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Yebra G, Mrochen D, Fischer S, Pfaff F, Ulrich RG, Pritchett-Corning K, Holtfreter S, Fitzgerald JR. Bacteriophage-driven emergence and expansion of Staphylococcus aureus in rodent populations. PLoS Pathog 2024; 20:e1012378. [PMID: 39047021 PMCID: PMC11299810 DOI: 10.1371/journal.ppat.1012378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/05/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Human activities such as agriculturalization and domestication have led to the emergence of many new pathogens via host-switching events between humans, domesticated and wild animals. Staphylococcus aureus is a multi-host opportunistic pathogen with a global healthcare and economic burden. Recently, it was discovered that laboratory and wild rodents can be colonised and infected with S. aureus, but the origins and zoonotic potential of rodent S. aureus is unknown. In order to trace their evolutionary history, we employed a dataset of 1249 S. aureus genome sequences including 393 of isolates from rodents and other small mammals (including newly determined sequences for 305 isolates from 7 countries). Among laboratory mouse populations, we identified multiple widespread rodent-specific S. aureus clones that likely originated in humans. Phylogeographic analysis of the most common murine lineage CC88 suggests that it emerged in the 1980s in laboratory mouse facilities most likely in North America, from where it spread to institutions around the world, via the distribution of mice for research. In contrast, wild rodents (mice, voles, squirrels) were colonized with a unique complement of S. aureus lineages that are widely disseminated across Europe. In order to investigate the molecular basis for S. aureus adaptation to rodent hosts, genome-wide association analysis was carried out revealing a unique complement of bacteriophages associated with a rodent host ecology. Of note, we identified novel prophages and pathogenicity islands in rodent-derived S. aureus that conferred the potential for coagulation of rodent plasma, a key phenotype of abscess formation and persistence. Our findings highlight the remarkable capacity of S. aureus to expand into new host populations, driven by the acquisition of genes promoting survival in new host-species.
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Affiliation(s)
- Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Mrochen
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Kathleen Pritchett-Corning
- Charles River, Research and Professional Services, Wilmington, Massachusetts, United States of America
- Office of Animal Resources, Harvard University Faculty of Arts and Sciences, Cambridge, Massachusetts, United States of America
| | - Silva Holtfreter
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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2
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Fernandez JE, Egli A, Overesch G, Perreten V. Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution. Nat Commun 2024; 15:5526. [PMID: 38951499 PMCID: PMC11217367 DOI: 10.1038/s41467-024-49644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.
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Affiliation(s)
- Javier Eduardo Fernandez
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gudrun Overesch
- Center for Zoonoses, Animal Bacterial Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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3
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Kerro Dego O, Vidlund J. Staphylococcal mastitis in dairy cows. Front Vet Sci 2024; 11:1356259. [PMID: 38863450 PMCID: PMC11165426 DOI: 10.3389/fvets.2024.1356259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Bovine mastitis is one of the most common diseases of dairy cattle. Even though different infectious microorganisms and mechanical injury can cause mastitis, bacteria are the most common cause of mastitis in dairy cows. Staphylococci, streptococci, and coliforms are the most frequently diagnosed etiological agents of mastitis in dairy cows. Staphylococci that cause mastitis are broadly divided into Staphylococcus aureus and non-aureus staphylococci (NAS). NAS is mainly comprised of coagulase-negative Staphylococcus species (CNS) and some coagulase-positive and coagulase-variable staphylococci. Current staphylococcal mastitis control measures are ineffective, and dependence on antimicrobial drugs is not sustainable because of the low cure rate with antimicrobial treatment and the development of resistance. Non-antimicrobial effective and sustainable control tools are critically needed. This review describes the current status of S. aureus and NAS mastitis in dairy cows and flags areas of knowledge gaps.
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Affiliation(s)
- Oudessa Kerro Dego
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
| | - Jessica Vidlund
- Department of Animal Science, University of Tennessee, Knoxville, TN, United States
- East Tennessee AgResearch and Education Center-Little River Animal and Environmental Unit, University of Tennessee, Walland, TN, United States
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4
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Cuny C, Layer-Nicolaou F, Werner G, Witte W. A look at staphylococci from the one health perspective. Int J Med Microbiol 2024; 314:151604. [PMID: 38367509 DOI: 10.1016/j.ijmm.2024.151604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.
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Affiliation(s)
- Christiane Cuny
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.
| | - Franziska Layer-Nicolaou
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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5
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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6
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Chen Q, Zhao G, Yang W, Chen F, Qi Y, Lou Z. Investigation into the prevalence of enterotoxin genes and genetic background of Staphylococcus aureus isolates from retain foods in Hangzhou, China. BMC Microbiol 2023; 23:294. [PMID: 37848808 PMCID: PMC10580612 DOI: 10.1186/s12866-023-03027-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Staphylococcus aureus expresses numerous toxins, many of which are strongly believed to be responsible for specific symptoms and even diseases, making it significant in the pathogenesis of human health. Enterotoxins, which are vital toxins, are associated with foodborne illnesses that manifest through symptoms like vomiting and diarrhea. In the present study, 264 S. aureus isolates obtained from various retail foods in Hangzhou, China were further investigated the profiles of enterotoxin genes and genetic backgrounds. RESULTS Approximately, 64.02% of the isolates from diverse sources contained at least one Staphylococcal Enterotoxin (SE) genes, displaying a total of 36 distinct combinations. Enterotoxin gene cluster (egc) encoded enterotoxin genes, normally designated by seg, sei, sem, sen, seo and selu, plus with sep were more frequently detected (33.73%, each). In contrast, see, ses and set were absent in any of the isolates tested. A total of 44 sequence types (STs), 20 clonal complexes (CCs) and 66 different staphylococcal protein A (spa) types (including six novel types) were identified among those 169 SE-positive isolates. Moreover, nineteen methicillin-resistant Staphylococcus aureus (MRSA) isolates were identified. The majority of those isolates belonged to the CC59-Sccmec IVa cluster and carried the seb-sek-seq gene cluster. The egc cluster, either coexisting with or without other enterotoxin genes, was observed in all isolates allocated into CC5, CC9, CC20, CC25, CC72 and ST672. Irrespective of the spa types and origins of the food, it appeared that seh was a distinct genetic element present in isolates belonging to the CC1 clonal lineage. CONCLUSIONS The results not only proposed a suspected relationship between distribution of enterotoxigenic strains and genetic backgrounds, but also attributed the presence of novel enterotoxins to potential hazards in food safety.
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Affiliation(s)
- Qi Chen
- Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, 310000, Hangzhou, China.
| | - Gang Zhao
- Hangzhou Center for Disease Control and Prevention, 310021, Hangzhou, China
| | - Wei Yang
- Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, 310000, Hangzhou, China
| | - Fuhong Chen
- Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, 310000, Hangzhou, China
| | - Yan Qi
- Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, 310000, Hangzhou, China
| | - Zhengqing Lou
- Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, 310000, Hangzhou, China.
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7
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Cheung GYC, Otto M. Virulence Mechanisms of Staphylococcal Animal Pathogens. Int J Mol Sci 2023; 24:14587. [PMID: 37834035 PMCID: PMC10572719 DOI: 10.3390/ijms241914587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Staphylococci are major causes of infections in mammals. Mammals are colonized by diverse staphylococcal species, often with moderate to strong host specificity, and colonization is a common source of infection. Staphylococcal infections of animals not only are of major importance for animal well-being but have considerable economic consequences, such as in the case of staphylococcal mastitis, which costs billions of dollars annually. Furthermore, pet animals can be temporary carriers of strains infectious to humans. Moreover, antimicrobial resistance is a great concern in livestock infections, as there is considerable antibiotic overuse, and resistant strains can be transferred to humans. With the number of working antibiotics continuously becoming smaller due to the concomitant spread of resistant strains, alternative approaches, such as anti-virulence, are increasingly being investigated to treat staphylococcal infections. For this, understanding the virulence mechanisms of animal staphylococcal pathogens is crucial. While many virulence factors have similar functions in humans as animals, there are increasingly frequent reports of host-specific virulence factors and mechanisms. Furthermore, we are only beginning to understand virulence mechanisms in animal-specific staphylococcal pathogens. This review gives an overview of animal infections caused by staphylococci and our knowledge about the virulence mechanisms involved.
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Affiliation(s)
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20814, USA;
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8
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Rhoads DD, Pummil J, Ekesi NS, Alrubaye AAK. Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis. PLoS One 2023; 18:e0283914. [PMID: 37406030 DOI: 10.1371/journal.pone.0283914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.
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Affiliation(s)
- Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
| | - Jeff Pummil
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR, United States of America
| | - Nnamdi S Ekesi
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, United States of America
| | - Adnan A K Alrubaye
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
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9
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Haag AF, Liljeroos L, Donato P, Pozzi C, Brignoli T, Bottomley MJ, Bagnoli F, Delany I. In Vivo Gene Expression Profiling of Staphylococcus aureus during Infection Informs Design of Stemless Leukocidins LukE and -D as Detoxified Vaccine Candidates. Microbiol Spectr 2023; 11:e0257422. [PMID: 36688711 PMCID: PMC9927290 DOI: 10.1128/spectrum.02574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/02/2023] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is a clinically important bacterial pathogen that has become resistant to treatment with most routinely used antibiotics. Alternative strategies, such as vaccination and phage therapy, are therefore actively being investigated to prevent or combat staphylococcal infections. Vaccination requires that vaccine targets are expressed at sufficient quantities during infection so that they can be targeted by the host's immune system. While our knowledge of in vitro expression levels of putative vaccine candidates is comprehensive, crucial in vivo expression data are scarce and promising vaccine candidates during in vitro assessment often prove ineffective in preventing S. aureus infection. Here, we show how a newly developed high-throughput quantitative reverse transcription-PCR (qRT-PCR) assay monitoring the expression of 84 staphylococcal genes encoding mostly virulence factors can inform the selection and design of effective vaccine candidates against staphylococcal infections. We show that this assay can accurately quantify mRNA expression levels of these genes in several host organs relying only on very limited amounts of bacterial mRNA in each sample. We selected two highly expressed genes, lukE and lukD, encoding pore-forming leukotoxins, to inform the design of detoxified recombinant proteins and showed that immunization with recombinant genetically detoxified LukED antigens conferred protection against staphylococcal skin infection in mice. Consequently, knowledge of in vivo-expressed virulence determinants can be successfully deployed to identify and select promising candidates for optimized design of effective vaccine antigens against S. aureus. Notably, this approach should be broadly applicable to numerous other pathogens. IMPORTANCE Vaccination is an attractive strategy for preventing bacterial infections in an age of increased antimicrobial resistance. However, vaccine development frequently suffers significant setbacks when candidate antigens that show promising results in in vitro experimentation fail to protect from disease. An alluring strategy is to focus resources on developing bacterial virulence factors that are expressed during disease establishment or maintenance and are critical for bacterial in-host survival as vaccine targets. While expression profiles of many virulence factors have been characterized in detail in vitro, our knowledge of their in vivo expression profiles is still scarce. Here, using a high-throughput qRT-PCR approach, we identified two highly expressed leukotoxins in a murine infection model and showed that genetically detoxified derivatives of these elicited a protective immune response in a murine skin infection model. Therefore, in vivo gene expression can inform the selection of promising candidates for the design of effective vaccine antigens.
