51
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Moura G, Gebreyes W, Marques M, Stipp D, Souza F, Da Costa L, Oliveira C. Short communication: Occurrence of methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococci in dairy goat herds in Ohio, United States. J Dairy Sci 2018; 101:7804-7807. [DOI: 10.3168/jds.2017-13361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 03/24/2018] [Indexed: 11/19/2022]
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52
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Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
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Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
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53
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Akkou M, Bouchiat C, Antri K, Bes M, Tristan A, Dauwalder O, Martins-Simoes P, Rasigade JP, Etienne J, Vandenesch F, Ramdani-Bouguessa N, Laurent F. New host shift from human to cows within Staphylococcus aureus involved in bovine mastitis and nasal carriage of animal's caretakers. Vet Microbiol 2018; 223:173-180. [PMID: 30173744 DOI: 10.1016/j.vetmic.2018.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022]
Abstract
Staphylococcus aureus is a commensal and pathogen of both humans and bovines. While the epidemiology of both groups has been extensively studied individually, little is known about the potential zoonotic transfer from animal strains to human being and vice versa. To determine the S. aureus prevalence of bovine mastitis in Algeria and the zoonotic transfer of strains to human beings, mastitis milk samples were collected, and professionals in a close contact with bovines were nasal swabbed. S. aureus isolates were all characterized by methicillin resistance and spa-typing. DNA microarrays analysis was performed on a subset of strains in order to detect other virulence factors, including toxins, and to assign the isolates to theirs MLST clonal complexes. Overall, 116/222 (52.3%) cows suffered from mastitis, whose 38.8% (45/116) infected with S. aureus. Human nasal carriage was of 38% (49/129), with only 4 MRSA carriers (3.1%). A higher diversity of spa-types was observed in human (35/50) than in bovine (18/67) isolates, with a predominance of clonal complexes CC97 and CC22 in bovines. The typical animal clone CC97 was occasionally detected in human beings. Conversely, the CC22 S. aureus clone largely switched from humans to bovines. Our study highlights the potential dynamics of animal and human S. aureus strains in the farm environment in Algeria, which may represent a health threat in both populations.
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Affiliation(s)
- Madjid Akkou
- Institut des Sciences Vétérinaires, Université Blida1, 09000, Blida, Algeria.
| | - Coralie Bouchiat
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Kenza Antri
- Département de Biologie Cellulaire et Moléculaire, USTHB, 16000, Alger, Algeria
| | - Michèle Bes
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Anne Tristan
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Olivier Dauwalder
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Patricia Martins-Simoes
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Jean-Philippe Rasigade
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - Jérôme Etienne
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | - François Vandenesch
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
| | | | - Frédéric Laurent
- Inserm U851, IFR 128, CNR des Staphylocoques, Université de Lyon1, 69008, Lyon, France; Centre de biologie Est, Hospices Civils de Lyon, 69500 Bron, France
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54
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Zhao X, Yu Z, Xu Z. Study the Features of 57 Confirmed CRISPR Loci in 38 Strains of Staphylococcus aureus. Front Microbiol 2018; 9:1591. [PMID: 30093886 PMCID: PMC6070637 DOI: 10.3389/fmicb.2018.01591] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus is a foodborne pathogen that causes food contamination and food poisoning, which poses great harm to health, agriculture and other hosts. Clustered regularly interspaced short palindromic repeats (CRISPR) are a recently discovered bacterial immune system that resists foreign genes such as phage DNA. This system inhibits the transfer of specific movable genetic elements that match the CRISPR spacer sequences, thereby preventing the spread of drug-resistant genes between pathogens. In this study, 57 CRISPR loci were screened from 38 strains of S. aureus based on the CRISPR database, and bioinformatics tools were used to investigate the structural features and potential functions of S. aureus CRISPR loci. The results showed that most strains contained only one CRISPR locus, a few strains contained multiple loci with sparsely distributed sites. These loci mainly included highly conserved direct repeat sequences and highly variable spacer sequences, as well as polymorphic cas genes. In addition, the analysis of secondary structure of direct repeat RNA showed that all sites can form stable RNA secondary structure. The results of constructing phylogenetic tree based on spacer sequence showed that some strains contained a high degree of phylogenetic relationship, while the differences among other strains in evolutionary processes were quite obvious. Of the 57 CRISPR loci identified, only the cas gene was found near the 4 CRISPR loci.
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Affiliation(s)
- Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Key Laboratory for Hubei Novel Reactor & Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Zhixue Yu
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Key Laboratory for Hubei Novel Reactor & Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Zhenbo Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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55
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Phumthanakorn N, Fungwithaya P, Chanchaithong P, Prapasarakul N. Enterotoxin gene profile of methicillin-resistant Staphylococcus pseudintermedius isolates from dogs, humans and the environment. J Med Microbiol 2018; 67:866-873. [PMID: 29724270 DOI: 10.1099/jmm.0.000748] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE This study aimed to detect and identify staphylococcal enterotoxin (SE) genes in methicillin-resistant Staphylococcus pseudintermedius (MRSP) strains from different sources, and to investigate the relationship between their sequence types (STs) and SE gene patterns. METHODOLOGY The profiles of 17 SE genes in 93 MRSP strains isolated from dogs (n=43), humans (n=18) and the environment (n=32) were detected by PCR. Multilocus sequence typing (MLST), SCCmec typing and pulsed-field gel electrophoresis (PFGE) were used to analyse the clonal relatedness between the molecular type and SE gene profiles.Results/Key findings. The human MRSP strains harboured the greatest number of SE genes (12/17; sea, sec, seg, sei, sek, sel, sem, sen, seo, sep, seq and tst-1) compared to those from dogs (5/17; sec, sel, sem, seq and tst-1) and environmental sources (3/17; sec, seq and tst-1). Using MLST and PFGE, different SE gene profiles were found within the same clonal type. CONCLUSION We show that isolates of MRSP vary in their virulence gene profiles, depending on the source from which they have been isolated. This insight should encourage the development of appropriate monitoring and mitigation strategies to reduce the transmission of MRSP in veterinary hospitals and households.
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Affiliation(s)
- Nathita Phumthanakorn
- Department of Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Punpichaya Fungwithaya
- Department of Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattrarat Chanchaithong
- Department of Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nuvee Prapasarakul
- Department of Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Diagnosis and Monitoring of Animal Pathogen Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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56
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Fisher EL, Otto M, Cheung GYC. Basis of Virulence in Enterotoxin-Mediated Staphylococcal Food Poisoning. Front Microbiol 2018; 9:436. [PMID: 29662470 PMCID: PMC5890119 DOI: 10.3389/fmicb.2018.00436] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/26/2018] [Indexed: 12/17/2022] Open
Abstract
The Staphylococcus aureus enterotoxins are a superfamily of secreted virulence factors that share structural and functional similarities and possess potent superantigenic activity causing disruptions in adaptive immunity. The enterotoxins can be separated into two groups; the classical (SEA-SEE) and the newer (SEG-SElY and counting) enterotoxin groups. Many members from both these groups contribute to the pathogenesis of several serious human diseases, including toxic shock syndrome, pneumonia, and sepsis-related infections. Additionally, many members demonstrate emetic activity and are frequently responsible for food poisoning outbreaks. Due to their robust tolerance to denaturing, the enterotoxins retain activity in food contaminated previously with S. aureus. The genes encoding the enterotoxins are found mostly on a variety of different mobile genetic elements. Therefore, the presence of enterotoxins can vary widely among different S. aureus isolates. Additionally, the enterotoxins are regulated by multiple, and often overlapping, regulatory pathways, which are influenced by environmental factors. In this review, we also will focus on the newer enterotoxins (SEG-SElY), which matter for the role of S. aureus as an enteropathogen, and summarize our current knowledge on their prevalence in recent food poisoning outbreaks. Finally, we will review the current literature regarding the key elements that govern the complex regulation of enterotoxins, the molecular mechanisms underlying their enterotoxigenic, superantigenic, and immunomodulatory functions, and discuss how these activities may collectively contribute to the overall manifestation of staphylococcal food poisoning.
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Affiliation(s)
- Emilie L Fisher
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gordon Y C Cheung
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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57
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Bacterial Pathogen Emergence Requires More than Direct Contact with a Novel Passerine Host. Infect Immun 2018; 86:IAI.00863-17. [PMID: 29311238 PMCID: PMC5820954 DOI: 10.1128/iai.00863-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
While direct contact may sometimes be sufficient to allow a pathogen to jump into a new host species, in other cases, fortuitously adaptive mutations that arise in the original donor host are also necessary. Viruses have been the focus of most host shift studies, so less is known about the importance of ecological versus evolutionary processes to successful bacterial host shifts. Here we tested whether direct contact with the novel host was sufficient to enable the mid-1990s jump of the bacterium Mycoplasma gallisepticum from domestic poultry to house finches (Haemorhous mexicanus). We experimentally inoculated house finches with two genetically distinct M. gallisepticum strains obtained either from poultry (Rlow) or from house finches (HF1995) during an epizootic outbreak. All 15 house finches inoculated with HF1995 became infected, whereas Rlow successfully infected 12 of 15 (80%) inoculated house finches. Comparisons among infected birds showed that, relative to HF1995, Rlow achieved substantially lower bacterial loads in the host respiratory mucosa and was cleared faster. Furthermore, Rlow-infected finches were less likely to develop clinical symptoms than HF1995-infected birds and, when they did, displayed milder conjunctivitis. The lower infection success of Rlow relative to HF1995 was not, however, due to a heightened host antibody response to Rlow. Taken together, our results indicate that contact between infected poultry and house finches was not, by itself, sufficient to explain the jump of M. gallisepticum to house finches. Instead, mutations arising in the original poultry host would have been necessary for successful pathogen emergence in the novel finch host.
