, cows and dogs. The maximum likelihood phylogenetic tree based on the alignment of 89,143 single nucleotide polymorphisms of 1173 core genes reveal 31 sequence types (STs). The most common STs were ST5, ST8, ST30, ST133 and ST2187. Every genome carried at least eight acquired resistance genes. Genes related to resistance found in all genomes included norA (fluoroquinolone), arlRS (fluoroquinolone), lmrS (multidrug), tet(38) (tetracycline) and mepAR (multidrug and tigecycline resistance). The most common superantigen genes were tsst-1, sea and sec. Acquired antibiotic resistance (n = 10) and superantigen (n = 9) genes of S. aureus were widely shared between S. aureus lineages and between strains from different animal hosts. These analyses provide insights for considering bacterial gene sharing when developing strategies to combat the emergence of high-risk clones in animals.
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Park S, Jung D, O'Brien B, Ruffini J, Dussault F, Dube-Duquette A, Demontier É, Lucier JF, Malouin F, Dufour S, Ronholm J. Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation. Microb Genom 2022; 8. [PMID: 35179459 PMCID: PMC8942034 DOI: 10.1099/mgen.0.000779] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. The versatile and adaptative evolutionary strategies of this bacterium have challenged mastitis control and prevention globally, and the high incidence of S. aureus mastitis increases concerns about antimicrobial resistance (AMR) and zoonosis. This study aims to describe the evolutionary relationship between bovine intramammary infection (IMI)-associated S. aureus and human pathogenic S. aureus and further elucidate the specific genetic composition that leads to the emergence of successful bovine IMI-associated S. aureus lineages. We performed a phylogenomic analysis of 187 S. aureus isolates that originated from either dairy cattle or humans. Our results revealed that bovine IMI-associated S. aureus isolates showed distinct clades compared to human-originated S. aureus isolates. From a pan-genome analysis, 2070 core genes were identified. Host-specific genes and clonal complex (CC)-specific genes were also identified in bovine S. aureus isolates, mostly located in mobile genetic elements (MGEs). Additionally, the genome sequences of three apparent human-adapted isolates (two from CC97 and one from CC8), isolated from bovine mastitis samples, may provide an snapshot of the genomic characteristics in early host spillover events. Virulence and AMR genes were not conserved among bovine IMI-associated S. aureus isolates. Restriction-modification (R-M) genes in bovine IMI-associated S. aureus demonstrated that the Type I R-M system was lineage-specific and Type II R-M system was sequence type (ST)-specific. The distribution of exclusive, virulence, and AMR genes were closely correlated with the presence of R-M systems in S. aureus, suggesting that R-M systems may contribute to shaping clonal diversification by providing a genetic barrier to the horizontal gene transfer (HGT). Our findings indicate that the CC or ST lineage-specific R-M systems may limit genetic exchange between bovine-adapted S. aureus isolates from different lineages.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Bridget O'Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | - Janina Ruffini
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | | | - Alexis Dube-Duquette
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Élodie Demontier
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Jean-François Lucier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - François Malouin
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
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46
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Zou G, Matuszewska M, Jia M, Zhou J, Ba X, Duan J, Zhang C, Zhao J, Tao M, Fan J, Zhang X, Jin W, Cui T, Zeng X, Jia M, Qian X, Huang C, Zhuo W, Yao Z, Zhang L, Li S, Li L, Huang Q, Wu B, Chen H, Tucker AW, Grant AJ, Holmes MA, Zhou R. A Survey of Chinese Pig Farms and Human Healthcare Isolates Reveals Separate Human and Animal Methicillin-Resistant Staphylococcus aureus Populations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103388. [PMID: 34894204 PMCID: PMC8811834 DOI: 10.1002/advs.202103388] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/10/2021] [Indexed: 06/14/2023]
Abstract
There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern.