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Affiliation(s)
- Andreas F. Haag
- GSK, Siena, Italy
- School of Medicine, University of St. Andrews, St. Andrews, United Kingdom
| | | | | | | | - Tarcisio Brignoli
- GSK, Siena, Italy
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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10
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Shoaib M, Aqib AI, Muzammil I, Majeed N, Bhutta ZA, Kulyar MFEA, Fatima M, Zaheer CNF, Muneer A, Murtaza M, Kashif M, Shafqat F, Pu W. MRSA compendium of epidemiology, transmission, pathophysiology, treatment, and prevention within one health framework. Front Microbiol 2023; 13:1067284. [PMID: 36704547 PMCID: PMC9871788 DOI: 10.3389/fmicb.2022.1067284] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Staphylococcus aureus is recognized as commensal as well as opportunistic pathogen of humans and animals. Methicillin resistant strain of S. aureus (MRSA) has emerged as a major pathogen in hospitals, community and veterinary settings that compromises the public health and livestock production. MRSA basically emerged from MSSA after acquiring SCCmec element through gene transfer containing mecA gene responsible for encoding PBP-2α. This protein renders the MRSA resistant to most of the β-lactam antibiotics. Due to the continuous increasing prevalence and transmission of MRSA in hospitals, community and veterinary settings posing a major threat to public health. Furthermore, high pathogenicity of MRSA due to a number of virulence factors produced by S. aureus along with antibiotic resistance help to breach the immunity of host and responsible for causing severe infections in humans and animals. The clinical manifestations of MRSA consist of skin and soft tissues infection to bacteremia, septicemia, toxic shock, and scalded skin syndrome. Moreover, due to the increasing resistance of MRSA to number of antibiotics, there is need to approach alternatives ways to overcome economic as well as human losses. This review is going to discuss various aspects of MRSA starting from emergence, transmission, epidemiology, pathophysiology, disease patterns in hosts, novel treatment, and control strategies.
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Affiliation(s)
- Muhammad Shoaib
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Iqra Muzammil
- Department of Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Noreen Majeed
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Mahreen Fatima
- Faculty of Biosciences, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | | | - Afshan Muneer
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Maheen Murtaza
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Kashif
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Furqan Shafqat
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Lanzhou, China
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11
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Chaguza C, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. CELL GENOMICS 2022; 2:100194. [PMID: 36465278 PMCID: PMC9718559 DOI: 10.1016/j.xgen.2022.100194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA,Corresponding author
| | | | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA,Corresponding author
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12
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Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors. Cell 2022; 185:3248-3262.e20. [PMID: 35985290 DOI: 10.1016/j.cell.2022.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 01/26/2023]
Abstract
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
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13
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Ibarra-Chávez R, Brady A, Chen J, Penadés JR, Haag AF. Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis. PLoS Genet 2022; 18:e1010146. [PMID: 35344558 PMCID: PMC8989297 DOI: 10.1371/journal.pgen.1010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 04/07/2022] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
Phage-inducible chromosomal islands (PICIs) are a widespread family of highly mobile genetic elements that disseminate virulence and toxin genes among bacterial populations. Since their life cycle involves induction by helper phages, they are important players in phage evolution and ecology. PICIs can interfere with the lifecycle of their helper phages at different stages resulting frequently in reduced phage production after infection of a PICI-containing strain. Since phage defense systems have been recently shown to be beneficial for the acquisition of exogenous DNA via horizontal gene transfer, we hypothesized that PICIs could provide a similar benefit to their hosts and tested the impact of PICIs in recipient strains on host cell viability, phage propagation and transfer of genetic material. Here we report an important role for PICIs in bacterial evolution by promoting the survival of phage-mediated transductants of chromosomal or plasmid DNA. The presence of PICIs generates favorable conditions for population diversification and the inheritance of genetic material being transferred, such as antibiotic resistance and virulence genes. Our results show that by interfering with phage reproduction, PICIs can protect the bacterial population from phage attack, increasing the overall survival of the bacterial population as well as the transduced cells. Moreover, our results also demonstrate that PICIs reduce the frequency of lysogenization after temperate phage infection, creating a more genetically diverse bacterial population with increased bet-hedging opportunities to adapt to new niches. In summary, our results identify a new role for the PICIs and highlight them as important drivers of bacterial evolution.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - José R. Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
- Universidad CEU Cardenal Herrera, Moncada, Spain
- * E-mail: (JRP); (AFH)
| | - Andreas F. Haag
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Medicine, University of St Andrews, North Haugh, St Andrews, United Kingdom
- * E-mail: (JRP); (AFH)
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14
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Diversity and pathogenesis of Staphylococcus aureus from bovine mastitis: current understanding and future perspectives. BMC Vet Res 2022; 18:115. [PMID: 35331225 PMCID: PMC8944054 DOI: 10.1186/s12917-022-03197-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/03/2022] [Indexed: 11/10/2022] Open
Abstract
Staphylococcus aureus is a leading cause of bovine mastitis worldwide. Despite some improved understanding of disease pathogenesis, progress towards new methods for the control of intramammary infections (IMI) has been limited, particularly in the field of vaccination. Although herd management programs have helped to reduce the number of clinical cases, S. aureus mastitis remains a major disease burden. This review summarizes the past 16 years of research on bovine S. aureus population genetics, and molecular pathogenesis that have been conducted worldwide. We describe the diversity of S. aureus associated with bovine mastitis and the geographical distribution of S. aureus clones in different continents. We also describe studies investigating the evolution of bovine S. aureus and the importance of host-adaptation in its emergence as a mastitis pathogen. The available information on the prevalence of virulence determinants and their functional relevance during the pathogenesis of bovine mastitis are also discussed. Although traits such as biofilm formation and innate immune evasion are critical for the persistence of bacteria, the current understanding of the key host-pathogen interactions that determine the outcome of S. aureus IMI is very limited. We suggest that greater investment in research into the genetic and molecular basis of bovine S. aureus pathogenesis is essential for the identification of novel therapeutic and vaccine targets.
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15
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Park S, Jung D, O'Brien B, Ruffini J, Dussault F, Dube-Duquette A, Demontier É, Lucier JF, Malouin F, Dufour S, Ronholm J. Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation. Microb Genom 2022; 8. [PMID: 35179459 PMCID: PMC8942034 DOI: 10.1099/mgen.0.000779] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus is a major etiological agent of clinical and subclinical bovine mastitis. The versatile and adaptative evolutionary strategies of this bacterium have challenged mastitis control and prevention globally, and the high incidence of S. aureus mastitis increases concerns about antimicrobial resistance (AMR) and zoonosis. This study aims to describe the evolutionary relationship between bovine intramammary infection (IMI)-associated S. aureus and human pathogenic S. aureus and further elucidate the specific genetic composition that leads to the emergence of successful bovine IMI-associated S. aureus lineages. We performed a phylogenomic analysis of 187 S. aureus isolates that originated from either dairy cattle or humans. Our results revealed that bovine IMI-associated S. aureus isolates showed distinct clades compared to human-originated S. aureus isolates. From a pan-genome analysis, 2070 core genes were identified. Host-specific genes and clonal complex (CC)-specific genes were also identified in bovine S. aureus isolates, mostly located in mobile genetic elements (MGEs). Additionally, the genome sequences of three apparent human-adapted isolates (two from CC97 and one from CC8), isolated from bovine mastitis samples, may provide an snapshot of the genomic characteristics in early host spillover events. Virulence and AMR genes were not conserved among bovine IMI-associated S. aureus isolates. Restriction-modification (R-M) genes in bovine IMI-associated S. aureus demonstrated that the Type I R-M system was lineage-specific and Type II R-M system was sequence type (ST)-specific. The distribution of exclusive, virulence, and AMR genes were closely correlated with the presence of R-M systems in S. aureus, suggesting that R-M systems may contribute to shaping clonal diversification by providing a genetic barrier to the horizontal gene transfer (HGT). Our findings indicate that the CC or ST lineage-specific R-M systems may limit genetic exchange between bovine-adapted S. aureus isolates from different lineages.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Bridget O'Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | - Janina Ruffini
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada
| | | | - Alexis Dube-Duquette
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Élodie Demontier
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Jean-François Lucier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - François Malouin
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada.,Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Québec, Canada.,Mastitis Network, Saint-Hyacinthe, Québec, Canada.,Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
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16
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Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R, Deplano A, Vandendriessche S, Černá Bolfíková B, Hulva P, Arendrup MC, Hare RK, Barnadas C, Stegger M, Sieber RN, Skov RL, Petersen A, Angen Ø, Rasmussen SL, Espinosa-Gongora C, Aarestrup FM, Lindholm LJ, Nykäsenoja SM, Laurent F, Becker K, Walther B, Kehrenberg C, Cuny C, Layer F, Werner G, Witte W, Stamm I, Moroni P, Jørgensen HJ, de Lencastre H, Cercenado E, García-Garrote F, Börjesson S, Hæggman S, Perreten V, Teale CJ, Waller AS, Pichon B, Curran MD, Ellington MJ, Welch JJ, Peacock SJ, Seilly DJ, Morgan FJE, Parkhill J, Hadjirin NF, Lindsay JA, Holden MTG, Edwards GF, Foster G, Paterson GK, Didelot X, Holmes MA, Harrison EM, Larsen AR. Emergence of methicillin resistance predates the clinical use of antibiotics. Nature 2022; 602:135-141. [PMID: 34987223 PMCID: PMC8810379 DOI: 10.1038/s41586-021-04265-w] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
The discovery of antibiotics more than 80 years ago has led to considerable improvements in human and animal health. Although antibiotic resistance in environmental bacteria is ancient, resistance in human pathogens is thought to be a modern phenomenon that is driven by the clinical use of antibiotics1. Here we show that particular lineages of methicillin-resistant Staphylococcus aureus-a notorious human pathogen-appeared in European hedgehogs in the pre-antibiotic era. Subsequently, these lineages spread within the local hedgehog populations and between hedgehogs and secondary hosts, including livestock and humans. We also demonstrate that the hedgehog dermatophyte Trichophyton erinacei produces two β-lactam antibiotics that provide a natural selective environment in which methicillin-resistant S. aureus isolates have an advantage over susceptible isolates. Together, these results suggest that methicillin resistance emerged in the pre-antibiotic era as a co-evolutionary adaptation of S. aureus to the colonization of dermatophyte-infected hedgehogs. The evolution of clinically relevant antibiotic-resistance genes in wild animals and the connectivity of natural, agricultural and human ecosystems demonstrate that the use of a One Health approach is critical for our understanding and management of antibiotic resistance, which is one of the biggest threats to global health, food security and development.