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58
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Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli. Sci Rep 2018; 8:3028. [PMID: 29445215 PMCID: PMC5813019 DOI: 10.1038/s41598-018-21438-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 01/04/2023] Open
Abstract
Campylobacter jejuni and Campylobacter coli are the most common cause of bacterial gastroenteritis worldwide. Additionally, C. jejuni is the most common bacterial etiological agent in the autoimmune Guillain-Barré syndrome (GBS). Ganglioside mimicry by C. jejuni lipooligosaccharide (LOS) is the triggering factor of the disease. LOS-associated genes involved in the synthesis and transfer of sialic acid (glycosyltranferases belonging to family GT-42) are essential in C. jejuni to synthesize ganglioside-like LOS. Despite being isolated from GBS patients, scarce genetic evidence supports C. coli role in the disease. In this study, through data mining and bioinformatics analysis, C. coli is shown to possess a larger GT-42 glycosyltransferase repertoire than C. jejuni. Although GT-42 glycosyltransferases are widely distributed in C. coli population, only a fraction of C. coli strains (1%) are very likely able to express ganglioside mimics. Even though the activity of C. coli specific GT-42 enzymes and their role in shaping the bacterial population are yet to be explored, evidence presented herein suggest that loss of function of some LOS-associated genes occurred during agriculture niche adaptation.
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59
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A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. PLoS Comput Biol 2018; 14:e1005958. [PMID: 29401456 PMCID: PMC5814097 DOI: 10.1371/journal.pcbi.1005958] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 02/15/2018] [Accepted: 12/30/2017] [Indexed: 11/28/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) in microbial organisms have the potential to vastly improve the way we understand, manage, and treat infectious diseases. Yet, microbial GWAS methods established thus far remain insufficiently able to capitalise on the growing wealth of bacterial and viral genetic sequence data. Facing clonal population structure and homologous recombination, existing GWAS methods struggle to achieve both the precision necessary to reject spurious findings and the power required to detect associations in microbes. In this paper, we introduce a novel phylogenetic approach that has been tailor-made for microbial GWAS, which is applicable to organisms ranging from purely clonal to frequently recombining, and to both binary and continuous phenotypes. Our approach is robust to the confounding effects of both population structure and recombination, while maintaining high statistical power to detect associations. Thorough testing via application to simulated data provides strong support for the power and specificity of our approach and demonstrates the advantages offered over alternative cluster-based and dimension-reduction methods. Two applications to Neisseria meningitidis illustrate the versatility and potential of our method, confirming previously-identified penicillin resistance loci and resulting in the identification of both well-characterised and novel drivers of invasive disease. Our method is implemented as an open-source R package called treeWAS which is freely available at https://github.com/caitiecollins/treeWAS. Measurable differences often exist within a microbial population, with important ecological or epidemiological consequences. Examples include differences in growth rates, host range, transmissibility, antimicrobial resistance, virulence, etc. Understanding the genetic factors involved in these phenotypic properties is a crucial aim in microbial genomics. A fundamental approach for doing so is to perform a Genome-Wide Association Study (GWAS), where genomes are compared to search for genetic markers systematically correlated with the property of interest. If this strategy were implemented naively in microbes, it could lead to spurious results due to the confounding effects of population structure and recombination. Here we present treeWAS, a new phylogenetic method to perform microbial GWAS that avoids these pitfalls. We show, using simulated datasets, that treeWAS is able to distinguish between genetic markers that are truly associated with the property of interest and those that are not. Furthermore, we demonstrate that treeWAS offers advantages in both sensitivity and specificity over alternative cluster-based and dimension-reduction techniques. We also showcase treeWAS in two applications to real datasets from N. meningitidis. We have developed an easy-to-use implementation of treeWAS in the R environment, which should be useful to a wide range of researchers in microbial genomics.
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60
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de Jong NWM, Vrieling M, Garcia BL, Koop G, Brettmann M, Aerts PC, Ruyken M, van Strijp JAG, Holmes M, Harrison EM, Geisbrecht BV, Rooijakkers SHM. Identification of a staphylococcal complement inhibitor with broad host specificity in equid Staphylococcus aureus strains. J Biol Chem 2018; 293:4468-4477. [PMID: 29414776 PMCID: PMC5868266 DOI: 10.1074/jbc.ra117.000599] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/25/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus aureus is a versatile pathogen capable of causing a broad range of diseases in many different hosts. S. aureus can adapt to its host through modification of its genome (e.g. by acquisition and exchange of mobile genetic elements that encode host-specific virulence factors). Recently, the prophage φSaeq1 was discovered in S. aureus strains from six different clonal lineages almost exclusively isolated from equids. Within this phage, we discovered a novel variant of staphylococcal complement inhibitor (SCIN), a secreted protein that interferes with activation of the human complement system, an important line of host defense. We here show that this equine variant of SCIN, eqSCIN, is a potent blocker of equine complement system activation and subsequent phagocytosis of bacteria by phagocytes. Mechanistic studies indicate that eqSCIN blocks equine complement activation by specific inhibition of the C3 convertase enzyme (C3bBb). Whereas SCIN-A from human S. aureus isolates exclusively inhibits human complement, eqSCIN represents the first animal-adapted SCIN variant that functions in a broader range of hosts (horses, humans, and pigs). Binding analyses suggest that the human-specific activity of SCIN-A is related to amino acid differences on both sides of the SCIN-C3b interface. These data suggest that modification of this phage-encoded complement inhibitor plays a role in the host adaptation of S. aureus and are important to understand how this pathogen transfers between different hosts.
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Affiliation(s)
- Nienke W M de Jong
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Manouk Vrieling
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.,the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom
| | - Brandon L Garcia
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Gerrit Koop
- the Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Matt Brettmann
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Piet C Aerts
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Maartje Ruyken
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Jos A G van Strijp
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Mark Holmes
- the Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom, and
| | - Ewan M Harrison
- the Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Brian V Geisbrecht
- the Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Suzan H M Rooijakkers
- From the Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands,
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61
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Young BC, Wu CH, Gordon NC, Cole K, Price JR, Liu E, Sheppard AE, Perera S, Charlesworth J, Golubchik T, Iqbal Z, Bowden R, Massey RC, Paul J, Crook DW, Peto TE, Walker AS, Llewelyn MJ, Wyllie DH, Wilson DJ. Severe infections emerge from commensal bacteria by adaptive evolution. eLife 2017; 6. [PMID: 29256859 PMCID: PMC5736351 DOI: 10.7554/elife.30637] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/02/2017] [Indexed: 12/23/2022] Open
Abstract
Bacteria responsible for the greatest global mortality colonize the human microbiota far more frequently than they cause severe infections. Whether mutation and selection among commensal bacteria are associated with infection is unknown. We investigated de novo mutation in 1163 Staphylococcus aureus genomes from 105 infected patients with nose colonization. We report that 72% of infections emerged from the nose, with infecting and nose-colonizing bacteria showing parallel adaptive differences. We found 2.8-to-3.6-fold adaptive enrichments of protein-altering variants in genes responding to rsp, which regulates surface antigens and toxin production; agr, which regulates quorum-sensing, toxin production and abscess formation; and host-derived antimicrobial peptides. Adaptive mutations in pathogenesis-associated genes were 3.1-fold enriched in infecting but not nose-colonizing bacteria. None of these signatures were observed in healthy carriers nor at the species-level, suggesting infection-associated, short-term, within-host selection pressures. Our results show that signatures of spontaneous adaptive evolution are specifically associated with infection, raising new possibilities for diagnosis and treatment.
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Affiliation(s)
- Bernadette C Young
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Chieh-Hsi Wu
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - N Claire Gordon
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom
| | - James R Price
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom.,Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Elian Liu
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Anna E Sheppard
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
| | - Sanuki Perera
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jane Charlesworth
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Tanya Golubchik
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - John Paul
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Timothy E Peto
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research, Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, United Kingdom.,Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - David H Wyllie
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Centre for Molecular and Cellular Physiology, Jenner Institute, Oxford, United Kingdom
| | - Daniel J Wilson
- Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, United Kingdom.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, United Kingdom
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62
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Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H, Lawley TD. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 2017; 8:1367. [PMID: 29118316 PMCID: PMC5678084 DOI: 10.1038/s41467-017-01449-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022] Open
Abstract
Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen.
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Affiliation(s)
- Gregorio Iraola
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay. .,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay. .,Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK
| | - Philippe Lehours
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3.,Départment de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, QC, Canada, H3T 1J4
| | - Francisco J García-Peña
- Departamento de Bacteriología, Laboratorio Central de Veterinaria de Algete (MAGRAMA), 28110, Algete, Spain
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Claudia Morsella
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743, Jena, Germany
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Ana Vidal
- Animal and Plant Health Association (APHA), Addlestone, KT15 3NB, UK
| | - Simon Lévesque
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3
| | - Wataru Yamazaki
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Claudia Balzan
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Agueda Vargas
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, 35122, Italy
| | - Bonnie Chaban
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatchewan, SK, Canada, S7N 5A2
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, 11600, Uruguay
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5090000, Valdivia, Chile
| | - Isabelle Truyers
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anne C Midwinter
- EpiLab, Infectious Disease Research Centre, Massey University, Palmerston North, 4442, New Zealand
| | - Hatice T Dagi
- Department of Microbiology, Faculty of Medicine, Selçuk University, Selçuklu, 42250, Turkey
| | - Francis Mégraud
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, 12900, Montevideo, Uruguay
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
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63
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Sun J, Yang M, Sreevatsan S, Bender JB, Singer RS, Knutson TP, Marthaler DG, Davies PR. Longitudinal study of Staphylococcus aureus colonization and infection in a cohort of swine veterinarians in the United States. BMC Infect Dis 2017; 17:690. [PMID: 29052523 PMCID: PMC5649086 DOI: 10.1186/s12879-017-2802-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/04/2017] [Indexed: 12/04/2022] Open
Abstract
Background People working with pigs are at elevated risk of harboring methicillin resistant S. aureus (MRSA) in their nose, which is attributable to occupational exposure to animals harboring livestock adapted S. aureus. To obtain insight into the biological nature of occupationally related nasal culture positivity, we conducted a longitudinal study of 66 swine veterinarians in the USA. Methods The study cohort resided in 15 US states and worked predominantly with swine. Monthly for 18 months, participants self-collected nasal swabs and completed a survey to report recent exposure to pigs and other animals; the occurrence of work related injuries; and any relevant health events such as skin and soft tissue infections or confirmed staphylococcal infections. Nasal swabs were cultured using selective methods to determine the presence of MRSA and methicillin susceptible S. aureus (MSSA), and isolates were characterized by spa typing and MLST. Results Prevalences of S. aureus (64%, monthly range from 58 to 82%) and MRSA (9.5%; monthly range from 6 to15%) were higher than reported for the US population (30% and 1.5% respectively). Predominant spa types were t034 (ST398, 37%), t002 (ST5, 17%) and t337 (ST9/ST398 13%), a distribution similar to that found in a concurrent study in pigs in the USA. Veterinarians were classified into three groups: Persistent carriers (PC, 52%), Intermittent carriers (IC, 47%) and Non-carriers (NC, 1%). Persistent carriage of a single spa type was observed in 14 (21%) of participants, and paired (first and last) isolates from PC subjects had minor genetic differences. Swabs from PC veterinarians carried higher numbers of S. aureus. Among IC veterinarians, culture positivity was significantly associated with recent contact with pigs. Conclusions Exposure to pigs did not lead to prolonged colonization in most subjects, and the higher numbers of S. aureus in PC subjects suggests that unknown host factors may determine the likelihood of prolonged colonization by S. aureus of livestock origin. Exposure to S. aureus and persistent colonization of swine veterinarians was common but rarely associated with S. aureus disease. Electronic supplementary material The online version of this article (10.1186/s12879-017-2802-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jisun Sun
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - My Yang
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - Jeffrey B Bender
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, 55108, USA
| | - Todd P Knutson
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA
| | - Peter R Davies
- Department of Veterinary Population Medicine, University of Minnesota, 385 ASVM, 1988 Fitch Ave, St. Paul, MN, 55108, USA.
