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Yebra G, Mrochen D, Fischer S, Pfaff F, Ulrich RG, Pritchett-Corning K, Holtfreter S, Fitzgerald JR. Bacteriophage-driven emergence and expansion of Staphylococcus aureus in rodent populations. PLoS Pathog 2024; 20:e1012378. [PMID: 39047021 PMCID: PMC11299810 DOI: 10.1371/journal.ppat.1012378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/05/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Human activities such as agriculturalization and domestication have led to the emergence of many new pathogens via host-switching events between humans, domesticated and wild animals. Staphylococcus aureus is a multi-host opportunistic pathogen with a global healthcare and economic burden. Recently, it was discovered that laboratory and wild rodents can be colonised and infected with S. aureus, but the origins and zoonotic potential of rodent S. aureus is unknown. In order to trace their evolutionary history, we employed a dataset of 1249 S. aureus genome sequences including 393 of isolates from rodents and other small mammals (including newly determined sequences for 305 isolates from 7 countries). Among laboratory mouse populations, we identified multiple widespread rodent-specific S. aureus clones that likely originated in humans. Phylogeographic analysis of the most common murine lineage CC88 suggests that it emerged in the 1980s in laboratory mouse facilities most likely in North America, from where it spread to institutions around the world, via the distribution of mice for research. In contrast, wild rodents (mice, voles, squirrels) were colonized with a unique complement of S. aureus lineages that are widely disseminated across Europe. In order to investigate the molecular basis for S. aureus adaptation to rodent hosts, genome-wide association analysis was carried out revealing a unique complement of bacteriophages associated with a rodent host ecology. Of note, we identified novel prophages and pathogenicity islands in rodent-derived S. aureus that conferred the potential for coagulation of rodent plasma, a key phenotype of abscess formation and persistence. Our findings highlight the remarkable capacity of S. aureus to expand into new host populations, driven by the acquisition of genes promoting survival in new host-species.
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Affiliation(s)
- Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Mrochen
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Kathleen Pritchett-Corning
- Charles River, Research and Professional Services, Wilmington, Massachusetts, United States of America
- Office of Animal Resources, Harvard University Faculty of Arts and Sciences, Cambridge, Massachusetts, United States of America
| | - Silva Holtfreter
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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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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Ibraheim HK, Fayez RA, Jasim AS, Gharban HAJ. Role of nuc gene in Staphylococcus aureus to phagocytic activity in different cattle infections. Open Vet J 2023; 13:1021-1026. [PMID: 37701667 PMCID: PMC10495089 DOI: 10.5455/ovj.2023.v13.i8.8] [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: 05/22/2023] [Accepted: 07/30/2023] [Indexed: 09/14/2023] Open
Abstract
Background Staphylococcus aureus is a typical pathogenic agent that causes several morbidities and mortalities which variable largely following the severity of bacteria and activity of host immunity. Aim Isolation of S. aureus from different cattle infections, molecular detection of nuc gene in positive S. aureus isolates, and identification of the effectiveness of the phagocytic activity. Methods Totally, 100 cattle with various infections (25 wounds, 25 abscesses, 25 nasal discharges, and 25 ear swaps) were selected and subjected to collection of swabs under controlled conditions. All collected samples were cultured on mannitol salt agar (MSA) and assessed by biochemical tests. Targeting the nuc gene, all study MSA positive isolates were examined molecularly by conventional polymerase chain reaction (PCR), and then subjected to antibiotic susceptibility test. Jugular venous blood was collected from all infected animals in addition to 20 healthy cattle that were selected as a control group to estimate the phagocytic activity of S. aureus isolates. Results The findings of MSA culture revealed a total of 80 positive samples of S. aureus as 23, 21, 20, and 16 positive isolates for nasal discharge, abscess, wound, and ear swab, respectively; based on its morphology, cultural trait, and biochemical test. Subsequently, PCR assaying of MSA-positive isolates demonstrated an overall 59 positive samples as 14, 16, 12, and 17 positive isolates for nasal discharge, abscess, wound, and ear swabs, respectively. Antibiotic susceptibility testing of S. aureus-positive PCR isolates reported a significantly high sensitivity to chloramphenicol and vancomycin, and a high resistance to penicillin. Finally, there was a considerable decline in phagocytic activity in particular 2 weeks post-infection as a result of bacterial invasion. Conclusion This study shows a high prevalence of S. aureus in cattle infections, and the protocol includes a regular screening of cattle infection and suitable therapy based on antibacterial susceptibility test is of great importance in the long-term control of the pathogen. However, additional molecular studies targeting other genes of S. aureus and the role of immune markers in different infections should be aimed.