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Affiliation(s)
- Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Stien Vandendriessche
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
- Laboratory for Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Maiken C Arendrup
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus K Hare
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Céline Barnadas
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert L Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Petersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sophie L Rasmussen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Wildlife Conservation Research Unit (WildCRU), Department of Zoology, University of Oxford, Tubney, UK
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Laura J Lindholm
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Frederic Laurent
- Bacteriology Department and French National Reference Center for Staphylococci, Hospices Civils de Lyon, University of Lyon, Lyon, France
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Walther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig University Giessen, Giessen, Germany
| | - Christiane Cuny
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | - Wolfgang Witte
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
| | | | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Fernando García-Garrote
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
- Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sara Hæggman
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Andrew S Waller
- Animal Health Trust, Newmarket, UK
- Intervacc AB, Stockholm, Stockholm, Sweden
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bruno Pichon
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - David J Seilly
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Fiona J E Morgan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nazreen F Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jodi A Lindsay
- Institute of Infection and Immunity, St George's, University of London, London, UK
| | | | - Giles F Edwards
- Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK
| | | | - Gavin K Paterson
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Anders R Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
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17
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Borodovich T, Shkoporov AN, Ross RP, Hill C. OUP accepted manuscript. Gastroenterol Rep (Oxf) 2022; 10:goac012. [PMID: 35425613 PMCID: PMC9006064 DOI: 10.1093/gastro/goac012] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/26/2022] Open
Abstract
Horizontal gene transfer (HGT) in the microbiome has profound consequences for human health and disease. The spread of antibiotic resistance genes, virulence, and pathogenicity determinants predominantly occurs by way of HGT. Evidence exists of extensive horizontal transfer in the human gut microbiome. Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another. The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome. Here we review in detail the known mechanisms of phage-mediated HGT, namely specialized and generalized transduction, lateral transduction, gene-transfer agents, and molecular piracy, as well as methods used to detect phage-mediated HGT, and discuss its potential implications for the human gut microbiome.
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Affiliation(s)
- Tatiana Borodovich
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Corresponding author. APC Microbiome Ireland, Biosciences Institute, University College Cork, Room 3.63, College Road, Cork, T12 YT20, Ireland.
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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18
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Ibarra-Chávez R, Hansen MF, Pinilla-Redondo R, Seed KD, Trivedi U. Phage satellites and their emerging applications in biotechnology. FEMS Microbiol Rev 2021; 45:fuab031. [PMID: 34104956 PMCID: PMC8632786 DOI: 10.1093/femsre/fuab031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
The arms race between (bacterio)phages and their hosts is a recognised hot spot for genome evolution. Indeed, phages and their components have historically paved the way for many molecular biology techniques and biotech applications. Further exploration into their complex lifestyles has revealed that phages are often parasitised by distinct types of hyperparasitic mobile genetic elements. These so-called phage satellites exploit phages to ensure their own propagation and horizontal transfer into new bacterial hosts, and their prevalence and peculiar lifestyle has caught the attention of many researchers. Here, we review the parasite-host dynamics of the known phage satellites, their genomic organisation and their hijacking mechanisms. Finally, we discuss how these elements can be repurposed for diverse biotech applications, kindling a new catalogue of exciting tools for microbiology and synthetic biology.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
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19
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Shape shifter: redirection of prolate phage capsid assembly by staphylococcal pathogenicity islands. Nat Commun 2021; 12:6408. [PMID: 34737316 PMCID: PMC8569155 DOI: 10.1038/s41467-021-26759-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus pathogenicity islands (SaPIs) are molecular parasites that hijack helper phages for their transfer. SaPIbov5, the prototypical member of a family of cos type SaPIs, redirects the assembly of ϕ12 helper capsids from prolate to isometric. This size and shape shift is dependent on the SaPIbov5-encoded protein Ccm, a homolog of the ϕ12 capsid protein (CP). Using cryo-electron microscopy, we have determined structures of prolate ϕ12 procapsids and isometric SaPIbov5 procapsids. ϕ12 procapsids have icosahedral end caps with Tend = 4 architecture and a Tmid = 14 cylindrical midsection, whereas SaPIbov5 procapsids have T = 4 icosahedral architecture. We built atomic models for CP and Ccm, and show that Ccm occupies the pentameric capsomers in the isometric SaPIbov5 procapsids, suggesting that preferential incorporation of Ccm pentamers prevents the cylindrical midsection from forming. Our results highlight that pirate elements have evolved diverse mechanisms to suppress phage multiplication, including the acquisition of phage capsid protein homologs. Phage-inducible chromosomal islands (PICIs) are a group of mobile genetic elements that hijack the replication and assembly machinery of helper bacteriophages. Here the authors describe a mechanism by which a group of PICIs from Staphylococcus aureus re-direct the assembly pathway of their helpers using a capsid protein homolog.
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20
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Pickering AC, Yebra G, Gong X, Goncheva MI, Wee BA, MacFadyen AC, Muehlbauer LF, Alves J, Cartwright RA, Paterson GK, Fitzgerald JR. Evolutionary and Functional Analysis of Coagulase Positivity among the Staphylococci. mSphere 2021; 6:e0038121. [PMID: 34346700 PMCID: PMC8386474 DOI: 10.1128/msphere.00381-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/30/2021] [Indexed: 11/20/2022] Open
Abstract
The bacterial genus Staphylococcus comprises a large group of pathogenic and nonpathogenic species associated with an array of host species. Staphylococci are differentiated into coagulase-positive or coagulase-negative groups based on the capacity to promote clotting of plasma, a phenotype historically associated with the ability to cause disease. However, the genetic basis of this important diagnostic and pathogenic trait across the genus has not been examined to date. Here, we selected 54 representative staphylococcal species and subspecies to examine coagulation of plasma derived from six representative host species. In total, 13 staphylococcal species mediated coagulation of plasma from at least one host species including one previously identified as coagulase negative (Staphylococcus condimenti). Comparative genomic analysis revealed that coagulase activity correlated with the presence of a gene (vwb) encoding the von Willebrand binding protein (vWbp) whereas only the Staphylococcus aureus complex contained a gene encoding staphylocoagulase (Coa), the classical mediator of coagulation. Importantly, S. aureus retained vwb-dependent coagulase activity in an S. aureus strain deleted for coa whereas deletion of vwb in Staphylococcus pseudintermedius resulted in loss of coagulase activity. Whole-genome-based phylogenetic reconstruction of the Staphylococcus genus revealed that the vwb gene has been acquired on at least four different occasions during the evolution of the Staphylococcus genus followed by allelic diversification via mutation and recombination. Allelic variants of vWbp from selected coagulase-positive staphylococci mediated coagulation in a host-dependent manner indicative of host-adaptive evolution. Taken together, we have determined the genetic and evolutionary basis of staphylococcal coagulation, revealing vWbp to be its archetypal determinant. IMPORTANCE The ability of some species of staphylococci to promote coagulation of plasma is a key pathogenic and diagnostic trait. Here, we provide a comprehensive analysis of the coagulase positivity of the staphylococci and its evolutionary genetic basis. We demonstrate that the von Willebrand binding protein rather than staphylocoagulase is the archetypal coagulation factor of the staphylococci and that the vwb gene has been acquired several times independently during the evolution of the staphylococci. Subsequently, vwb has undergone adaptive diversification to facilitate host-specific functionality. Our findings provide important insights into the evolution of pathogenicity among the staphylococci and the genetic basis for a defining diagnostic phenotype.
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Affiliation(s)
- Amy C. Pickering
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Gonzalo Yebra
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Xiangyu Gong
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Mariya I. Goncheva
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Bryan A. Wee
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Alison C. MacFadyen
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Lukas F. Muehlbauer
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Joana Alves
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Robyn A. Cartwright
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Gavin K. Paterson
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - J. Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
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21
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Abstract
Staphylococcus aureus can target a variety of tissues, causing life-threatening infections. The basis for this diversity stems from the microorganism’s ability to spread in the vascular system throughout the body. To survive in blood, S. aureus coats itself with a fibrinogen (Fg)/fibrin shield. The protective shield is assembled by the coordinated actions of a number of Fg-binding bacterial proteins that manipulate the host’s blood coagulation system. Several of the Fg binders appear redundant, sharing similar functional motifs. This observation led us to screen for the presence of novel proteins with significant amino acid identities to von Willebrand factor-binding protein (vWbp), a key component in the shield assembly machinery. One identified protein showed significant sequence identity with the C-terminal region of vWbp, and we consequently named it vWbp homologous protein (vhp). The vhp gene lies within a cluster of genes that encode other virulence factors in S. aureus. Although each isolate only contains one copy of the vhp gene, S. aureus has at least three distinct alleles, vhpA, B, and C, that are present in the core genome. All three vhp isoforms bind Fg with high affinity, targeting a site located in the D fragment of Fg. We further identified an ∼79 amino acid-long, conserved segment within the C-terminal region of vWbp that shares high sequence identities (54 to 67%) with the vhps and binds soluble Fg with high affinity. Further analysis of this conserved motif and the intact vhps revealed intriguing differences in the Fg binding behavior, perhaps suggesting that these proteins have similar but discrete functions in the shield assembly.