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64
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Rainard P, Foucras G, Fitzgerald JR, Watts JL, Koop G, Middleton JR. Knowledge gaps and research priorities in Staphylococcus aureus mastitis control. Transbound Emerg Dis 2017; 65 Suppl 1:149-165. [PMID: 28984427 DOI: 10.1111/tbed.12698] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 12/31/2022]
Abstract
This study assessed knowledge gaps and suggested research priorities in the field of Staphylococcus aureus mastitis. Staphylococcus aureus infecting the mammary gland remains a major problem to the dairy industry worldwide because of its pathogenicity, contagiousness, persistence in the cow environment, colonization of skin or mucosal epithelia, and the poor curing efficacy of treatments. Staphylococcus aureus also constitutes a threat to public health due to food safety and antibiotic usage issues and the potential for bidirectional transmission of strains between humans and dairy animals (cows and small ruminants). Gaps have been identified in (i) understanding the molecular basis for pathogenesis of S. aureus mastitis, (ii) identifying staphylococcal antigens inducing protection and (iii) determining the cell-mediated immune responses to infection and vaccination. The recommended priorities for research are (i) improved diagnostic methods for early detection of infection and intervention through treatment or management, (ii) development of experimental models to investigate the strategies used by S. aureus to survive within the mammary gland and resist treatment with anti-microbials, (iii) investigation of the basis for cow-to-cow variation in response to S. aureus mastitis, (iv) identification of the immune responses (adaptive and innate) induced by infection or vaccination and (v) antibacterial discovery programmes to develop new, more effective, narrow spectrum antibacterial agents for the treatment of S. aureus mastitis. With the availability and ongoing improvement of molecular research tools, these objectives may not be out of reach in the future.
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Affiliation(s)
- P Rainard
- ISP, INRA, Université de Tours, UMR1282, Nouzilly, France
| | - G Foucras
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | - J R Fitzgerald
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - J L Watts
- Zoetis, External Innovation-Anti-Infectives, VMRD, Kalamazoo, MI, USA
| | - G Koop
- Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - J R Middleton
- Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, MO, USA
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65
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Xue H, Wu Z, Qiao D, Tong C, Zhao X. Global acquisition of genetic material from different bacteria into the staphylococcal cassette chromosome elements of a Staphylococcus epidermidis isolate. Int J Antimicrob Agents 2017; 50:581-587. [DOI: 10.1016/j.ijantimicag.2017.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/24/2017] [Indexed: 10/19/2022]
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66
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Mrochen DM, Schulz D, Fischer S, Jeske K, El Gohary H, Reil D, Imholt C, Trübe P, Suchomel J, Tricaud E, Jacob J, Heroldová M, Bröker BM, Strommenger B, Walther B, Ulrich RG, Holtfreter S. Wild rodents and shrews are natural hosts of Staphylococcus aureus. Int J Med Microbiol 2017; 308:590-597. [PMID: 28967544 DOI: 10.1016/j.ijmm.2017.09.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/12/2017] [Accepted: 09/19/2017] [Indexed: 11/16/2022] Open
Abstract
Laboratory mice are the most commonly used animal model for Staphylococcus aureus infection studies. We have previously shown that laboratory mice from global vendors are frequently colonized with S. aureus. Laboratory mice originate from wild house mice. Hence, we investigated whether wild rodents, including house mice, as well as shrews are naturally colonized with S. aureus and whether S. aureus adapts to the wild animal host. 295 animals of ten different species were caught in different locations over four years (2012-2015) in Germany, France and the Czech Republic. 45 animals were positive for S. aureus (15.3%). Three animals were co-colonized with two different isolates, resulting in 48 S. aureus isolates in total. Positive animals were found in Germany and the Czech Republic in each studied year. The S. aureus isolates belonged to ten different spa types, which grouped into six lineages (clonal complex (CC) 49, CC88, CC130, CC1956, sequence type (ST) 890, ST3033). CC49 isolates were most abundant (17/48, 35.4%), followed by CC1956 (14/48, 29.2%) and ST890 (9/48, 18.8%). The wild animal isolates lacked certain properties that are common among human isolates, e.g., a phage-encoded immune evasion cluster, superantigen genes on mobile genetic elements and antibiotic resistance genes, which suggests long-term adaptation to the wild animal host. One CC130 isolate contained the mecC gene, implying wild rodents might be both reservoir and vector for methicillin-resistant . In conclusion, we demonstrated that wild rodents and shrews are naturally colonized with S. aureus, and that those S. aureus isolates show signs of host adaptation.
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Affiliation(s)
- Daniel M Mrochen
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany
| | - Daniel Schulz
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Kathrin Jeske
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Heba El Gohary
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany
| | - Daniela Reil
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Toppheideweg 88, 48161 Münster, Germany
| | - Christian Imholt
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Toppheideweg 88, 48161 Münster, Germany
| | - Patricia Trübe
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic
| | - Emilie Tricaud
- Institut Claude Bourgelat, Laboratoire de Toxicologie, BIOLYTICS, 1 Avenue Bourgelat, 69280 Marcy-l'Étoile, France
| | - Jens Jacob
- Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Toppheideweg 88, 48161 Münster, Germany
| | - Marta Heroldová
- Department of Forest Ecology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Barbara M Bröker
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch-Institut, Burgstraße 37, 38855 Wernigerode, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Robert-von-Ostertag Straße 7-13, 14163 Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Silva Holtfreter
- Department of Immunology, University Medicine Greifswald, Sauerbruchstraße DZ7, 17475 Greifswald, Germany.
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Cooper LP, Roberts GA, White JH, Luyten YA, Bower EKM, Morgan RD, Roberts RJ, Lindsay JA, Dryden DTF. DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus. Nucleic Acids Res 2017; 45:3395-3406. [PMID: 28180279 PMCID: PMC5399793 DOI: 10.1093/nar/gkx067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/03/2017] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction–modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range of biochemical assays on purified enzymes and single molecule real-time sequencing on genomic DNA to determine these target sequences and their patterns of methylation. Knowledge of the main target sequences for Sau1 will facilitate the synthesis of new vectors for transformation of the most prevalent lineages of this ‘untransformable’ bacterium.
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Affiliation(s)
- Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3FJ, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - Edward K M Bower
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3FJ, UK
| | - Richard D Morgan
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | | | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - David T F Dryden
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
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Harrison EM, Coll F, Toleman MS, Blane B, Brown NM, Török ME, Parkhill J, Peacock SJ. Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England. Sci Rep 2017; 7:7406. [PMID: 28785112 PMCID: PMC5547075 DOI: 10.1038/s41598-017-07662-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/22/2017] [Indexed: 11/28/2022] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. LA-MRSA has been isolated previously from animals and humans in the United Kingdom (UK), but the prevalence is unknown. The aim of this study was to determine the prevalence and to describe the molecular epidemiology of LA-MRSA isolated in the East of England (broadly Cambridge and the surrounding area). We accessed whole genome sequence data for 2,283 MRSA isolates from 1,465 people identified during a 12-month prospective study between 2012 and 2013 conducted in the East of England, United Kingdom. This laboratory serves four hospitals and 75 general practices. We screened the collection for multilocus sequence types (STs) and for host specific resistance and virulence factors previously associated with LA-MRSA. We identified 13 putative LA-MRSA isolates from 12 individuals, giving an estimated prevalence of 0.82% (95% CI 0.47% to 1.43%). Twelve isolates were mecC-MRSA (ten CC130, one ST425 and one ST1943) and single isolate was ST398. Our data demonstrate a low burden of LA-MRSA in the East of England, but the detection of mecC-MRSA and ST398 indicates the need for vigilance. Genomic surveillance provides a mechanism to detect and track the emergence and spread of MRSA clones of human importance.
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Affiliation(s)
- Ewan M Harrison
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom.
| | - Francesc Coll
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Michelle S Toleman
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, United Kingdom
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, United Kingdom
- Public Health England, Clinical Microbiology and Public Health Laboratory, Box 236, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, United Kingdom
| | - M Estee Török
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, United Kingdom
- Public Health England, Clinical Microbiology and Public Health Laboratory, Box 236, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QW, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, United Kingdom
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, United Kingdom
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Grinberg A, Biggs PJ, Zhang J, Ritchie S, Oneroa Z, O'Neill C, Karkaba A, Velathanthiri NS, Coombs GW. Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection. J Infect 2017; 75:326-335. [PMID: 28782565 DOI: 10.1016/j.jinf.2017.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/29/2017] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains. METHODS We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets. RESULTS Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%). CONCLUSIONS In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk.