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Affiliation(s)
- Hanaa Khaleel Ibraheim
- Microbiology Department, College of Veterinary Medicine, University of Basrah, Basrah, Iraq
| | - Rana A. Fayez
- Microbiology Department, College of Veterinary Medicine, University of Basrah, Basrah, Iraq
| | - Alyaa S. Jasim
- Microbiology Department, College of Veterinary Medicine, University of Basrah, Basrah, Iraq
| | - Hasanain A. J. Gharban
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Wasit, Wasit, Iraq
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Campos J, Pires MF, Sousa M, Campos C, da Costa CFFA, Sampaio-Maia B. Unveiling the Relevance of the Oral Cavity as a Staphylococcus aureus Colonization Site and Potential Source of Antimicrobial Resistance. Pathogens 2023; 12:765. [PMID: 37375455 DOI: 10.3390/pathogens12060765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Staphylococcus aureus is both a human commensal and a pathogen, that causes serious nosocomial and community-acquired infections. Despite nostrils being considered its preferred host habitat, the oral cavity has been demonstrated to be an ideal starting point for auto-infection and transmission. The antibiotic resistance assessment of S. aureus is a priority and is often reported in clinical settings. This study aimed to explore the prevalence and antimicrobial susceptibility of S. aureus in the oral and nasal cavities of healthy individuals. The participants (n = 101) were subjected to a demographic and clinical background survey, a caries evaluation, and to oral and nasal swabbing. Swabs were cultured in differential/selective media and S. aureus isolates were identified (MALDI-TOF MS) and tested for antibiotic susceptibility (EUCAST/CLSI). Similar S. aureus prevalence was found exclusively on nasal (13.9%) or oral (12.0%) habitats, whereas 9.9% of the population were simultaneous nasal and oral carriers. In oro-nasal cavities, similar antibiotic resistance rates (83.3-81.5%), including MDR (20.8-29.6%), were observed. Notably, 60% (6/10) of the simultaneous nasal and oral carriers exhibited different antibiotic resistance profiles between cavities. This study demonstrates the relevance of the oral cavity as an independent colonization site for S. aureus and as a potential source of antimicrobial resistance, a role which has been widely neglected so far.
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Affiliation(s)
- Joana Campos
- INEB-Instituto Nacional de Engenharia Biomédica, 4200-135 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Mariana Faria Pires
- Faculdade de Medicina Dentária, Universidade do Porto, 4200-393 Porto, Portugal
| | - Marta Sousa
- Faculdade de Medicina Dentária, Universidade do Porto, 4200-393 Porto, Portugal
| | - Carla Campos
- Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal
- Escola Superior de Saúde, Instituto Politécnico do Porto, 4200-072 Porto, Portugal
| | - Carolina Fernandes Ferreira Alves da Costa
- INEB-Instituto Nacional de Engenharia Biomédica, 4200-135 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Benedita Sampaio-Maia
- INEB-Instituto Nacional de Engenharia Biomédica, 4200-135 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina Dentária, Universidade do Porto, 4200-393 Porto, Portugal
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Rodrigues RA, Pizauro LJL, Varani ADM, de Almeida CC, Silva SR, Cardozo MV, MacInnes JI, Kropinski AM, Melo PDC, Ávila FA. Comparative genomics study of Staphylococcus aureus isolated from cattle and humans reveals virulence patterns exclusively associated with bovine clinical mastitis strains. Front Microbiol 2022; 13:1033675. [PMID: 36419431 PMCID: PMC9676464 DOI: 10.3389/fmicb.2022.1033675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 12/08/2023] Open
Abstract
Staphylococcus aureus causes nosocomial and intramammary infections in humans and cattle, respectively. A large number of virulence factors are thought to play important roles in the pathogenesis of this bacterium. Currently, genome-wide and data-analysis studies are being used to better understand its epidemiology. In this study, we conducted a genome wide comparison and phylogenomic analyses of S. aureus to find specific virulence patterns associated with clinical and subclinical mastitis strains in cattle and compare them with those of human origin. The presence/absence of key virulence factors such as adhesin, biofilm, antimicrobial resistance, and toxin genes, as well as the phylogeny and sequence type of the isolates were evaluated. A total of 248 genomes (27 clinical mastitis, 43 subclinical mastitis, 21 milk, 53 skin-related abscesses, 49 skin infections, and 55 pus from cellulitis) isolated from 32 countries were evaluated. We found that the cflA, fnbA, ebpS, spa, sdrC, coa, emp, vWF, atl, sasH, sasA, and sasF adhesion genes, as well as the aur, hglA, hglB, and hglC toxin genes were highly associated in clinical mastitis strains. The strains had diverse genetic origins (72 protein A and 48 sequence types with ST97, ST8 and ST152 being frequent in isolates from clinical mastitis, abscess, and skin infection, respectively). Further, our phylogenomic analyses suggested that zoonotic and/or zooanthroponotic transmission may have occurred. These findings contribute to a better understanding of S. aureus epidemiology and the relationships between adhesion mechanisms, biofilm formation, antimicrobial resistance, and toxins and could aid in the development of improved vaccines and strain genotyping methods.