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22
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Ji X, Krüger H, Tao J, Wang Y, Feßler AT, Bai R, Wang S, Dong Y, Shen J, Wang Y, Schwarz S, Wu C. Comparative analysis of genomic characteristics, fitness and virulence of MRSA ST398 and ST9 isolated from China and Germany. Emerg Microbes Infect 2021; 10:1481-1494. [PMID: 34210245 PMCID: PMC8300935 DOI: 10.1080/22221751.2021.1951125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) of sequence types ST398 and ST9 are dominant lineages among livestock in Europe and Asia, respectively. Although both STs were commonly found as colonizers of the skin and the mucosal membranes, MRSA ST398, rather than MRSA ST9, has been reported to cause infections in humans and animals. Herein, we comparatively analyzed the genomic characteristics, fitness and virulence of MRSA ST398 and ST9 isolated from pigs in both China (CHN) and Germany (GER) to explore the factors that lead to differences in their epidemics and pathogenicity. We observed that the CHN-MRSA ST9 and the GER-MRSA ST9 have evolved independently, whereas the CHN-MRSA ST398 and GER-MRSA ST398 had close evolutionary relationships. Resistance to antimicrobial agents commonly used in livestock, the enhanced ability of biofilm formation, and the resistance to desiccation contribute to the success of the dominant clones of CHN-MRSA ST9 and GER-MRSA ST398, and the vwbνSaα gene on the genomic island might in part contribute to their colonization fitness in pigs. All MRSA ST398 strains revealed more diverse genome structures, higher tolerance to acids and high osmotic pressure, and greater competitive fitness in co-culture experiments. Notably, we identified and characterized a novel hysAνSaβ gene, which was located on the genomic island νSaβ of MRSA ST398 but was absent in MRSA ST9. The enhanced pathogenicity of the MRSA ST398 strains due to hysAνSaβ might in part explain why MRSA ST398 strains are more likely to cause infections.
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Affiliation(s)
- Xing Ji
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Henrike Krüger
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jin Tao
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yaxin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Andrea T Feßler
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Rina Bai
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yanjun Dong
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Stefan Schwarz
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
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Molecular Evolution and Adaptation of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) Sequence Type 9. mSystems 2021; 6:e0049221. [PMID: 34156294 PMCID: PMC8269235 DOI: 10.1128/msystems.00492-21] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 9 (ST9) has emerged and disseminated in Asia. It is associated with colonization or infection in both humans and animal hosts; however, the genetic factors underpinning its adaptation to animal and human population remain to be determined. Here, we conducted a genomic analysis of 191 ST9 S. aureus genomes collected from 12 different countries, including 174 genomes retrieved from public databases and 17 sequenced in this study. In silico spa typing, staphylococcal cassette chromosome mec (SCCmec) typing, and antimicrobial resistance and virulence gene mining were conducted, and the temporal phylogenetic signal was assessed by Bayesian inference. Our results point toward a human methicillin-susceptible S. aureus (MSSA) origin of ST9 that evolved approximately 2 centuries ago. Three major genetic events occurred during ST9 host shift from human to animals: the loss of the immune evasion cluster genes (scn, chp, and sak), which were reported to contribute to virulence in human infections, the acquisition of the SaPIbov4-like element-encoding vwb gene, which is an animal-specific virulence factor responsible for the clotting of animal plasma, and the acquisition of antibiotic resistance genes, including SCCmec, quinolone resistance-determining region (QRDR) mutations, and a multidrug resistance genetic element (MDRST9). Evidence of direct transmission of animal-adapted strains to human hosts also suggest that transmission could potentially reshape the resistance and virulence genetic pool in these isolates. The rapid clonal expansion of MDR ST9 strains in mainland China and Taiwan highlights the increasing need for effective surveillance of antibiotic consumption in animal husbandry to control antimicrobial resistance spread. IMPORTANCEStaphylococcus aureus sequence type 9 (ST9) is the main LA-MRSA clone spreading in the Asian continent. It can colonize and cause mild to severe infections both in animal and humans. Previous work described its genotypic characteristics; however, the molecular history of global spread of ST9 strains remains largely unclear. We conducted a detailed analysis of genomic evolution of global ST9 strains and identified key genetic changes associated with its adaptation to specific hosts. Our results suggest that the ST9 clone originated from human-adapted strains, which lost genes related to the evasion of the immune system. The introduction of ST9 strains in animal populations was aligned with the acquisition of animal-specific virulent factors and mobile elements harboring multiple antimicrobial resistance genes, especially in isolates from mainland China and Taiwan.
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Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen. PLoS Pathog 2021; 17:e1009606. [PMID: 34015034 PMCID: PMC8171923 DOI: 10.1371/journal.ppat.1009606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/02/2021] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel. The emergence of new pathogens is a major threat to public and veterinary health. Some bacteria such as Staphylococcus aureus, have the capacity to infect many different host species including humans and livestock while others such as the closely-related S. aureus subsp. anaerobius, associated with a single type of pathology called Morel’s disease in small ruminants, are highly niche-restricted. However, our understanding of the genetic basis for such differences in bacterial host-tropism is very limited. Here, we discovered that S. aureus subsp. anaerobius evolved from an S. aureus ancestor and underwent an array of extensive changes to its genome that accompanied the transition to its current restricted lifestyle. We observed genome decay involving loss of function of hundreds of genes, large intra-chromosomal rearrangements affecting most of the genome, acquisition of a pathogenicity island, and expansion of large numbers of insertion sequences that are inserted at intergenic sites around the genome. Importantly, we found that IS elements affect the expression of neighbouring genes in different ways including a novel mechanism of IS-enabled disruption of ancestral gene repression. Taken together, we provide a remarkable example of radical genomic changes associated with evolutionary transition from a multi-host to highly restricted host ecology.
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25
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Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands. mSphere 2021; 6:6/3/e00223-21. [PMID: 33980677 PMCID: PMC8125051 DOI: 10.1128/msphere.00223-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. Staphylococcus epidermidis is a leading opportunistic pathogen causing nosocomial infections that is notable for its ability to form a biofilm and for its high rates of antibiotic resistance. It serves as a reservoir of multiple antimicrobial resistance genes that spread among the staphylococcal population by horizontal gene transfer such as transduction. While phage-mediated transduction is well studied in Staphylococcus aureus, S. epidermidis transducing phages have not been described in detail yet. Here, we report the characteristics of four phages, 27, 48, 456, and 459, previously used for S. epidermidis phage typing, and the newly isolated phage E72, from a clinical S. epidermidis strain. The phages, classified in the family Siphoviridae and genus Phietavirus, exhibited an S. epidermidis-specific host range, and together they infected 49% of the 35 strains tested. A whole-genome comparison revealed evolutionary relatedness to transducing S. aureus phietaviruses. In accordance with this, all the tested phages were capable of transduction with high frequencies up to 10−4 among S. epidermidis strains from different clonal complexes. Plasmids with sizes from 4 to 19 kb encoding resistance to streptomycin, tetracycline, and chloramphenicol were transferred. We provide here the first evidence of a phage-inducible chromosomal island transfer in S. epidermidis. Similarly to S. aureus pathogenicity islands, the transfer was accompanied by phage capsid remodeling; however, the interfering protein encoded by the island was distinct. Our findings underline the role of S. epidermidis temperate phages in the evolution of S. epidermidis strains by horizontal gene transfer, which can also be utilized for S. epidermidis genetic studies. IMPORTANCE Multidrug-resistant strains of S. epidermidis emerge in both nosocomial and livestock environments as the most important pathogens among coagulase-negative staphylococcal species. The study of transduction by phages is essential to understanding how virulence and antimicrobial resistance genes spread in originally commensal bacterial populations. In this work, we provide a detailed description of transducing S. epidermidis phages. The high transduction frequencies of antimicrobial resistance plasmids and the first evidence of chromosomal island transfer emphasize the decisive role of S. epidermidis phages in attaining a higher pathogenic potential of host strains. To date, such importance has been attributed only to S. aureus phages, not to those of coagulase-negative staphylococci. This study also proved that the described transducing bacteriophages represent valuable genetic modification tools in S. epidermidis strains where other methods for gene transfer fail.
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Etter D, Jenni C, Tasara T, Johler S. Mild Lactic Acid Stress Causes Strain-Dependent Reduction in SEC Protein Levels. Microorganisms 2021; 9:1014. [PMID: 34066749 PMCID: PMC8151770 DOI: 10.3390/microorganisms9051014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Staphylococcal enterotoxin C (SEC) is a major cause of staphylococcal food poisoning in humans and plays a role in bovine mastitis. Staphylococcus aureus (S. aureus) benefits from a competitive growth advantage under stress conditions encountered in foods such as a low pH. Therefore, understanding the role of stressors such as lactic acid on SEC production is of pivotal relevance to food safety. However, stress-dependent cues and their effects on enterotoxin expression are still poorly understood. In this study, we used human and animal strains harboring different SEC variants in order to evaluate the influence of mild lactic acid stress (pH 6.0) on SEC expression both on transcriptional and translational level. Although only a modest decrease in sec mRNA levels was observed under lactic acid stress, protein levels showed a significant decrease in SEC levels for some strains. These findings indicate that post-transcriptional modifications can act in SEC expression under lactic acid stress.
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Affiliation(s)
- Danai Etter
- Institute for Food Safety and Hygiene, University of Zurich, 8057 Zurich, Switzerland; (D.E.); (T.T.)