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Affiliation(s)
- Alex Grinberg
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand.
| | - Patrick J Biggs
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ji Zhang
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Stephen Ritchie
- University of Auckland, Faculty of Medical and Health Sciences, Molecular Medicine and Pathology, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Zachary Oneroa
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Charlotte O'Neill
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ali Karkaba
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Niluka S Velathanthiri
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, Australia
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Conceição T, de Lencastre H, Aires-de-Sousa M. Healthy Bovines as Reservoirs of Major Pathogenic Lineages of Staphylococcus aureus in Portugal. Microb Drug Resist 2017. [PMID: 28650693 DOI: 10.1089/mdr.2017.0074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nosocomial prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Portugal is close to 50% and remains one of the highest in Europe. MRSA reservoirs in the animal setting in Portugal have been very poorly investigated, namely among animal husbandry. A total of 52 samples (nasal, inguinal region, and milk) were obtained from bovine animals and analyzed for the presence of S. aureus. The isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, SCCmec typing, and multilocus sequence typing and tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants. Overall, 54% of the screened animals were colonized with S. aureus in at least one body site. Notably, S. aureus nasal carriage followed an increasing trend with animal age (p = 0.0006). None of the isolates harbored the mecA or mecC genes. Resistance to penicillin, rifampicin, and tetracycline was observed in 24%, 18%, and 6% of the isolates, respectively. The isolates were distributed into three clonal lineages: PFGE type A, spa type t1166, ST1247-CC133 (43%), PFGE B-t267-ST352-CC97 (30%), and PFGE C-t091-ST7-CC7 (27%). CC133 was associated to older animals (p = 0.0025), whereas CC97 was isolated from calves (p = 0.0016). Virulence determinants commonly found in mastitis were widely detected in carriage isolates: lukDE and hlgv (100%), hlb (76%), and lukM (35%). Although healthy bovines do not represent a MRSA reservoir in Portugal, they are mainly colonized with S. aureus pathogenic lineages associated to mastitis in cattle (CC97 and CC133).
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Affiliation(s)
- Teresa Conceição
- 1 Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Hermínia de Lencastre
- 1 Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal .,2 Laboratory of Microbiology and Infectious Diseases, The Rockefeller University , New York, New York
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71
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Macori G, Giacinti G, Bellio A, Gallina S, Bianchi DM, Sagrafoli D, Marri N, Giangolini G, Amatiste S, Decastelli L. Molecular Epidemiology of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus in the Ovine Dairy Chain and in Farm-Related Humans. Toxins (Basel) 2017; 9:E161. [PMID: 28509842 PMCID: PMC5450709 DOI: 10.3390/toxins9050161] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/14/2023] Open
Abstract
Staphylococcus aureus is a major cause of clinical infections in humans and its enterotoxins cause foodborne disease. In the present study, we tested a total of 51 isolates of S. aureus from small-ruminant dairy farms with artisan dairy facilities, all located in Latium, Italy. The farms have a known history of a high prevalence of methicillin-resistant S. aureus (MRSA). Most of the MRSA isolates (27 of 51) belonged to spa-type t127 (43.1%), followed by t2678 (3.9%), t044 (2%), t1166 (2%), and t1773 (2%). PFGE performed on mecA positive strains identified one cluster (≥ 80% of similarity), comprising 22 MRSA. Nine of twenty-two MRSA isolates were assigned human host origin, and 13 isolates did not belong to a specific host. During the characterization study, one strain isolated from bulk tank milk samples harbored the pvl gene; the strain was not enterotoxigenic with a non-specific host according to the biotyping scheme, highlighting the possible emerging risk of transmission of bacterial virulence factors by foods, the environment, and foodhandlers. These findings stress the importance of hygienic measures at all processing steps of the food production chain and underline that monitoring for the presence of MRSA throughout the food chain is essential for public health.
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Affiliation(s)
- Guerrino Macori
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
| | - Giuseppina Giacinti
- Centro di Referenza Nazionale Della Qualità Del Latte E Dei Derivati Ovini E Caprini, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana , Via Appia Nuova, 1411, 00178 Roma, Italy.
| | - Alberto Bellio
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
| | - Silvia Gallina
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
| | - Daniele Sagrafoli
- Centro di Referenza Nazionale Della Qualità Del Latte E Dei Derivati Ovini E Caprini, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana , Via Appia Nuova, 1411, 00178 Roma, Italy.
| | - Nicla Marri
- Centro di Referenza Nazionale Della Qualità Del Latte E Dei Derivati Ovini E Caprini, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana , Via Appia Nuova, 1411, 00178 Roma, Italy.
| | - Gilberto Giangolini
- Centro di Referenza Nazionale Della Qualità Del Latte E Dei Derivati Ovini E Caprini, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana , Via Appia Nuova, 1411, 00178 Roma, Italy.
| | - Simonetta Amatiste
- Centro di Referenza Nazionale Della Qualità Del Latte E Dei Derivati Ovini E Caprini, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana , Via Appia Nuova, 1411, 00178 Roma, Italy.
| | - Lucia Decastelli
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.
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72
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Murray S, Pascoe B, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Wilkinson TS, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK. Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus. Genome Biol Evol 2017; 9:830-842. [PMID: 28338786 PMCID: PMC5469444 DOI: 10.1093/gbe/evx037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex. Poultry and human CC5 isolates were significantly distinct from each other and more recombination events were detected in the poultry isolates. We identified 44 recombination events in 33 genes along the branch extending to the poultry-specific CC5 cluster, and 47 genes were found more often in CC5 poultry isolates compared with those from humans. Many of these gene sequences were common in chicken isolates from other clonal complexes suggesting horizontal gene transfer among poultry associated lineages. Consistent with functional predictions for putative poultry-associated genes, poultry isolates showed enhanced growth at 42 °C and greater erythrocyte lysis on chicken blood agar in comparison with human isolates. By combining phenotype information with evolutionary analyses of staphylococcal genomes, we provide evidence of adaptation, following a human-to-poultry host transition. This has important implications for the emergence and dissemination of new pathogenic clones associated with modern agriculture.
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Affiliation(s)
- Susan Murray
- Swansea University Medical School, Swansea University, United Kingdom
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom.,MRC CLIMB Consortium, United Kingdom
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom
| | | | - Koji Yahara
- Swansea University Medical School, Swansea University, United Kingdom.,The Biostatistics Center, Kurume University, Fukuoka, Japan
| | | | - Yasmin Friedmann
- Swansea University Medical School, Swansea University, United Kingdom
| | | | - Fraser J Gormley
- Brewdog PLC, Balmacassie Industrial Estate, Ellon, Aberdeenshire, United Kingdom
| | - Dietrich Mack
- Bioscientia Labor Ingelheim, Institut für Medizinische Diagnostik GmbH, Ingelheim, Germany
| | - James E Bray
- Department of Zoology, University of Oxford, United Kingdom
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, United Kingdom
| | | | - Sarah Wendlandt
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt, Germany
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Finland.,Department of Biostatistics, University of Oslo, Norway
| | - J Ross Fitzgerald
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, United Kingdom.,MRC CLIMB Consortium, United Kingdom.,Department of Zoology, University of Oxford, United Kingdom
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73
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Schulz D, Grumann D, Trübe P, Pritchett-Corning K, Johnson S, Reppschläger K, Gumz J, Sundaramoorthy N, Michalik S, Berg S, van den Brandt J, Fister R, Monecke S, Uy B, Schmidt F, Bröker BM, Wiles S, Holtfreter S. Laboratory Mice Are Frequently Colonized with Staphylococcus aureus and Mount a Systemic Immune Response-Note of Caution for In vivo Infection Experiments. Front Cell Infect Microbiol 2017; 7:152. [PMID: 28512627 PMCID: PMC5411432 DOI: 10.3389/fcimb.2017.00152] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/11/2017] [Indexed: 11/16/2022] Open
Abstract
Whether mice are an appropriate model for S. aureus infection and vaccination studies is a matter of debate, because they are not considered as natural hosts of S. aureus. We previously identified a mouse-adapted S. aureus strain, which caused infections in laboratory mice. This raised the question whether laboratory mice are commonly colonized with S. aureus and whether this might impact on infection experiments. Publicly available health reports from commercial vendors revealed that S. aureus colonization is rather frequent, with rates as high as 21% among specific-pathogen-free mice. In animal facilities, S. aureus was readily transmitted from parents to offspring, which became persistently colonized. Among 99 murine S. aureus isolates from Charles River Laboratories half belonged to the lineage CC88 (54.5%), followed by CC15, CC5, CC188, and CC8. A comparison of human and murine S. aureus isolates revealed features of host adaptation. In detail, murine strains lacked hlb-converting phages and superantigen-encoding mobile genetic elements, and were frequently ampicillin-sensitive. Moreover, murine CC88 isolates coagulated mouse plasma faster than human CC88 isolates. Importantly, S. aureus colonization clearly primed the murine immune system, inducing a systemic IgG response specific for numerous S. aureus proteins, including several vaccine candidates. Phospholipase C emerged as a promising test antigen for monitoring S. aureus colonization in laboratory mice. In conclusion, laboratory mice are natural hosts of S. aureus and therefore, could provide better infection models than previously assumed. Pre-exposure to the bacteria is a possible confounder in S. aureus infection and vaccination studies and should be monitored.