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Affiliation(s)
- Romário Alves Rodrigues
- Department of Reproduction Pathology and One Health, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Lucas José Luduverio Pizauro
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Alessandro de Mello Varani
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Camila Chioda de Almeida
- Department of Reproduction Pathology and One Health, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Saura Rodrigues Silva
- Department of Agricultural and Environmental Biotechnology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Marita Vedovelli Cardozo
- Laboratory of Microorganism Physiology, Minas Gerais State University, Passos, Minas Gerais, Brazil
| | - Janet I. MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Poliana de Castro Melo
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus, Bahia, Brazil
| | - Fernando Antonio Ávila
- Department of Reproduction Pathology and One Health, Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
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Molecular Mechanisms of Drug Resistance in Staphylococcus aureus. Int J Mol Sci 2022; 23:ijms23158088. [PMID: 35897667 PMCID: PMC9332259 DOI: 10.3390/ijms23158088] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
This paper discusses the mechanisms of S. aureus drug resistance including: (1) introduction. (2) resistance to beta-lactam antibiotics, with particular emphasis on the mec genes found in the Staphylococcaceae family, the structure and occurrence of SCCmec cassettes, as well as differences in the presence of some virulence genes and its expression in major epidemiological types and clones of HA-MRSA, CA-MRSA, and LA-MRSA strains. Other mechanisms of resistance to beta-lactam antibiotics will also be discussed, such as mutations in the gdpP gene, BORSA or MODSA phenotypes, as well as resistance to ceftobiprole and ceftaroline. (3) Resistance to glycopeptides (VRSA, VISA, hVISA strains, vancomycin tolerance). (4) Resistance to oxazolidinones (mutational and enzymatic resistance to linezolid). (5) Resistance to MLS-B (macrolides, lincosamides, ketolides, and streptogramin B). (6) Aminoglycosides and spectinomicin, including resistance genes, their regulation and localization (plasmids, transposons, class I integrons, SCCmec), and types and spectrum of enzymes that inactivate aminoglycosides. (7). Fluoroquinolones (8) Tetracyclines, including the mechanisms of active protection of the drug target site and active efflux of the drug from the bacterial cell. (9) Mupirocin. (10) Fusidic acid. (11) Daptomycin. (12) Resistance to other antibiotics and chemioterapeutics (e.g., streptogramins A, quinupristin/dalfopristin, chloramphenicol, rifampicin, fosfomycin, trimethoprim) (13) Molecular epidemiology of MRSA.
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Akoua-Koffi C, Kacou N’Douba A, Djaman JA, Herrmann M, Schaumburg F, Niemann S. Staphylococcus schweitzeri—An Emerging One Health Pathogen? Microorganisms 2022; 10:microorganisms10040770. [PMID: 35456820 PMCID: PMC9026344 DOI: 10.3390/microorganisms10040770] [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: 03/17/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 11/22/2022] Open
Abstract
The Staphylococcus aureus-related complex is formed by the Staphylococcus aureus, Staphylococcus schweitzeri, Staphylococcus argenteus, Staphylococcus roterodami and Staphylococcus singaporensis. Within this complex, S. schweitzeri is the only species mainly found in African wildlife, but it is rarely detected as a colonizer in humans or as a contaminant of fomites. The few detections in humans are most likely spillover events after contact with wildlife. However, since S. schweitzeri can be misidentified as S. aureus using culture-based routine techniques, it is likely that S. schweitzeri is under-reported in humans. The low number of isolates in humans, though, is consistent with the fact that the pathogen has typical animal adaptation characteristics (e.g., growth kinetics, lack of immune evasion cluster and antimicrobial resistance); however, evidence from selected in vitro assays (e.g., host cell invasion, cell activation, cytotoxicity) indicate that S. schweitzeri might be as virulent as S. aureus. In this case, contact with animals colonized with S. schweitzeri could constitute a risk for zoonotic infections. With respect to antimicrobial resistance, all described isolates were found to be susceptible to all antibiotics tested, and so far no data on the development of spontaneous resistance or the acquisition of resistance genes such the mecA/mecC cassette are available. In summary, general knowledge about this pathogen, specifically on the potential threat it may incur to human and animal health, is still very poor. In this review article, we compile the present state of scientific research, and identify the knowledge gaps that need to be filled in order to reliably assess S. schweitzeri as an organism with global One Health implications.
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Affiliation(s)
- Chantal Akoua-Koffi
- Centre Hospitalier Universitaire de Bouaké, Bouaké P.O. Box BP 1174, Côte d’Ivoire;
- Department of Biology, Université Alassane Ouattara de Bouaké, Bouaké P.O. Box BP V18, Côte d’Ivoire
| | - Adèle Kacou N’Douba
- Training and Research Unit of Medical Sciences, Félix Houphouët-Boigny University, Abidjan P.O. Box BP 44, Côte d’Ivoire;
- Centre Hospitalier Universitaire Angré, Abidjan P.O. Box BP 1530, Côte d’Ivoire
| | - Joseph Allico Djaman
- Training and Research Unit of Biosciences, Félix Houphouët Boigny University, Abidjan P.O. Box BP V 34, Côte d’Ivoire;
| | - Mathias Herrmann
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (M.H.); (F.S.)
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (M.H.); (F.S.)
| | - Silke Niemann
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (M.H.); (F.S.)
- Correspondence: ; Tel.: +49-251-835-5369
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