- Laboratory of Food Microbiology, Institute for Food, Nutrition and Health (IFNH), ETH Zurich, 8092 Zurich, Switzerland;
| | - Céline Jenni
- Laboratory of Food Microbiology, Institute for Food, Nutrition and Health (IFNH), ETH Zurich, 8092 Zurich, Switzerland;
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, University of Zurich, 8057 Zurich, Switzerland; (D.E.); (T.T.)
| | - Sophia Johler
- Institute for Food Safety and Hygiene, University of Zurich, 8057 Zurich, Switzerland; (D.E.); (T.T.)
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27
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Gómez P, Ruiz-Ripa L, Fernández-Fernández R, Gharsa H, Ben Slama K, Höfle U, Zarazaga M, Holmes MA, Torres C. Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins. Front Microbiol 2021; 12:655994. [PMID: 33841383 PMCID: PMC8027229 DOI: 10.3389/fmicb.2021.655994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/03/2021] [Indexed: 02/02/2023] Open
Abstract
Most methicillin resistant Staphylococcus aureus (MRSA) isolates harboring mecC gene belong to clonal complex CC130. This lineage has traditionally been regarded as animal-associated as it lacks the human specific immune evasion cluster (IEC), and has been recovered from a broad range of animal hosts. Nevertheless, sporadic mecC-MRSA human infections have been reported, with evidence of zoonotic transmission in some cases. The objective of this study was to investigate the whole-genome sequences of 18 S. aureus CC130 isolates [13 methicillin-resistant (mecC-MRSA) and five methicillin-susceptible (MSSA)] from different sequences types, obtained from a variety of host species and origins (human, livestock, wild birds and mammals, and water), and from different geographic locations, in order to identify characteristic markers and genomic features. Antibiotic resistance genes found among MRSA-CC130 were those associated with the SSCmecXI element. Most MRSA-CC130 strains carried a similar virulence gene profile. Additionally, six MRSA-CC130 possessed scn-sak and one MSSA-ST130 had lukMF'. The MSSA-ST700 strains were most divergent in their resistance and virulence genes. The pan-genome analysis showed that 29 genes were present solely in MRSA-CC130 (associated with SCCmecXI) and 21 among MSSA-CC130 isolates (associated with phages). The SCCmecXI, PBP3, GdpP, and AcrB were identical at the amino acid level in all strains, but some differences were found in PBP1, PBP2, PBP4, and YjbH proteins. An examination of the host markers showed that the 3' region of the bacteriophage φ3 was nearly identical to the reference sequence. Truncated hlb gene was also found in scn-negative strains (two of them carrying sak-type gene). The dtlB gene of wild rabbit isolates included novel mutations. The vwbp gene was found in the three MSSA-ST700 strains from small ruminants and in one MSSA-ST130 from a red deer; these strains also carried a scn-type gene, different from the human and equine variants. Finally, a phylogenetic analysis showed that the three MSSA-ST700 strains and the two MSSA-ST130 strains cluster separately from the remaining MRSA-CC130 strains with the etD2 gene as marker for the main lineage. The presence of the human IEC cluster in some mecC-MRSA-CC130 strains suggests that these isolates may have had a human origin.
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Affiliation(s)
- Paula Gómez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Laura Ruiz-Ripa
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Ursula Höfle
- Health and Biotechnology SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
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Park S, Ronholm J. Staphylococcus aureus in Agriculture: Lessons in Evolution from a Multispecies Pathogen. Clin Microbiol Rev 2021; 34:e00182-20. [PMID: 33568553 PMCID: PMC7950364 DOI: 10.1128/cmr.00182-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is a formidable bacterial pathogen that is responsible for infections in humans and various species of wild, companion, and agricultural animals. The ability of S. aureus to move between humans and livestock is due to specific characteristics of this bacterium as well as modern agricultural practices. Pathoadaptive clonal lineages of S. aureus have emerged and caused significant economic losses in the agricultural sector. While humans appear to be a primary reservoir for S. aureus, the continued expansion of the livestock industry, globalization, and ubiquitous use of antibiotics has increased the dissemination of pathoadaptive S. aureus in this environment. This review comprehensively summarizes the available literature on the epidemiology, pathophysiology, genomics, antibiotic resistance (ABR), and clinical manifestations of S. aureus infections in domesticated livestock. The availability of S. aureus whole-genome sequence data has provided insight into the mechanisms of host adaptation and host specificity. Several lineages of S. aureus are specifically adapted to a narrow host range on a short evolutionary time scale. However, on a longer evolutionary time scale, host-specific S. aureus has jumped the species barrier between livestock and humans in both directions several times. S. aureus illustrates how close contact between humans and animals in high-density environments can drive evolution. The use of antibiotics in agriculture also drives the emergence of antibiotic-resistant strains, making the possible emergence of human-adapted ABR strains from agricultural practices concerning. Addressing the concerns of ABR S. aureus, without negatively affecting agricultural productivity, is a challenging priority.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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29
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Lee GY, Seong HJ, Sul WJ, Yang SJ. Genomic Information on Linezolid-Resistant Sequence-Type 398 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolated from a Pig. Foodborne Pathog Dis 2021; 18:378-387. [PMID: 33656917 DOI: 10.1089/fpd.2020.2882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The frequent occurrence of sequence-type 398 (ST398) livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in pigs has become a major public health concern owing to the increased zoonotic potential of the pathogen. Recently, a novel oxazolidinone resistance gene, chloramphenicol-florfenicol resistant (cfr), conferring multiresistance phenotypes to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A (PhLOPSA), has been found among ST398 LA-MRSA strains isolated from pigs. In this study, we report the first in silico genome analysis of a linezolid-resistant ST398 LA-MRSA strain, designated PJFA-521M, recovered from a pig in Korea. Genomic analyses revealed that the presence of the cfr gene was responsible for the observed linezolid resistance in the PJFA-521M strain. Moreover, newer antimicrobial resistance genes, such as the dfrG, aadE, spw, lsa(E), lnu(B), and fexA genes, were found in the PJFA-521M strain. In addition to the genetic elements for antimicrobial resistance, the carriage of various virulence genes for adherence, invasion, and immunomodulation was identified in the genome, especially within several mobile genetic elements (MGEs). The presence of multiple antimicrobial resistance genes and virulence genes on MGEs in the genome of a linezolid-resistant ST398 LA-MRSA should raise awareness regarding the use of other antimicrobial agents in pig farms and may also provide selective pressure for the prevalence of the cfr gene and the associated multidrug-resistant phenotype.
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Affiliation(s)
- Gi Yong Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Korea
| | - Soo-Jin Yang
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Korea
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30
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Chueahiran S, Yindee J, Boonkham P, Suanpairintr N, Chanchaithong P. Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 as a Major MRSA Lineage in Dogs and Cats in Thailand. Antibiotics (Basel) 2021; 10:antibiotics10030243. [PMID: 33671008 PMCID: PMC7997496 DOI: 10.3390/antibiotics10030243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to present molecular and antimicrobial resistance characteristics of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC) 398 isolated from diseased dogs and cats in Thailand. A total of 20 MRSA isolates of 134 Staphylococcus aureus isolated from canine and feline clinical samples during 2017-2020 were CC398, consisting of sequence type (ST) 398 (18 isolates), ST5926 (1 isolate), and ST6563 (1 isolate) by multilocus sequence typing. spa t034 and staphylococcal cassette chromosome mec (SCCmec) V were predominantly associated with ST398. Intraclonal differentiation was present by additional spa (t1255, t4653), non-detectable spa, composite SCCmec with a hybrid of ccrA1B1+ccrC and class A mec complex, and DNA fingerprints by pulsed-field gel electrophoresis. The isolates essentially carried antimicrobial resistance genes, mediating multiple resistance to β-lactams (mecA, blaZ), tetracyclines [tet(M)], aminoglycosides [aac(6')-Ie-aph(2')-Ia], and trimethoprim (dfr). Livestock-associated MRSA ST398 resistance genes including lnu(B), lsa(E), spw, fexA, and tet(L) were heterogeneously found and lost in subpopulation, with the absence or presence of additional erm(A), erm(B), and ileS2 genes that corresponded to resistance phenotypes. As only a single CC398 was detected with the presence of intraclonal variation, CC398 seems to be the successful MRSA clone colonizing in small animals as a pet-associated MRSA in Thailand.
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Affiliation(s)
- Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.C.); (J.Y.)
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.C.); (J.Y.)
| | - Pongthai Boonkham
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Nipattra Suanpairintr
- Department of Pharmacology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.C.); (J.Y.)
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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Lienen T, Schnitt A, Hammerl JA, Maurischat S, Tenhagen BA. Genomic Distinctions of LA-MRSA ST398 on Dairy Farms From Different German Federal States With a Low Risk of Severe Human Infections. Front Microbiol 2021; 11:575321. [PMID: 33488532 PMCID: PMC7820121 DOI: 10.3389/fmicb.2020.575321] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) have been found on German dairy farms and may be the cause of difficult-to-treat bovine mastitis. Considering the one health approach, MRSA might be transmitted from animals to humans raising the risk for severe infections. On 17 German dairy farms with a history of MRSA detection, MRSA strains were isolated from quarter milk, bulk tank milk, and swab samples of calves, heifers, pigs, and the environment. A selection of 33 isolates was analyzed using whole-genome sequencing and antimicrobial resistance testing. All detected MRSA strains were attributed to the livestock-associated sequence type 398. Methicillin-resistance was associated with the mecA gene in the staphylococcal cassette chromosome (SCC)mec types IVa (7/33) or V (26/33). The MRSA strains across the German federal states showed large allelic differences indicating independent development and distribution. On one farm, a clonal MRSA isolate was widely spread among different animals and the milking equipment. Moreover, MRSA transmission between two dairy farms in one federal state seems to be likely. In depth studies indicated that the resistance gene prediction and phenotypic resistance are in good agreement. Twenty eight strains were determined to exhibit a non-wildtype phenotype (resistant) against up to seven antimicrobial substances with an overall resistance to β-lactams and tetracycline. Ten different phenotypic antimicrobial resistance patterns were found among the MRSA strains. The strains harbored a wide virulence gene repertoire, of which some of them are related to bovine mastitis. However, the isolates lacked typical human infection associated factors such as the immune evasion cluster genes, staphylococcal enterotoxin genes, or Panton-Valentine leukocidin genes leading to the assumption for a low risk for severe human infections and foodborne diseases.