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Affiliation(s)
- Daniel Schulz
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | - Dorothee Grumann
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | - Patricia Trübe
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | | | - Sarah Johnson
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of AucklandAuckland, New Zealand
| | - Kevin Reppschläger
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | - Janine Gumz
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | - Nandakumar Sundaramoorthy
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, ZIK FunGene, University Medicine GreifswaldGreifswald, Germany
| | - Stephan Michalik
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, ZIK FunGene, University Medicine GreifswaldGreifswald, Germany
| | - Sabine Berg
- Central Core and Research Facility of Laboratory Animals, University Medicine GreifswaldGreifswald, Germany
| | - Jens van den Brandt
- Central Core and Research Facility of Laboratory Animals, University Medicine GreifswaldGreifswald, Germany
| | - Richard Fister
- Charles River, Research and Professional ServicesWilmington, MA, USA
| | - Stefan Monecke
- Alere TechnologiesJena, Germany.,Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus"Dresden, Germany
| | - Benedict Uy
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of AucklandAuckland, New Zealand
| | - Frank Schmidt
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, ZIK FunGene, University Medicine GreifswaldGreifswald, Germany
| | - Barbara M Bröker
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of AucklandAuckland, New Zealand.,Maurice Wilkins Centre for Molecular BiodiscoveryAuckland, New Zealand
| | - Silva Holtfreter
- Department of Immunology, University Medicine GreifswaldGreifswald, Germany
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74
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Ben Said M, Abbassi MS, Gómez P, Ruiz-Ripa L, Sghaier S, El Fekih O, Hassen A, Torres C. Genetic characterization of Staphylococcus aureus isolated from nasal samples of healthy ewes in Tunisia. High prevalence of CC130 and CC522 lineages. Comp Immunol Microbiol Infect Dis 2017; 51:37-40. [PMID: 28504093 DOI: 10.1016/j.cimid.2017.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/23/2017] [Accepted: 03/09/2017] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus is a versatile bacterium, which can infect or colonize a variety of host species. The objective of this study was to characterize S. aureus isolates recovered from nasal swabs of 167 healthy ewes sampled from 12 farms in different areas of Tunisia during the period of 2014-2015. Genetic lineages, virulence factors and antibiotic resistance mechanisms were determined for recovered isolates. S. aureus was detected in 45 out of 167 tested samples (26.9%). All isolates were methicillin-susceptible (MSSA) and the majority of them were susceptible to tested antibiotics with few exceptions (% of resistance): penicillin (8.8), ciprofloxacin (4.4), and tobramycin or tetracycline (2.2, each). Twelve different spa types were detected (t15098, t15099, t1773, t3576, t1534, t5428, t3750, t5970 t254, t2883, t127 and t933), two of them were new (t15098 and t15099). S. aureus isolates were ascribed to agrI (n=23), agrII (n=1) and agrIII (n=20), and one was non-typeable. According to the sequence-type (ST) determined and/or the spa-type detected, the 45S. aureus isolates were assigned to six clonal complexes, with CC522 (44.4%) and CC130 (37.7%) being the most common lineages. Twenty-one (46.6%) and two (4.2%) isolates harbored the tst and eta genes encoding TSST-1 and ETA, respectively. In conclusion, nares of healthy ewes could be a reservoir of MSSA CC522 and CC130, lineages associated with TSST-1 and ETA that might represent a risk to human health.
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Affiliation(s)
- Meriam Ben Said
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia; Laboratoire de Traitement des Eaux Usées, Centre de Recherche et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia; Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunisia
| | - Paula Gómez
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - Laura Ruiz-Ripa
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - Senda Sghaier
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia; Laboratoire de Traitement des Eaux Usées, Centre de Recherche et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Oussama El Fekih
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre de Recherche et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain.
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75
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Koop G, Vrieling M, Storisteanu DML, Lok LSC, Monie T, van Wigcheren G, Raisen C, Ba X, Gleadall N, Hadjirin N, Timmerman AJ, Wagenaar JA, Klunder HM, Fitzgerald JR, Zadoks R, Paterson GK, Torres C, Waller AS, Loeffler A, Loncaric I, Hoet AE, Bergström K, De Martino L, Pomba C, de Lencastre H, Ben Slama K, Gharsa H, Richardson EJ, Chilvers ER, de Haas C, van Kessel K, van Strijp JAG, Harrison EM, Holmes MA. Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus. Sci Rep 2017; 7:40660. [PMID: 28106142 PMCID: PMC5247767 DOI: 10.1038/srep40660] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/08/2016] [Indexed: 11/09/2022] Open
Abstract
Bicomponent pore-forming leukocidins are a family of potent toxins secreted by Staphylococcus aureus, which target white blood cells preferentially and consist of an S- and an F-component. The S-component recognizes a receptor on the host cell, enabling high-affinity binding to the cell surface, after which the toxins form a pore that penetrates the cell lipid bilayer. Until now, six different leukocidins have been described, some of which are host and cell specific. Here, we identify and characterise a novel S. aureus leukocidin; LukPQ. LukPQ is encoded on a 45 kb prophage (ΦSaeq1) found in six different clonal lineages, almost exclusively in strains cultured from equids. We show that LukPQ is a potent and specific killer of equine neutrophils and identify equine-CXCRA and CXCR2 as its target receptors. Although the S-component (LukP) is highly similar to the S-component of LukED, the species specificity of LukPQ and LukED differs. By forming non-canonical toxin pairs, we identify that the F-component contributes to the observed host tropism of LukPQ, thereby challenging the current paradigm that leukocidin specificity is driven solely by the S-component.
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Affiliation(s)
- Gerrit Koop
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Manouk Vrieling
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Daniel M. L. Storisteanu
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Laurence S. C. Lok
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Tom Monie
- Medical Research Council Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge CB1 9NL, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Glenn van Wigcheren
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nicholas Gleadall
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
- Central Veterinary Institute of Wageningen UR, 8200 AB Lelystad, The Netherlands
| | - Heleen M. Klunder
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, United Kingdom
| | - Ruth Zadoks
- Moredun Research Institute, Bush Loan, Penicuik EH26 0PZ, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Gavin K. Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, Logroño 26006, Spain
| | - Andrew S. Waller
- Animal Health Trust, Lanwades Park, Kentford, Newmarket CB8 7UU, United Kingdom
| | - Anette Loeffler
- Department of Clinical Sciences and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, North Mymms, Hertfordshire AL9 7TA, United Kingdom
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Armando E. Hoet
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
- Veterinary Public Health Program, College of Public Health, The Ohio State University, 1900 Coffey Road, Columbus, OH 43210, USA
| | - Karin Bergström
- Department of Animal Health and Antimicrobial Strategies, SVA, SE-751 89 Uppsala, Sweden
| | - Luisa De Martino
- Department of Veterinary Medicine and Animal Production, Infectious Diseases Section, University of Naples “Federico II”, 80137 Naples, Italy
| | - Constança Pomba
- Interdisciplinary Centre of Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 LISBOA, Portugal
| | - Hermínia de Lencastre
- Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY10065, USA
| | - Karim Ben Slama
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Haythem Gharsa
- Laboratoire de Microorganismes et Biomolécules actives, Département de Biologie, Faculté de Sciences de Tunis, 2092 Tunis, Tunisia
| | - Emily J. Richardson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Edwin R. Chilvers
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s and Papworth Hospitals, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Carla de Haas
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Kok van Kessel
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jos A. G. van Strijp
- Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
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76
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Collins C, Didelot X. Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes. Methods Mol Biol 2017; 1535:109-137. [PMID: 27914076 DOI: 10.1007/978-1-4939-6673-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.
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Affiliation(s)
- Caitlin Collins
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
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77
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LukMF' is the major secreted leukocidin of bovine Staphylococcus aureus and is produced in vivo during bovine mastitis. Sci Rep 2016; 6:37759. [PMID: 27886237 PMCID: PMC5123576 DOI: 10.1038/srep37759] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/31/2016] [Indexed: 01/18/2023] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen and a common cause of mastitis in cattle. S. aureus secretes several leukocidins that target bovine neutrophils, crucial effector cells in the defence against bacterial pathogens. In this study, we investigated the role of staphylococcal leukocidins in the pathogenesis of bovine S. aureus disease. We show that LukAB, in contrast to the γ-hemolysins, LukED, and LukMF′, was unable to kill bovine neutrophils, and identified CXCR2 as a bovine receptor for HlgAB and LukED. Furthermore, we assessed functional leukocidin secretion by bovine mastitis isolates and observed that, although leukocidin production was strain dependent, LukMF′ was most abundantly secreted and the major toxin killing bovine neutrophils. To determine the role of LukMF′ in bovine mastitis, cattle were challenged with high (S1444) or intermediate (S1449, S1463) LukMF′-producing isolates. Only animals infected with S1444 developed severe clinical symptoms. Importantly, LukM was produced in vivo during the course of infection and levels in milk were associated with the severity of mastitis. Altogether, these findings underline the importance of LukMF′ as a virulence factor and support the development of therapeutic approaches targeting LukMF′ to control S. aureus mastitis in cattle.
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78
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Aires-de-Sousa M. Methicillin-resistant Staphylococcus aureus among animals: current overview. Clin Microbiol Infect 2016; 23:373-380. [PMID: 27851997 DOI: 10.1016/j.cmi.2016.11.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 01/04/2023]
Abstract
Currently, methicillin-resistant Staphylococcus aureus (MRSA) is a universal threat. After being well established in the healthcare setting, it has emerged in the community among people with no risk factors for MRSA acquisition, therefore imposing a new threat. The subsequent detection of MRSA colonizing or infecting animals as well as in food of animal origin was of major concern, revealing new reservoirs for MRSA. The major MRSA clonal lineages circulating in the different settings, i.e. in hospitals, in the community and among animals, are described here, differentiating between clones colonizing companion and food-chain animals. Particular attention is given to the widely spread livestock-associated MRSA clonal complex (CC) 398, which is mainly associated with professional exposure but may be of high pathogenicity. The recent detection of a mecA homologue, designated mecC, with a wide geographical distribution in Europe, and including a large diversity of hosts (food-chain, companion and wildlife animals and also detected in water samples) adds to the threat. Domestication as well as globalization of the livestock industry have intensified exchanges between human and animal bacteria. We report here several cases of transmission of MRSA between companion or food-chain animals and humans, as well as some MRSA clones of human origin that have adapted to new animal hosts eventually by losing useless virulence factors or acquiring new mobile genetic elements.
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Affiliation(s)
- M Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa, Lisboa, Portugal.
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79
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Penadés JR, Christie GE. The Phage-Inducible Chromosomal Islands: A Family of Highly Evolved Molecular Parasites. Annu Rev Virol 2016; 2:181-201. [PMID: 26958912 DOI: 10.1146/annurev-virology-031413-085446] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phage-inducible chromosomal islands (PICIs) are a family of highly mobile genetic elements that contribute substantively to horizontal gene transfer, host adaptation, and virulence. Initially identified in Staphylococcus aureus, these elements are now thought to occur widely in gram-positive bacteria. They are molecular parasites that exploit certain temperate phages as helpers, using a variety of elegant strategies to manipulate the phage life cycle and promote their own spread, both intra- and intergenerically. At the same time, these PICI-encoded mechanisms severely interfere with helper phage reproduction, thereby enhancing survival of the bacterial population. In this review we discuss the genetics and the life cycle of these elements, with special emphasis on how they interact and interfere with the helper phage machinery for their own benefit. We also analyze the role that these elements play in driving bacterial and viral evolution.