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Affiliation(s)
- Geng Zou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Marta Matuszewska
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Ming Jia
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Jianwei Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Xiaoliang Ba
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Juan Duan
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | | | - Jian Zhao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Meng Tao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Jingyan Fan
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | | | | | | | | | - Min Jia
- Wuhan First HospitalWuhan430014China
| | | | - Chao Huang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Wenxiao Zhuo
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Zhiming Yao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Lijun Zhang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Shaowen Li
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
| | - Lu Li
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Qi Huang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Bin Wu
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | - Huanchun Chen
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
| | | | - Andrew J. Grant
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Mark A. Holmes
- Department of Veterinary MedicineUniversity of CambridgeCambridgeCB3 0ESUK
| | - Rui Zhou
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural University College of Veterinary MedicineWuhan430070China
- Cooperative Innovation Center of Sustainable Pig ProductionWuhan430070China
- International Research Center for Animal Diseases (MOST)Wuhan430070China
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47
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Zawierucha K, Trzebny A, Buda J, Bagshaw E, Franzetti A, Dabert M, Ambrosini R. Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms. PLoS One 2022; 17:e0262039. [PMID: 35020747 PMCID: PMC8754347 DOI: 10.1371/journal.pone.0262039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.
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Affiliation(s)
- Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznań, Poland
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Poznań, Poland
| | - Elizabeth Bagshaw
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Andrea Franzetti
- Earth and Environmental Sciences Department, University of Milano-Bicocca, Milan, Italy
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
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48
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:910-920. [DOI: 10.1093/jac/dkac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/26/2021] [Indexed: 11/13/2022] Open
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49
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Peptidoglycan-Free Bacterial Ghosts Confer Enhanced Protection against Yersinia pestis Infection. Vaccines (Basel) 2021; 10:vaccines10010051. [PMID: 35062712 PMCID: PMC8777944 DOI: 10.3390/vaccines10010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
To develop a modern plague vaccine, we used hypo-endotoxic Yersinia pestis bacterial ghosts (BGs) with combinations of genes encoding the bacteriophage ɸX174 lysis-mediating protein E and/or holin-endolysin systems from λ or L-413C phages. Expression of the protein E gene resulted in the BGs that retained the shape of the original bacterium. Co-expression of this gene with genes coding for holin-endolysin system of the phage L-413C caused formation of structures resembling collapsed sacs. Such structures, which have lost their rigidity, were also formed as a result of the expression of only the L-413C holin-endolysin genes. A similar holin-endolysin system from phage λ containing mutated holin gene S and intact genes R-Rz coding for the endolysins caused generation of mixtures of BGs that had (i) practically preserved and (ii) completely lost their original rigidity. The addition of protein E to the work of this system shifted the equilibrium in the mixture towards the collapsed sacs. The collapse of the structure of BGs can be explained by endolysis of peptidoglycan sacculi. Immunizations of laboratory animals with the variants of BGs followed by infection with a wild-type Y. pestis strain showed that bacterial envelopes protected only cavies. BGs with maximally hydrolyzed peptidoglycan had a greater protectivity compared to BGs with a preserved peptidoglycan skeleton.
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50
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Abstract
Bacterial pathogens commonly carry prophages that express virulence factors, and human strains of Staphylococcus aureus carry Sa3int phages, which promote immune evasion. Recently, however, these phages have been found in livestock-associated, methicillin-resistant S. aureus (LA-MRSA). This is surprising, as LA-MRSA strains contain a mutated primary bacterial integration site, which likely explains why the rare integration events that do occur mostly happen at alternative locations. Using deep sequencing, we show that after initial integration at secondary sites, Sa3int phages adapt through nucleotide changes in their attachment sequences to increase homology with alternative bacterial attachment sites. Importantly, this homology significantly enhances integrations in new rounds of infections. We propose that promiscuity of the phage-encoded tyrosine recombinase is responsible for establishment of Sa3int phages in LA-MRSA. Our results demonstrate that phages can adopt extensive population heterogeneity, leading to establishment in strains lacking bona fide integration sites. Ultimately, their presence may increase virulence and zoonotic potential of pathogens with major implications for human health.
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