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Affiliation(s)
- Tobias Lienen
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Arne Schnitt
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens Andre Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sven Maurischat
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Genomic analysis of European bovine Staphylococcus aureus from clinical versus subclinical mastitis. Sci Rep 2020; 10:18172. [PMID: 33097797 PMCID: PMC7584570 DOI: 10.1038/s41598-020-75179-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Intramammary infections (IMI) with Staphylococcus aureus are a common cause of bovine mastitis and can result in both clinical (CM) or subclinical mastitis (SCM). Although bacterial isolates of S. aureus differ in their virulence potential it is largely unclear which bacterial virulence factors are responsible for increased clinical severity. We performed a genome wide association study and used a generalized linear mixed model to investigate the correlation between gene carriage, lineage and clinical outcome of IMI in a collection of S. aureus isolates from cattle with CM (n = 125) and SCM (n = 151) from 11 European countries. An additional aim was to describe the genetic variation of bovine S. aureus in Europa. The dominant lineages in our collection were clonal complex (CC) 151 (81/276, 29.3%), CC97 (54/276, 19.6%), CC479 (32/276, 11.6%) and CC398 (19/276, 6.9%). Virulence and antimicrobial resistance (AMR) gene carriage was highly associated with CC. Among a selection of nine virulence and AMR genes, CC151, CC479 and CC133 carried more virulence genes than other CCs, and CC398 was associated with AMR gene carriage. Whereas CC151, CC97 were widespread in Europe, CC479, CC398 and CC8 were only found in specific countries. Compared to CC151, CC479 was associated with CM rather than SCM (OR 3.62; 95% CI 1.38-9.50) and the other CCs were not. Multiple genes were associated with CM, but due to the clustering within CC of carriage of these genes, it was not possible to differentiate between the effect of gene carriage and CC on clinical outcome of IMI. Nevertheless, this study demonstrates that characterization of S. aureus CC and virulence genes helps to predict the likelihood of the occurrence of CM following S. aureus IMI and highlights the potential benefit of diagnostics tools to identify S. aureus CC during bovine mastitis.
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Mrochen DM, Fernandes de Oliveira LM, Raafat D, Holtfreter S. Staphylococcus aureus Host Tropism and Its Implications for Murine Infection Models. Int J Mol Sci 2020; 21:E7061. [PMID: 32992784 PMCID: PMC7582387 DOI: 10.3390/ijms21197061] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a pathobiont of humans as well as a multitude of animal species. The high prevalence of multi-resistant and more virulent strains of S. aureus necessitates the development of new prevention and treatment strategies for S. aureus infection. Major advances towards understanding the pathogenesis of S. aureus diseases have been made using conventional mouse models, i.e., by infecting naïve laboratory mice with human-adapted S.aureus strains. However, the failure to transfer certain results obtained in these murine systems to humans highlights the limitations of such models. Indeed, numerous S. aureus vaccine candidates showed promising results in conventional mouse models but failed to offer protection in human clinical trials. These limitations arise not only from the widely discussed physiological differences between mice and humans, but also from the lack of attention that is paid to the specific interactions of S. aureus with its respective host. For instance, animal-derived S. aureus lineages show a high degree of host tropism and carry a repertoire of host-specific virulence and immune evasion factors. Mouse-adapted S.aureus strains, humanized mice, and microbiome-optimized mice are promising approaches to overcome these limitations and could improve transferability of animal experiments to human trials in the future.
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Affiliation(s)
- Daniel M. Mrochen
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Liliane M. Fernandes de Oliveira
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
| | - Dina Raafat
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Silva Holtfreter
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse DZ 7, 17475 Greifswald, Germany; (L.M.F.d.O.); (D.R.); (S.H.)
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Etter D, Schelin J, Schuppler M, Johler S. Staphylococcal Enterotoxin C-An Update on SEC Variants, Their Structure and Properties, and Their Role in Foodborne Intoxications. Toxins (Basel) 2020; 12:E584. [PMID: 32927913 PMCID: PMC7551944 DOI: 10.3390/toxins12090584] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022] Open
Abstract
Staphylococcal enterotoxins are the most common cause of foodborne intoxications (staphylococcal food poisoning) and cause a wide range of diseases. With at least six variants staphylococcal enterotoxin C (SEC) stands out as particularly diverse amongst the 25 known staphylococcal enterotoxins. Some variants present unique and even host-specific features. Here, we review the role of SEC in human and animal health with a particular focus on its role as a causative agent for foodborne intoxications. We highlight structural features unique to SEC and its variants, particularly, the emetic and superantigen activity, as well as the roles of SEC in mastitis and in dairy products. Information about the genetic organization as well as regulatory mechanisms including the accessory gene regulator and food-related stressors are provided.
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Affiliation(s)
- Danai Etter
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland;
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zürich, Switzerland;
| | - Jenny Schelin
- Division of Applied Microbiology, Department of Chemistry, Lund University, 22100 Lund, Sweden;
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zürich, Switzerland;
| | - Sophia Johler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland;
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Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome. Sci Rep 2020; 10:8467. [PMID: 32439871 PMCID: PMC7242376 DOI: 10.1038/s41598-020-64952-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is an important opportunistic pathogen of humans and animals. It produces extracellular vesicles (EVs) that are involved in cellular communication and enable inter-kingdom crosstalk, the delivery of virulence factors and modulation of the host immune response. The protein content of EVs determines their biological functions. Clarifying which proteins are selected, and how, is of crucial value to understanding the role of EVs in pathogenesis and the development of molecular delivery systems. Here, we postulated that S. aureus EVs share a common proteome containing components involved in cargo sorting. The EV proteomes of five S. aureus strains originating from human, bovine, and ovine hosts were characterised. The clustering of EV proteomes reflected the diversity of the producing strains. A total of 253 proteins were identified, 119 of which composed a core EV proteome with functions in bacterial survival, pathogenesis, and putatively in EV biology. We also identified features in the sequences of EV proteins and the corresponding genes that could account for their packaging into EVs. Our findings corroborate the hypothesis of a selective sorting of proteins into EVs and offer new perspectives concerning the roles of EVs in S. aureus pathogenesis in specific host niches.
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Molecular Epidemiology of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus in Wild, Captive and Laboratory Rats: Effect of Habitat on the Nasal S. aureus Population. Toxins (Basel) 2020; 12:toxins12020080. [PMID: 31991690 PMCID: PMC7076793 DOI: 10.3390/toxins12020080] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/10/2020] [Accepted: 01/20/2020] [Indexed: 11/16/2022] Open
Abstract
Rats are a reservoir of human- and livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). However, the composition of the natural S. aureus population in wild and laboratory rats is largely unknown. Here, 144 nasal S. aureus isolates from free-living wild rats, captive wild rats and laboratory rats were genotyped and profiled for antibiotic resistances and human-specific virulence genes. The nasal S. aureus carriage rate was higher among wild rats (23.4%) than laboratory rats (12.3%). Free-living wild rats were primarily colonized with isolates of clonal complex (CC) 49 and CC130 and maintained these strains even in husbandry. Moreover, upon livestock contact, CC398 isolates were acquired. In contrast, laboratory rats were colonized with many different S. aureus lineages—many of which are commonly found in humans. Five captive wild rats were colonized with CC398-MRSA. Moreover, a single CC30-MRSA and two CC130-MRSA were detected in free-living or captive wild rats. Rat-derived S. aureus isolates rarely harbored the phage-carried immune evasion gene cluster or superantigen genes, suggesting long-term adaptation to their host. Taken together, our study revealed a natural S. aureus population in wild rats, as well as a colonization pressure on wild and laboratory rats by exposure to livestock- and human-associated S. aureus, respectively.
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Matuszewska M, Murray GGR, Harrison EM, Holmes MA, Weinert LA. The Evolutionary Genomics of Host Specificity in Staphylococcus aureus. Trends Microbiol 2020; 28:465-477. [PMID: 31948727 DOI: 10.1016/j.tim.2019.12.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/18/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Ewan M Harrison
- Wellcome Sanger Institute, University of Cambridge, Cambridge, CB10 1SA, UK; Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
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38
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Muthukrishnan G, Masters EA, Daiss JL, Schwarz EM. Mechanisms of Immune Evasion and Bone Tissue Colonization That Make Staphylococcus aureus the Primary Pathogen in Osteomyelitis. Curr Osteoporos Rep 2019; 17:395-404. [PMID: 31721069 PMCID: PMC7344867 DOI: 10.1007/s11914-019-00548-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Staphylococcus aureus is the primary pathogen responsible for osteomyelitis, which remains a major healthcare burden. To understand its dominance, here we review the unique pathogenic mechanisms utilized by S. aureus that enable it to cause incurable osteomyelitis. RECENT FINDINGS Using an arsenal of toxins and virulence proteins, S. aureus kills and usurps immune cells during infection, to produce non-neutralizing pathogenic antibodies that thwart adaptive immunity. S. aureus also has specific mechanisms for distinct biofilm formation on implants, necrotic bone tissue, bone marrow, and within the osteocyte lacuno-canicular networks (OLCN) of live bone. In vitro studies have also demonstrated potential for intracellular colonization of osteocytes, osteoblasts, and osteoclasts. S. aureus has evolved a multitude of virulence mechanisms to achieve life-long infection of the bone, most notably colonization of OLCN. Targeting S. aureus proteins involved in these pathways could provide new targets for antibiotics and immunotherapies.
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Affiliation(s)
- Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
| | - Elysia A Masters
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA
| | - John L Daiss
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA
| | - Edward M Schwarz
- Center for Musculoskeletal Research, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA.
- Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA.