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Affiliation(s)
- José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8TA Glasgow, United Kingdom;
| | - Gail E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298;
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80
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Abstract
Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. The first S. aureus genomes to be published, 15 years ago, provided the first view of genome structure and gene content. Since then, thousands of genomes from a wide array of strains from different sources have been sequenced. Comparison of these sequences has resulted in broad insights into population structure, bacterial evolution, clone emergence and expansion, and the molecular basis of niche adaptation. Furthermore, this information is now being applied clinically in outbreak investigations to inform infection control measures and to determine appropriate treatment regimens. In this review, we summarize some of the broad insights into S. aureus biology gained from the analysis of genomes and discuss future directions and opportunities in this dynamic field of research.
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Affiliation(s)
- J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom;
| | - Matthew T G Holden
- School of Medicine, University of St. Andrews, St. Andrews, Fife KY16 9S5, United Kingdom;
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81
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Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe. mBio 2016; 7:mBio.00444-16. [PMID: 27150362 PMCID: PMC4959656 DOI: 10.1128/mbio.00444-16] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools. The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.
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82
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Gharsa H, Ben Slama K, Gómez-Sanz E, Lozano C, Zarazaga M, Messadi L, Boudabous A, Torres C. Molecular characterization of Staphylococcus aureus from nasal samples of healthy farm animals and pets in Tunisia. Vector Borne Zoonotic Dis 2016; 15:109-15. [PMID: 25700041 DOI: 10.1089/vbz.2014.1655] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A total of 261 healthy farm and pet animals (75 cattle, 52 goats, 100 dogs, and 34 cats) from different regions of Tunisia were screened for Staphylococcus aureus nasal carriage. Molecular typing of isolates (by spa- and multilocus sequence-typing) was performed, and their antimicrobial resistance and virulence genotypes were determined by PCR and sequencing. S. aureus isolates were detected in 17 of 261 tested samples (6.5%). All S. aureus isolates recovered were methicillin-susceptible (MSSA), and one isolate/sample was further studied. Eight different spa types were detected (t189, t279, t582, t701, t1166, t1268, t1534, and t1773), and eight different sequence types were identified (ST6, ST15, ST45, ST133, ST188, ST700 [clonal complex CC130], ST2057, and a new ST2121). MSSA from pets (six isolates) showed resistance to (number of isolates, resistance gene): penicillin (six, blaZ), tetracycline (one, tet[M]), erythromycin one, erm[A]), streptomycin (one, ant[6]-Ia), and ciprofloxacin (one). All isolates from farm animals showed susceptibility to the tested antimicrobials, except for two penicillin-resistant isolates. Five S. aureus isolates from goats and cats harbored the lukF/lukS-PV genes, encoding the Panton-Valentine leukocidin, and six isolates from goats harbored the tst virulence gene. In addition, diverse combinations of enterotoxin genes were detected, including two variants of the egc cluster. Goats and cats could represent a reservoir of important toxin genes, with potential implications in animal and human health.
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Affiliation(s)
- Haythem Gharsa
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis-El Manar , Tunis, Tunisia
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83
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Molecular characterization of Staphylococcus aureus isolated from humans related to a livestock farm in Spain, with detection of MRSA-CC130 carrying mecC gene: A zoonotic case? Enferm Infecc Microbiol Clin 2016; 34:280-5. [DOI: 10.1016/j.eimc.2015.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/11/2022]
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84
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Merz A, Stephan R, Johler S. Staphylococcus aureus Isolates from Goat and Sheep Milk Seem to Be Closely Related and Differ from Isolates Detected from Bovine Milk. Front Microbiol 2016; 7:319. [PMID: 27014240 PMCID: PMC4789554 DOI: 10.3389/fmicb.2016.00319] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/29/2016] [Indexed: 11/13/2022] Open
Abstract
Dairy goat and sheep farms suffer severe economic losses due to intramammary infections, with Staphylococcus aureus representing the main cause of clinical mastitis in small ruminants. In addition, S. aureus contamination of goat and sheep milk may cause staphylococcal food poisoning, as many traditional caprine and ovine milk products are not subjected to pasteurization. Data on virulence and antimicrobial resistance genes, as well as on the clonality of S. aureus detected in goat and sheep milk is scarce. Therefore, it was the aim of this study to determine (i) spa types and clonal complexes (CC) and (ii) virulence and resistance gene profiles of S. aureus isolated from goat and sheep milk. A total of 162 milk samples from sheep and goats presenting signs of an intramammary infection and 104 bulk milk samples were collected. While low prevalence rates of S. aureus was detected on single animal level, 46% of the bulk tank milk samples from small ruminants were positive for S. aureus. All isolates were spa typed and CC and virulence and resistance gene patterns were determined using a DNA microarray. Data from 49 S. aureus isolates was included in the statistical analysis and the construction of a SplitsTree. The analyzed isolates could be assigned to eleven CC, with the large majority of goat and sheep isolates being assigned to CC130 and CC133. The findings of this study suggest that S. aureus shows pronounced adaptation to small ruminants in general, but not to sheep or goats in particular. Although some common characteristics among S. aureus from caprine, ovine, and bovine milk samples were observed, S. aureus from small ruminants seem to form a distinct population. As 67% of the detected S. aureus strains exhibited at least one enterotoxin gene, many caprine, or ovine raw milk products may be contaminated with low levels of enterotoxigenic S. aureus, stressing the importance of strict maintenance of the cold chain.
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Affiliation(s)
- Axel Merz
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich, Switzerland
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85
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Draft Genome Sequences of Staphylococcus aureus Strains Isolated from Subclinical Bovine Mastitis in Brazil. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01594-15. [PMID: 26893417 PMCID: PMC4759064 DOI: 10.1128/genomea.01594-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the draft genome sequences of four Staphylococcus aureus strains isolated from mastitic milk collected from animals with subclinical manifestations. Three of them were typed as sequence type 126 (ST126), a genotype with no genome sequence available. ST126 is found in several herds of southern Brazil and is described as a bovine pathogen strongly associated with milk around the world.
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86
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Lozano C, Gharsa H, Ben Slama K, Zarazaga M, Torres C. Staphylococcus aureus in Animals and Food: Methicillin Resistance, Prevalence and Population Structure. A Review in the African Continent. Microorganisms 2016; 4:microorganisms4010012. [PMID: 27681906 PMCID: PMC5029517 DOI: 10.3390/microorganisms4010012] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/19/2016] [Accepted: 01/29/2016] [Indexed: 12/30/2022] Open
Abstract
The interest about Staphylococcus aureus (S. aureus) and methicillin resistant S. aureus (MRSA) in livestock, and domestic and wild animals has significantly increased. The spread of different clonal complexes related to livestock animals, mainly CC398, and the recent description of the new mecC gene, make it necessary to know more about the epidemiology and population structure of this microorganism all over the world. Nowadays, there are several descriptions about the presence of S. aureus and/or MRSA in different animal species (dogs, sheep, donkeys, bats, pigs, and monkeys), and in food of animal origin in African countries. In this continent, there is a high diversity of ethnicities, cultures or religions, as well as a high number of wild animal species and close contact between humans and animals, which can have a relevant impact in the epidemiology of this microorganism. This review shows that some clonal lineages associated with humans (CC1, CC15, CC72, CC80, CC101, and CC152) and animals (CC398, CC130 and CC133) are present in this continent in animal isolates, although the mecC gene has not been detected yet. However, available studies are limited to a few countries, very often with incomplete information, and many more studies are necessary to cover a larger number of African countries.
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Affiliation(s)
- Carmen Lozano
- Area of Biochemistry and Molecular Biology, University of La Rioja, Madre de Dios 53, Logroño 26006, Spain.
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis 1006, Tunisia.
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis 1006, Tunisia.
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, University of La Rioja, Madre de Dios 53, Logroño 26006, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, University of La Rioja, Madre de Dios 53, Logroño 26006, Spain.
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87
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Chen K, Stephanou AS, Roberts GA, White JH, Cooper LP, Houston PJ, Lindsay JA, Dryden DTF. The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:81-97. [PMID: 27193539 DOI: 10.1007/978-3-319-32189-9_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Type I DNA restriction-modification (RM) systems of Staphylococcus aureus are known to act as a significant barrier to horizontal gene transfer between S. aureus strains belonging to different clonal complexes. The livestock-associated clonal complexes CC133/771 and CC398 contain Type I RM systems not found in human MRSA strains as yet but at some point transfer will occur. When this does take place, horizontal gene transfer of resistance will happen more easily between these strains. The reservoir of antibiotic resistance, virulence and host-adaptation genes present in livestock-associated MRSA will then potentially contribute to the development of newly evolving MRSA clones. The target sites recognised by the Type I RM systems of CC133/771 and CC398 were identified as CAG(N)5RTGA and ACC(N)5RTGA, respectively. Assuming that these enzymes recognise the methylation state of adenine, the underlined A and T bases indicate the unique positions of methylation. Target methylation points for enzymes from CC1 were also identified. The methylation points for CC1-1 are CCAY(N)5TTAA and those for CC1-2 are CCAY(N)6 TGT with the underline indicating the adenine methylation site thus clearing up the ambiguity noted previously (Roberts et al. 2013, Nucleic Acids Res 41:7472-7484) for the half sites containing two adenine bases.
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Affiliation(s)
- Kai Chen
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK.,Shenyang Research Institute of Chemical Industry, 8 Shenliao Dong Road, Shenyang, Liaoning, People's Republic of China
| | - Augoustinos S Stephanou
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK
| | - Gareth A Roberts
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK
| | - Laurie P Cooper
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK
| | - Patrick J Houston
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.,The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - David T F Dryden
- EaStCHEM School of Chemistry, University of Edinburgh the King's Buildings, Edinburgh, EH9 3JJ, UK.
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88
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Rossi G, Cerquetella M, Attili AR. Amphixenosic Aspects of Staphylococcus aureus Infection in Man and Animals. Curr Top Microbiol Immunol 2016; 409:297-323. [PMID: 27023699 DOI: 10.1007/82_2016_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
According to the mode of transmission, Staphylococcus aureus infection between hosts is classified as "direct zoonoses," or infection that is transmitted from an infected vertebrate host to a susceptible host (man) by direct contact, by contact with a fomite or by a mechanical vector. The agent itself undergoes little or no propagative or developmental changes during transmission. According to the reservoir host, staphylococcosis is most precisely defined as "zooanthroponoses" or infections transmitted from man to lower vertebrate animals (e.g., streptococci, diphtheria, Enterobacteriaceae, human tuberculosis in cattle and parrots), but also "anthropozoonoses" or infections transmitted to man from lower vertebrate animals. In particular, actually, the correct definition of S. aureus infections between humans and animals is "amphixenoses" or infections maintained in both man and lower vertebrate animals and transmitted in either direction. S. aureus exhibits tropisms to many distinct animal hosts. While spillover events can occur wherever there is an interface between host species, changes in host tropism only occur with the establishment of sustained transmission in the new host species, leading to clonal expansion. Although the genomic variation underpinning adaptation in S. aureus genotypes infecting bovids and poultry has been well characterized, the frequency of switches from one host to another remains obscure. In this review, we sought to identify the sustained switches in host tropism in the S. aureus population, both anthroponotic and zoonotic, and their distribution over the species phylogeny. S. aureus is an organism with the capacity to switch into and adapt to novel hosts, even after long periods of isolation in a single host species. Based on this evidence, animal-adapted S. aureus lineages exhibiting resistance to antibiotics must be considered a major threat to public health, as they can adapt to the human population.
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Affiliation(s)
- Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024, Matelica, MC, Italy.
| | - Matteo Cerquetella
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024, Matelica, MC, Italy
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024, Matelica, MC, Italy
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89
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Zubair S, Fischer A, Liljander A, Meens J, Hegerman J, Gourlé H, Bishop RP, Roebbelen I, Younan M, Mustafa MI, Mushtaq M, Bongcam-Rudloff E, Jores J. Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. Stand Genomic Sci 2015; 10:109. [PMID: 26594310 PMCID: PMC4654806 DOI: 10.1186/s40793-015-0098-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 11/10/2015] [Indexed: 11/29/2022] Open
Abstract
We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), ~18 % were within the variable genome (shared among multiple but not all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.
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Affiliation(s)
- Saima Zubair
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Anne Fischer
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya ; International Center for Insect Physiology and Ecology, PO Box 30722, Nairobi, Kenya
| | - Anne Liljander
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
| | - Jochen Meens
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jan Hegerman
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany ; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany ; REBIRTH Cluster of Excellence, Hannover, Germany
| | - Hadrien Gourlé
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Richard P Bishop
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
| | - Ina Roebbelen
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
| | - Mario Younan
- Vétérinaires sans Frontières Germany, Nairobi, Kenya
| | - Mudassir Imran Mustafa
- Department of Public Health and Caring Science, Uppsala University, 751 22 Uppsala, Sweden
| | - Mamoona Mushtaq
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Joerg Jores
- International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
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90
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Boss R, Cosandey A, Luini M, Artursson K, Bardiau M, Breitenwieser F, Hehenberger E, Lam T, Mansfeld M, Michel A, Mösslacher G, Naskova J, Nelson S, Podpečan O, Raemy A, Ryan E, Salat O, Zangerl P, Steiner A, Graber HU. Bovine Staphylococcus aureus: Subtyping, evolution, and zoonotic transfer. J Dairy Sci 2015; 99:515-28. [PMID: 26601578 DOI: 10.3168/jds.2015-9589] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/27/2015] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus is globally one of the most important pathogens causing contagious mastitis in cattle. Previous studies using ribosomal spacer (RS)-PCR, however, demonstrated in Swiss cows that Staph. aureus isolated from bovine intramammary infections are genetically heterogeneous, with Staph. aureus genotype B (GTB) and GTC being the most prominent genotypes. Furthermore, Staph. aureus GTB was found to be contagious, whereas Staph. aureus GTC and all the remaining genotypes were involved in individual cow disease. In addition to RS-PCR, other methods for subtyping Staph. aureus are known, including spa typing and multilocus sequence typing (MLST). They are based on sequencing the spa and various housekeeping genes, respectively. The aim of the present study was to compare the 3 analytic methods using 456 strains of Staph. aureus isolated from milk of bovine intramammary infections and bulk tanks obtained from 12 European countries. Furthermore, the phylogeny of animal Staph. aureus was inferred and the zoonotic transfer of Staph. aureus between cattle and humans was studied. The analyzed strains could be grouped into 6 genotypic clusters, with CLB, CLC, and CLR being the most prominent ones. Comparing the 3 subtyping methods, RS-PCR showed the highest resolution, followed by spa typing and MLST. We found associations among the methods but in many cases they were unsatisfactory except for CLB and CLC. Cluster CLB was positive for clonal complex (CC)8 in 99% of the cases and typically positive for t2953; it is the cattle-adapted form of CC8. Cluster CLC was always positive for tbl 2645 and typically positive for CC705. For CLR and the remaining subtypes, links among the 3 methods were generally poor. Bovine Staph. aureus is highly clonal and a few clones predominate. Animal Staph. aureus always evolve from human strains, such that every human strain may be the ancestor of a novel animal-adapted strain. The zoonotic transfer of IMI- and milk-associated strains of Staph. aureus between cattle and humans seems to be very limited and different hosts are not considered as a source for mutual, spontaneous infections. Spillover events, however, may happen.
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Affiliation(s)
- R Boss
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland
| | - A Cosandey
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland; Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - M Luini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Einstein, 26900 Lodi, Italy
| | - K Artursson
- Department of Bacteriology, National Veterinary Institute, SE-751 89 Uppsala, Sweden
| | - M Bardiau
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, University of Liège, Avenue de Cureghem 6, 4000 Liège, Belgium
| | - F Breitenwieser
- Milchprüfring Baden-Württemberg e. V., Marie-Curie-Strasse 19, 73230 Kirchheim/Teck, Germany
| | - E Hehenberger
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - Th Lam
- GD Animal Health, Arnsbergstraat 7, PO Box 9, 7400 AA Deventer, the Netherlands
| | - M Mansfeld
- Carinthian Institute for Veterinary Disease Control, Kirchengasse 43, 9020 Klagenfurt, Austria
| | - A Michel
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - G Mösslacher
- Animal Health Organisation Upper Austria, Bahnhofplatz 1, 4021 Linz, Austria
| | - J Naskova
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland
| | - S Nelson
- Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Ullevalsvn 72, PO Box 8146 Dep, N-0033 Oslo, Norway
| | - O Podpečan
- Ambulatory Clinic for Large Animals, University of Ljubljana, Veterinary Faculty, Gerbičeva ul. 60, 1000 Ljubljana, Slovenia
| | - A Raemy
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - E Ryan
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - O Salat
- Veterinary Clinic of Haute Auvergne, Allauzier, 15100 Saint Flour, France
| | - P Zangerl
- Federal Institute for Alpine Dairying BAM, 6200 Jenbach, Austria
| | - A Steiner
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - H U Graber
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland.
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91
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Characterization of Insertion Sequence ISSau2 in the Human and Livestock-Associated Staphylococcus aureus. PLoS One 2015; 10:e0127183. [PMID: 25978410 PMCID: PMC4433286 DOI: 10.1371/journal.pone.0127183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/12/2015] [Indexed: 01/13/2023] Open
Abstract
Mobile genetic elements play important roles in evolution and diversification of bacterial genomes. ISSau2 is 1660bp in length with terminal 5’-TG and CA-3’ dinucleotides and has two overlapping reading frames orfA and orfB. It has been found in a wide range of S. aureus, such as HA-MRSA252, LGA251, MRSA S0385 and ED133. To determine distribution of ISSau2, 164 S. aureus isolates from milk samples of mastitic cows from our laboratory and all the S. aureus strains from the National Center for Biotechnology Information (NCBI) database were screened for the presence of ISSau2. Next, in order to explore a potential relationship among S. aureus ISSau2-containing strains and isolates, a relationship among 10 ISSau2-positive S. aureus isolates and 27 ISSau2-positive S. aureus strains was investigated by a phylogenetic analysis. These ISSau2 isolates and strains could be classified into four groups (A, B, C and D). The strains or isolates in Group D were all isolated from mammary glands, suggesting tissue specificity. All strains in Group B had an identical ISSau2 derivative, termed ISSau21628, with 32bp deletion at the 3’ terminus. ISSau21628 in strain ST398 from Group B was closely related to ISSau2 in strain LGA251 from Group D.
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92
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Phage-mediated horizontal transfer of a Staphylococcus aureus virulence-associated genomic island. Sci Rep 2015; 5:9784. [PMID: 25891795 PMCID: PMC4402969 DOI: 10.1038/srep09784] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/19/2015] [Indexed: 02/04/2023] Open
Abstract
Staphylococcus aureus is a major pathogen of humans and animals. The capacity of S. aureus to adapt to different host species and tissue types is strongly influenced by the acquisition of mobile genetic elements encoding determinants involved in niche adaptation. The genomic islands νSaα and νSaβ are found in almost all S. aureus strains and are characterized by extensive variation in virulence gene content. However the basis for the diversity and the mechanism underlying mobilization of the genomic islands between strains are unexplained. Here, we demonstrated that the genomic island, νSaβ, encoding an array of virulence factors including staphylococcal superantigens, proteases, and leukotoxins, in addition to bacteriocins, was transferrable in vitro to human and animal strains of multiple S. aureus clones via a resident prophage. The transfer of the νSaβ appears to have been accomplished by multiple conversions of transducing phage particles carrying overlapping segments of the νSaβ. Our findings solve a long-standing mystery regarding the diversification and spread of the genomic island νSaβ, highlighting the central role of bacteriophages in the pathogenic evolution of S. aureus.