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39
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Hansen JE, Ronco T, Stegger M, Sieber RN, Fertner ME, Martin HL, Farre M, Toft N, Larsen AR, Pedersen K. LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production. Front Microbiol 2019; 10:2733. [PMID: 31849885 PMCID: PMC6887863 DOI: 10.3389/fmicb.2019.02733] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/11/2019] [Indexed: 01/19/2023] Open
Abstract
The possible spillover from pigs into other production animals incites concern for unresolved reservoirs of human exposure. The present investigation was therefore initiated, to elucidate if Danish veal and dairy farms constitute a reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 and to potentially identify the source of introduction. We collected nasal swab samples from 17 Danish veal farms, 2 slaughterhouses, and received bulk tank milk samples from 286 dairy farms. All samples were analyzed by culturing and screening on MRSA selective plates and presumed MRSA was verified by MALDI-TOF and PCR. MRSA isolates were subjected to spa typing and whole-genome sequencing. LA-MRSA was found on two veal farms in one and three calves, respectively, with subsequent follow-up samples found negative. Eight of 286 dairy farms (2.8%) were found LA-MRSA positive and follow-up samples, from five farms showed intermittent detection of LA-MRSA. The spa types, t034 and t011, were the most common while a single isolate from a dairy farm belonged to spa type t843 associated to mecC-MRSA CC130 and is the first report of mecC-MRSA in the Danish dairy production. A phylogenetic analysis showed that some of the isolates grouped within or close to the dominant Danish pig clusters, suggesting spillover into cattle farms. Other isolates clustered outside the dominant pig clusters suggesting that other routes of introduction cannot be excluded. Results of the investigation indicated a contamination of veal farms while some dairy farms seemed to be a permanent reservoir. Thus, Danish cattle represent a low prevalence reservoir of LA-MRSA CC398, which at present, is not of major human health concern.
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Affiliation(s)
- Julie E Hansen
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Troels Ronco
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mette E Fertner
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Nils Toft
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Anders R Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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Imanishi I, Nicolas A, Caetano ACB, Castro TLDP, Tartaglia NR, Mariutti R, Guédon E, Even S, Berkova N, Arni RK, Seyffert N, Azevedo V, Nishifuji K, Le Loir Y. Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity. Sci Rep 2019; 9:16336. [PMID: 31704997 PMCID: PMC6841975 DOI: 10.1038/s41598-019-52777-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/21/2019] [Indexed: 11/24/2022] Open
Abstract
Exfoliative toxins (ETs) are secreted virulence factors produced by staphylococci. These serine proteases specifically cleave desmoglein 1 (Dsg1) in mammals and are key elements in staphylococcal skin infections. We recently identified a new et gene in S. aureus O46, a strain isolated from ovine mastitis. In the present study, we characterized the new et gene at a genetic level and the enzymatic activity of the deduced protein. The S. aureus O46 genome was re-assembled, annotated and compared with other publicly available S. aureus genomes. The deduced amino acid sequence of the new et gene shared 40%, 53% and 59% sequence identity to those of ETA, ETB and ETD, respectively. The new et gene shared the same genetic vicinity and was similar in other S. aureus strains bearing this gene. The recombinant enzyme of the new et gene caused skin exfoliation in vivo in neonatal mice. The new et-gene was thus named ete, encoding a new type (type E) of exfoliative toxin. We showed that ETE degraded the extracellular segments of Dsg1 in murine, ovine and caprine epidermis, as well as in ovine teat canal epithelia, but not that in bovine epidermis. We further showed that it directly hydrolyzed human and swine Dsg1 as well as murine Dsg1α and Dsg1β, but not canine Dsg1 or murine Dsg1γ. Molecular modeling revealed a correlation between the preferred orientation of ETE docking on its Dsg1 cleavage site and species-specific cleavage activity, suggesting that the docking step preceding cleavage accounts for the ETE species-specificity. This new virulence factor may contribute to the bacterial colonization on the stratified epithelia in certain ruminants with mastitis.
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Affiliation(s)
- Ichiro Imanishi
- Laboratory of Veterinary Internal Medicine, Division of Animal Life Science, Graduate School, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | | | - Ana-Carolina Barbosa Caetano
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Thiago Luiz de Paula Castro
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil.,Institute of Health Sciences, Federal University of Bahia, Salvador, BA, 40110-100, Brazil
| | - Natayme Rocha Tartaglia
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France.,Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | | | - Eric Guédon
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | - Sergine Even
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | - Nadia Berkova
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France
| | | | - Nubia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil.,Institute of Biology, Federal University of Bahia, Salvador, BA, 40170-115, Brazil
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 270-901, Brazil
| | - Koji Nishifuji
- Laboratory of Veterinary Internal Medicine, Division of Animal Life Science, Graduate School, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Yves Le Loir
- STLO, INRA, Agrocampus Ouest, F-35042, Rennes, France.
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41
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Dokland T. Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements. Viruses 2019; 11:v11111003. [PMID: 31683607 PMCID: PMC6893505 DOI: 10.3390/v11111003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/21/2023] Open
Abstract
Horizontal transfer of mobile genetic elements (MGEs) is a key aspect of the evolution of bacterial pathogens. Transduction by bacteriophages is especially important in this process. Bacteriophages—which assemble a machinery for efficient encapsidation and transfer of genetic material—often transfer MGEs and other chromosomal DNA in a more-or-less nonspecific low-frequency process known as generalized transduction. However, some MGEs have evolved highly specific mechanisms to take advantage of bacteriophages for their own propagation and high-frequency transfer while strongly interfering with phage production—“molecular piracy”. These mechanisms include the ability to sense the presence of a phage entering lytic growth, specific recognition and packaging of MGE genomes into phage capsids, and the redirection of the phage assembly pathway to form capsids with a size more appropriate for the size of the MGE. This review focuses on the process of assembly redirection, which has evolved convergently in many different MGEs from across the bacterial universe. The diverse mechanisms that exist suggest that size redirection is an evolutionarily advantageous strategy for many MGEs.
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Affiliation(s)
- Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35242, USA.
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Haag AF, Fitzgerald JR, Penadés JR. Staphylococcus aureus in Animals. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0060-2019. [PMID: 31124433 PMCID: PMC11257167 DOI: 10.1128/microbiolspec.gpp3-0060-2019] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus aureus is a mammalian commensal and opportunistic pathogen that colonizes niches such as skin, nares and diverse mucosal membranes of about 20-30% of the human population. S. aureus can cause a wide spectrum of diseases in humans and both methicillin-sensitive and methicillin-resistant strains are common causes of nosocomial- and community-acquired infections. Despite the prevalence of literature characterising staphylococcal pathogenesis in humans, S. aureus is a major cause of infection and disease in a plethora of animal hosts leading to a significant impact on public health and agriculture. Infections in animals are deleterious to animal health, and animals can act as a reservoir for staphylococcal transmission to humans.Host-switching events between humans and animals and amongst animals are frequent and have been accentuated with the domestication and/or commercialisation of specific animal species. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements such as phages, pathogenicity islands and plasmids as well as further host-specific mutations allowing it to expand into new host populations.In this chapter, we will be giving an overview of S. aureus in animals, how this bacterial species was, and is, being transferred to new host species and the key elements thought to be involved in its adaptation to new ecological host niches. We will also highlight animal hosts as a reservoir for the development and transfer of antimicrobial resistance determinants.
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Affiliation(s)
- Andreas F Haag
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, G12 8TA, Glasgow, UK
| | | | - José R Penadés
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, G12 8TA, Glasgow, UK
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43
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Novick RP. Pathogenicity Islands and Their Role in Staphylococcal Biology. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0062-2019. [PMID: 31172913 PMCID: PMC11257176 DOI: 10.1128/microbiolspec.gpp3-0062-2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 12/20/2022] Open
Abstract
Pathogenicity islands are members of a vast collection of genomic islands that encode important virulence, antibiotic resistance and other accessory functions and have a critical role in bacterial gene transfer. Staphylococcus aureus is host to a large family of such islands, known as SaPIs, which encode super antigen and other virulence determinants, are mobilized by helper phages and transferred at extremely high frequencies. They benefit their host cells by interfering with phage predation and enhancing horizontal gene transfer. This chapter describes their life cycle, the bases of their phage interference mechanisms, their transfer system and their conversion to antibacterial agents for treatment ofstaphylococcal infections.
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Affiliation(s)
- Richard P Novick
- NYU School of Medicine, Skirball Institute of Biomolecular Medicine and Departments of Medicine and Microbiology, New York, NY 10016
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44
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Tam K, Torres VJ. Staphylococcus aureus Secreted Toxins and Extracellular Enzymes. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0039-2018. [PMID: 30873936 PMCID: PMC6422052 DOI: 10.1128/microbiolspec.gpp3-0039-2018] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus aureus is a formidable pathogen capable of causing infections in different sites of the body in a variety of vertebrate animals, including humans and livestock. A major contribution to the success of S. aureus as a pathogen is the plethora of virulence factors that manipulate the host's innate and adaptive immune responses. Many of these immune modulating virulence factors are secreted toxins, cofactors for activating host zymogens, and exoenzymes. Secreted toxins such as pore-forming toxins and superantigens are highly inflammatory and can cause leukocyte cell death by cytolysis and clonal deletion, respectively. Coagulases and staphylokinases are cofactors that hijack the host's coagulation system. Exoenzymes, including nucleases and proteases, cleave and inactivate various immune defense and surveillance molecules, such as complement factors, antimicrobial peptides, and surface receptors that are important for leukocyte chemotaxis. Additionally, some of these secreted toxins and exoenzymes can cause disruption of endothelial and epithelial barriers through cell lysis and cleavage of junction proteins. A unique feature when examining the repertoire of S. aureus secreted virulence factors is the apparent functional redundancy exhibited by the majority of the toxins and exoenzymes. However, closer examination of each virulence factor revealed that each has unique properties that have important functional consequences. This chapter provides a brief overview of our current understanding of the major secreted virulence factors critical for S. aureus pathogenesis.