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93
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Lewis AM, Matzdorf SS, Endres JL, Windham IH, Bayles KW, Rice KC. Examination of the Staphylococcus aureus nitric oxide reductase (saNOR) reveals its contribution to modulating intracellular NO levels and cellular respiration. Mol Microbiol 2015; 96:651-69. [PMID: 25651868 DOI: 10.1111/mmi.12962] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2015] [Indexed: 12/21/2022]
Abstract
Staphylococcus aureus nitrosative stress resistance is due in part to flavohemoprotein (Hmp). Although hmp is present in all sequenced S. aureus genomes, 37% of analyzed strains also contain nor, encoding a predicted quinol-type nitric oxide (NO) reductase (saNOR). DAF-FM staining of NO-challenged wild-type, nor, hmp and nor hmp mutant biofilms suggested that Hmp may have a greater contribution to intracellular NO detoxification relative to saNOR. However, saNOR still had a significant impact on intracellular NO levels and complemented NO detoxification in a nor hmp mutant. When grown as NO-challenged static (low-oxygen) cultures, hmp and nor hmp mutants both experienced a delay in growth initiation, whereas the nor mutant's ability to initiate growth was comparable with the wild-type strain. However, saNOR contributed to cell respiration in this assay once growth had resumed, as determined by membrane potential and respiratory activity assays. Expression of nor was upregulated during low-oxygen growth and dependent on SrrAB, a two-component system that regulates expression of respiration and nitrosative stress resistance genes. High-level nor promoter activity was also detectable in a cell subpopulation near the biofilm substratum. These results suggest that saNOR contributes to NO-dependent respiration during nitrosative stress, possibly conferring an advantage to nor+ strains in vivo.
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Affiliation(s)
- A M Lewis
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA
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94
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Venkateswara Prasad U, Vasu D, Yeswanth S, Swarupa V, Sunitha MM, Choudhary A, Sarma PVGK. Phosphorylation controls the functioning ofStaphylococcus aureusisocitrate dehydrogenase – favours biofilm formation. J Enzyme Inhib Med Chem 2015; 30:655-61. [DOI: 10.3109/14756366.2014.959945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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95
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Viana D, Comos M, McAdam PR, Ward MJ, Selva L, Guinane CM, González-Muñoz BM, Tristan A, Foster SJ, Fitzgerald JR, Penadés JR. A single natural nucleotide mutation alters bacterial pathogen host tropism. Nat Genet 2015; 47:361-366. [PMID: 25685890 PMCID: PMC4824278 DOI: 10.1038/ng.3219] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/16/2015] [Indexed: 11/25/2022]
Abstract
The capacity of microbial pathogens to alter their host-tropism leading to epidemics in distinct host-species populations is a global public and veterinary health concern. In order to investigate the molecular basis of a bacterial host-switching event in a tractable host-species, we traced the evolutionary trajectory of the common rabbit clone of Staphylococcus aureus. We report that it evolved through a likely human-to-rabbit host jump over 40 years ago, and that only a single natural nucleotide mutation was required and sufficient to convert a human-specific S. aureus strain into one which could infect rabbits. Related mutations were identified at the same locus in other rabbit strains of distinct clonal origin, consistent with convergent evolution. This first report of a single mutation that was sufficient to alter the host-tropism of a micro-organism during its evolution highlights the capacity of some pathogens to readily expand into novel host-species populations.
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Affiliation(s)
- David Viana
- Universidad CEU Cardenal Herrera, 46113 Moncada, Valencia, Spain
| | - María Comos
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias(CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
| | - Paul R McAdam
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - Melissa J Ward
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH93JT
| | - Laura Selva
- Universidad CEU Cardenal Herrera, 46113 Moncada, Valencia, Spain
| | - Caitriona M Guinane
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - Beatriz M González-Muñoz
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Université Lyon, France
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - José R Penadés
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010, Valencia, Spain.,Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
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96
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Koymans KJ, Vrieling M, Gorham RD, van Strijp JAG. Staphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation. Curr Top Microbiol Immunol 2015; 409:441-489. [PMID: 26919864 DOI: 10.1007/82_2015_5017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.
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Affiliation(s)
- Kirsten J Koymans
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Manouk Vrieling
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ronald D Gorham
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Jos A G van Strijp
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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97
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Experimental model of toxin-induced subclinical mastitis and its effect on disruption of follicular function in cows. Theriogenology 2014; 82:1165-72. [DOI: 10.1016/j.theriogenology.2014.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/05/2014] [Accepted: 08/05/2014] [Indexed: 01/26/2023]
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98
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Peton V, Bouchard DS, Almeida S, Rault L, Falentin H, Jardin J, Jan G, Hernandez D, François P, Schrenzel J, Azevedo V, Miyoshi A, Berkova N, Even S, Le Loir Y. Fine-tuned characterization of Staphylococcus aureus Newbould 305, a strain associated with mild and chronic mastitis in bovines. Vet Res 2014; 45:106. [PMID: 25316113 PMCID: PMC4230361 DOI: 10.1186/s13567-014-0106-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/01/2014] [Indexed: 11/17/2022] Open
Abstract
S. aureus is a major aetiological agent of ruminant mastitis worldwide. The chronic nature of S. aureus mastitis makes it difficult to cure and prone to resurgence. In order to identify the bacterial factors involved in this chronicity, Newbould 305 (N305), a strain that can reproducibly induce mild and chronic mastitis in an experimental setting, was characterized in depth. We employed genomic and proteomic techniques combined with phenotype characterization, in order to comprehensively analyse N305. The results were compared with data obtained on S. aureus RF122, a strain representative of the major clone involved in severe bovine mastitis worldwide. Five mobile genetic elements were identified in the N305 genome as carrying virulence factors which correlated with phenotypic features such as cytotoxicity, mammary epithelial cell invasion or host-adaptation. In particular, the presence and characteristics of surface exposed proteins correlated well with the greater adhesion and internalization capacities of N305 in bovine mammary epithelial cells. N305 also displayed less diversity of toxin genes but secreted larger quantities of these toxins, associated with a higher cytotoxicity potential. Our data are consistent with the invasiveness and host-adaptation features which contribute to the chronicity of S. aureus mastitis. Mobile genetic elements, exoproteins and surface exposed proteins constitute good targets for further research to explore the underlying mechanisms related to mastitis chronicity.
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Affiliation(s)
- Vincent Peton
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Damien S Bouchard
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Sintia Almeida
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
| | - Lucie Rault
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Hélène Falentin
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Julien Jardin
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Gwénaël Jan
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - David Hernandez
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals (HUG), CH-1211, Geneva 14, Switzerland.
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals (HUG), CH-1211, Geneva 14, Switzerland.
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals (HUG), CH-1211, Geneva 14, Switzerland.
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
| | - Anderson Miyoshi
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
| | - Nadia Berkova
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Sergine Even
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Yves Le Loir
- INRA, UMR 1253 STLO, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. .,Agrocampus Ouest, UMR1253 STLO, 85 rue de Saint Brieuc, 35042, Rennes Cedex, France.
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99
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Woolfit M, Iturbe-Ormaetxe I, Brownlie JC, Walker T, Riegler M, Seleznev A, Popovici J, Rancès E, Wee BA, Pavlides J, Sullivan MJ, Beatson SA, Lane A, Sidhu M, McMeniman CJ, McGraw EA, O'Neill SL. Genomic evolution of the pathogenic Wolbachia strain, wMelPop. Genome Biol Evol 2014; 5:2189-204. [PMID: 24190075 PMCID: PMC3845649 DOI: 10.1093/gbe/evt169] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most strains of the widespread endosymbiotic bacterium Wolbachia pipientis are benign or behave as reproductive parasites. The pathogenic strain wMelPop is a striking exception, however: it overreplicates in its insect hosts and causes severe life shortening. The mechanism of this pathogenesis is currently unknown. We have sequenced the genomes of three variants of wMelPop and of the closely related nonpathogenic strain wMelCS. We show that the genomes of wMelCS and wMelPop appear to be identical in the nonrepeat regions of the genome and differ detectably only by the triplication of a 19-kb region that is unlikely to be associated with life shortening, demonstrating that dramatic differences in the host phenotype caused by this endosymbiont may be the result of only minor genetic changes. We also compare the genomes of the original wMelPop strain from Drosophila melanogaster and two sequential derivatives, wMelPop-CLA and wMelPop-PGYP. To develop wMelPop as a novel biocontrol agent, it was first transinfected into and passaged in mosquito cell lines for approximately 3.5 years, generating wMelPop-CLA. This cell line-passaged strain was then transinfected into Aedes aegypti mosquitoes, creating wMelPop-PGYP, which was sequenced after 4 years in the insect host. We observe a rapid burst of genomic changes during cell line passaging, but no further mutations were detected after transinfection into mosquitoes, indicating either that host preadaptation had occurred in cell lines, that cell lines are a more selectively permissive environment than animal hosts, or both. Our results provide valuable data on the rates of genomic and phenotypic change in Wolbachia associated with host shifts over short time scales.
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Affiliation(s)
- Megan Woolfit
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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100
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Bergonier D, Sobral D, Feßler AT, Jacquet E, Gilbert FB, Schwarz S, Treilles M, Bouloc P, Pourcel C, Vergnaud G. Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA). Vet Res 2014; 45:97. [PMID: 25315988 PMCID: PMC4195859 DOI: 10.1186/s13567-014-0097-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 09/05/2014] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes.
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Affiliation(s)
- Dominique Bergonier
- INRA, UMR1225, IHAP, 31076, Toulouse, France. .,Université de Toulouse, INP, ENVT, UMR1225, IHAP, 31076, Toulouse, France. .,UMT INRA-ENVT-Institut de l'Élevage "Small Ruminants Health Management", 31076, Toulouse, France.
| | - Daniel Sobral
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France. .,Ceeram (Centre Européen d'Expertise et de Recherche sur les Agents Microbiens), 44240, La Chapelle sur Erdre, France.
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute, 31535, Neustadt-Mariensee, Germany.
| | - Eric Jacquet
- ICSN, CNRS, UPR2301, IMAGIF qPCR-Platform, 91198, Gif-sur-Yvette, France.
| | | | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute, 31535, Neustadt-Mariensee, Germany.
| | - Michaël Treilles
- Laboratoire départemental d'analyses de la Manche (LDA50), 50000, Saint-Lô, France.
| | - Philippe Bouloc
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France.
| | - Christine Pourcel
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France.
| | - Gilles Vergnaud
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France. .,ENSTA ParisTech, 91762, Palaiseau, France.
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