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Affiliation(s)
- Kayan Tam
- Department of Microbiology, New York University School of Medicine, Alexandria Center for Life Science, New York, NY 10016
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, Alexandria Center for Life Science, New York, NY 10016
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45
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Buchan KD, Foster SJ, Renshaw SA. Staphylococcus aureus: setting its sights on the human innate immune system. MICROBIOLOGY-SGM 2019; 165:367-385. [PMID: 30625113 DOI: 10.1099/mic.0.000759] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Staphylococcus aureus has colonized humans for at least 10 000 years, and today inhabits roughly a third of the population. In addition, S. aureus is a major pathogen that is responsible for a significant disease burden, ranging in severity from mild skin and soft-tissue infections to life-threatening endocarditis and necrotizing pneumonia, with treatment often hampered by resistance to commonly available antibiotics. Underpinning its versatility as a pathogen is its ability to evade the innate immune system. S. aureus specifically targets innate immunity to establish and sustain infection, utilizing a large repertoire of virulence factors to do so. Using these factors, S. aureus can resist phagosomal killing, impair complement activity, disrupt cytokine signalling and target phagocytes directly using proteolytic enzymes and cytolytic toxins. Although most of these virulence factors are well characterized, their importance during infection is less clear, as many display species-specific activity against humans or against animal hosts, including cows, horses and chickens. Several staphylococcal virulence factors display species specificity for components of the human innate immune system, with as few as two amino acid changes reducing binding affinity by as much as 100-fold. This represents a major issue for studying their roles during infection, which cannot be examined without the use of humanized infection models. This review summarizes the major factors S. aureus uses to impair the innate immune system, and provides an in-depth look into the host specificity of S. aureus and how this problem is being approached.
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Affiliation(s)
- Kyle D Buchan
- 1The Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Simon J Foster
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Stephen A Renshaw
- 1The Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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46
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Magro G, Rebolini M, Beretta D, Piccinini R. Methicillin-resistant Staphylococcus aureus CC22-MRSA-IV as an agent of dairy cow intramammary infections. Vet Microbiol 2018; 227:29-33. [PMID: 30473348 DOI: 10.1016/j.vetmic.2018.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/19/2018] [Accepted: 10/23/2018] [Indexed: 11/30/2022]
Abstract
Methicillin-resistant S. aureus (MRSA) lineages have become major responsible of healthcare- and community-associated infections in human population. Bovine MRSA are sporadically detected in the dairy herd, but its presence enhances the risk of zoonosis. Some lineages are able to lose the specific host tropism, being easily transmitted from animals to humans and vice-versa. The present study aims at clarifying the epidemiology of MRSA intramammary infections in a closed dairy herd, which was running a mastitis control program since years. Quarter milk samples were collected from all lactating cows once a week for 9 weeks and bacteriologically tested. At the end of the follow-up period, also a self-taken nasal swab of the milker was analysed. Three cows (12.5%) were MRSA positive, a fourth showed a transient infection and MRSA was isolated also from the milker's nose. Somatic cell counts of infected quarters fluctuated from 1000 to 1,800,000 cells/mL. The isolates were genotyped using DNA microarrays and identified as the epidemic UK-EMRSA-15 grouping in CC22. All strains carried the genes for β-lactam and macrolide resistance. The milker isolate differed from cow isolates mainly for the absence of the untruncated β-haemolysin and the presence of the immune evasion cluster. The milker had been volunteering in a nursing home since months, thus playing the role of MRSA vector into the herd. Our results showed the adaptive capacity of such MRSA to the bovine host. Therefore, we suggest that CC22-MRSA should be regarded as a potential cause of reverse zoonosis in dairy cattle herds.
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Affiliation(s)
- Giada Magro
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milan, Italy
| | - Marta Rebolini
- Department of Agricultural and Environmental Sciences - Production, Land, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Daniele Beretta
- Allegrini S.p.A, Zootechnics division, Vicolo Salvo D'Acquisto 2, 24050, Grassobbio, Italy
| | - Renata Piccinini
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milan, Italy.
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47
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Walther B, Klein KS, Barton AK, Semmler T, Huber C, Merle R, Tedin K, Mitrach F, Lübke-Becker A, Gehlen H. Equine Methicillin-Resistant Sequence Type 398 Staphylococcus aureus (MRSA) Harbor Mobile Genetic Elements Promoting Host Adaptation. Front Microbiol 2018; 9:2516. [PMID: 30405574 PMCID: PMC6207647 DOI: 10.3389/fmicb.2018.02516] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022] Open
Abstract
Continuing introduction of multi-drug resistant, zoonotic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) in horse clinics challenges the biosafety of employees and animal patients. This study was aimed to determine the occurrence of mobile genetic elements facilitating survival in the early stages of invasive infection in different host species, including humans and horses, in MRSA carried by equine patients admitted to a large horse clinic. A total of 341 equine patients were investigated for carriage of MRSA by hygiene screening directly at hospital admission. MRSA were further investigated by antimicrobial susceptibility testing, whole-genome sequencing and genomic composition, including virulence factors involved in immune evasion and host adaption. From a total of 340 validated specimens from equine nostrils, 3.5% yielded positive results for MRSA. All MRSA were found to be closely related belonging to sequence type (ST) 398_t011 with up to four additional antimicrobial resistances. All MRSA harbored a specific Staphylococcal Pathogenicity Island (SaPIbov5) involved in facilitating survival in ruminant and equine plasma. Moreover, a β-hemolysin (hlb) converting ΦSa3 phage encoding the human-specific Immune Evasion Cluster (IEC) was present in 72% of the isolates. An equid-specific leukotoxin encoded by a further temperate phage (Saeq1) was only rarely detected (22%). Despite the absence of β-hemolysin production for all IEC-positive ST398, a prominent hemolysis zone was demonstrable on sheep blood agar. Thus, IEC might remain undetected among the ST398 lineage, since the presence of IEC is commonly associated with reduction of hemolysis in S. aureus belonging to other genetic backgrounds. Here we describe MRSA-ST398 harboring different mobile genetic elements encoding variants of immune evasion factors and toxins previously shown to contribute to S. aureus invasive diseases in specific host species or ecologic niches. We suggest these combinations contribute to the adaptation of MRSA belonging to ST398 with respect to epidemic spread across different habitats and hosts, and may therefore confer a host “generalist” phenotype.
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Affiliation(s)
- Birgit Walther
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, Berlin, Germany
| | - Katja-Sophia Klein
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Ann-Kristin Barton
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Charlotte Huber
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Roswitha Merle
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Karsten Tedin
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Franziska Mitrach
- Faculty of Environment and Natural Sciences, Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Antina Lübke-Becker
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Heidrun Gehlen
- Equine Clinic, Surgery and Radiology, Freie Universität Berlin, Berlin, Germany
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48
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Trübe P, Hertlein T, Mrochen DM, Schulz D, Jorde I, Krause B, Zeun J, Fischer S, Wolf SA, Walther B, Semmler T, Bröker BM, Ulrich RG, Ohlsen K, Holtfreter S. Bringing together what belongs together: Optimizing murine infection models by using mouse-adapted Staphylococcus aureus strains. Int J Med Microbiol 2018; 309:26-38. [PMID: 30391222 DOI: 10.1016/j.ijmm.2018.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/05/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus (S.) aureus is a leading cause of bacterial infection world-wide, and currently no vaccine is available for humans. Vaccine development relies heavily on clinically relevant infection models. However, the suitability of mice for S. aureus infection models has often been questioned, because experimental infection of mice with human-adapted S. aureus requires very high infection doses. Moreover, mice were not considered to be natural hosts of S. aureus. The latter has been disproven by our recent findings, showing that both laboratory mice, as well as wild small mammals including mice, voles, and shrews, are naturally colonized with S. aureus. Here, we investigated whether mouse-and vole-derived S. aureus strains show an enhanced virulence in mice as compared to the human-adapted strain Newman. Using a step-wise approach based on the bacterial genotype and in vitro assays for host adaptation, we selected the most promising candidates for murine infection models out of a total of 254 S. aureus isolates from laboratory mice as well as wild rodents and shrews. Four strains representing the clonal complexes (CC) 8, 49, and 88 (n = 2) were selected and compared to the human-adapted S. aureus strain Newman (CC8) in murine pneumonia and bacteremia models. Notably, a bank vole-derived CC49 strain, named DIP, was highly virulent in BALB/c mice in pneumonia and bacteremia models, whereas the other murine and vole strains showed virulence similar to or lower than that of Newman. At one tenth of the standard infection dose DIP induced disease severity, bacterial load and host cytokine and chemokine responses in the murine bacteremia model similar to that of Newman. In the pneumonia model, DIP was also more virulent than Newman but the effect was less pronounced. Whole genome sequencing data analysis identified a pore-forming toxin gene, lukF-PV(P83)/lukM, in DIP but not in the other tested S. aureus isolates. To conclude, the mouse-adapted S. aureus strain DIP allows a significant reduction of the inoculation dose in mice and is hence a promising tool to develop clinically more relevant infection models.
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Affiliation(s)
- Patricia Trübe
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology, University of Würzburg, Germany
| | - Daniel M Mrochen
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Daniel Schulz
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Ilka Jorde
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Bettina Krause
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Julia Zeun
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Silver A Wolf
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Barbara M Bröker
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Germany
| | - Silva Holtfreter
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany.
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49
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Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat Ecol Evol 2018; 2:1468-1478. [PMID: 30038246 PMCID: PMC7610605 DOI: 10.1038/s41559-018-0617-0] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/25/2018] [Indexed: 01/15/2023]
Abstract
The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S. aureus host-switching events linked to the emergence of endemic livestock strains, and cows as the main animal reservoir for the emergence of human epidemic clones. Such host-species transitions are associated with horizontal acquisition of genetic elements from host-specific gene pools conferring traits required for survival in the new host-niche. Importantly, genes associated with antimicrobial resistance are unevenly distributed among human and animal hosts, reflecting distinct antibiotic usage practices in medicine and agriculture. In addition to gene acquisition, genetic diversification has occurred in pathways associated with nutrient acquisition, implying metabolic remodelling after a host switch in response to distinct nutrient availability. For example, S. aureus from dairy cattle exhibit enhanced utilization of lactose-a major source of carbohydrate in bovine milk. Overall, our findings highlight the influence of human activities on the multi-host ecology of a major bacterial pathogen, underpinned by horizontal gene transfer and core genome diversification.
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Affiliation(s)
- Emily J Richardson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rodrigo Bacigalupe
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Lycett
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Manouk Vrieling
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital and The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Adebayo Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Hinxton, UK
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | | | - Jukka Corander
- Wellcome Trust Sanger Institute, Hinxton, UK
- Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J Ross Fitzgerald
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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50
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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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