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Wang Y, Zhang P, Wu J, Chen S, Jin Y, Long J, Duan G, Yang H. Transmission of livestock-associated methicillin-resistant Staphylococcus aureus between animals, environment, and humans in the farm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:86521-86539. [PMID: 37418185 DOI: 10.1007/s11356-023-28532-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/28/2023] [Indexed: 07/08/2023]
Abstract
Staphylococcus aureus (S. aureus) is a fearsome bacterial pathogen that can colonize and infect humans and animals. Depending on the different sources, MRSA is classified as hospital-associated methicillin-resistant S. aureus (HA-MRSA), community-associated MRSA (CA-MRSA), and livestock-associated MRSA (LA-MRSA). LA-MRSA is initially associated with livestock, and clonal complexes (CCs) were almost always 398. However, the continued development of animal husbandry, globalization, and the widespread use of antibiotics have increased the spread of LA-MRSA among humans, livestock, and the environment, and other clonal complexes such as CC9, CC5, and CC8 have gradually emerged in various countries. This may be due to frequent host switching between humans and animals, as well as between animals. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements (MGEs) such as phages, pathogenicity islands, and plasmids as well as further host-specific mutations allowing it to expand into new host populations. This review aimed to provide an overview of the transmission characteristics of S. aureus in humans, animals, and farm environments, and also to describe the main prevalent clones of LA-MRSA and the changes in MGEs during host switching.
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Affiliation(s)
- Ying Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Peihua Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Jian Wu
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China.
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Hong S, Kang HJ, Lee HY, Jung HR, Moon JS, Yoon SS, Kim HY, Lee YJ. Prevalence and characteristics of foodborne pathogens from slaughtered pig carcasses in Korea. Front Vet Sci 2023; 10:1158196. [PMID: 37065220 PMCID: PMC10103459 DOI: 10.3389/fvets.2023.1158196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
The introduction of bacteria into slaughterhouses can lead to microbial contamination in carcasses during slaughter, and the initial level of bacteria in carcasses is important because it directly affects spoilage and the shelf life. This study was conducted to investigate the microbiological quality, and the prevalence of foodborne pathogens in 200 carcasses from 20 pig slaughterhouses across Korea. Distribution of microbial counts were significantly higher for aerobic bacteria at 3.01–4.00 log10 CFU/cm2 (42.0%) and 2.01–3.00 log10 CFU/cm2 (28.5%), whereas most of Escherichia coli showed the counts under 1.00 log10 CFU/cm2 (87.0%) (P < 0.05). The most common pathogen isolated from 200 carcasses was Staphylococcus aureus (11.5%), followed by Yersinia enterocolitica (7.0%). In total, 17 S. aureus isolates from four slaughterhouses were divided into six pulsotypes and seven spa types, and showed the same or different types depending on the slaughterhouses. Interestingly, isolates from two slaughterhouses carried only LukED associated with the promotion of bacterial virulence, whereas, isolates from two other slaughterhouses carried one or more toxin genes associated with enterotoxins including sen. In total, 14 Y. enterocolitica isolates from six slaughterhouses were divided into nine pulsotypes, 13 isolates belonging to biotype 1A or 2 carried only ystB, whereas one isolate belonging to bio-serotype 4/O:3 carried both ail and ystA. This is the first study to investigate microbial quality and the prevalence of foodborne pathogens in carcasses from slaughterhouses nationally, and the findings support the need for ongoing slaughterhouse monitoring to improve the microbiological safety of pig carcasses.
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Affiliation(s)
- Serim Hong
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Hye Jeong Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hye-Young Lee
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hye-Ri Jung
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Jin-San Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Ha-Young Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
- *Correspondence: Ha-Young Kim
| | - Young Ju Lee
- College of Veterinary Medicine and Zoonoses Research Institute, Kyungpook National University, Daegu, Republic of Korea
- Young Ju Lee
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Panwar S, Kumari S, Verma J, Bakshi S, Narendrakumar L, Paul D, Das B. Toxin-linked mobile genetic elements in major enteric bacterial pathogens. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023; 4:e5. [PMID: 39295911 PMCID: PMC11406385 DOI: 10.1017/gmb.2023.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 12/31/2022] [Accepted: 02/24/2023] [Indexed: 09/21/2024]
Abstract
One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.
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Affiliation(s)
- Shruti Panwar
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Shashi Kumari
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Jyoti Verma
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Susmita Bakshi
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Lekshmi Narendrakumar
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Deepjyoti Paul
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Bhabatosh Das
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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Zhou W, Li Y, Xu X, Rao S, Wen H, Han Y, Deng A, Zhang Z, Yang Z, Zhu G. Whole-genome analysis showed the promotion of genetic diversity and coevolution in Staphylococcus aureus lytic bacteriophages and their hosts mediated by prophages via worldwide recombination events. Front Microbiol 2023; 14:1088125. [PMID: 36970693 PMCID: PMC10036374 DOI: 10.3389/fmicb.2023.1088125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Prophages as a part of Staphylococcus aureus genome contribute to the genetic diversity as well as survival strategies of their host. Some S. aureus prophages also have an imminent risk of host cell lysis and become a lytic phage. Nonetheless, interactions among S. aureus prophages, lytic phages, and their hosts, as well as the genetic diversity of S. aureus prophages, remain unclear. We identified 579 intact and 1,389 incomplete prophages in the genomes of 493 S. aureus isolates obtained from the NCBI database. The structural diversity and gene content of intact and incomplete prophages were investigated and compared with 188 lytic phages. Mosaic structure comparison, ortholog group clustering, phylogenetic analysis, and recombination network analysis were performed to estimate genetic relatedness among S. aureus intact prophages, incomplete prophages, and lytic phages. The intact and incomplete prophages harbored 148 and 522 distinct mosaic structures, respectively. The major difference between lytic phages and prophages was the lack of functional modules and genes. Compared to the lytic phages, both the S. aureus intact and incomplete prophages harbored multiple antimicrobial resistance (AMR) and virulence factor (VF) genes. Several functional modules of lytic phages 3_AJ_2017 and 23MRA shared more than 99% nucleotide sequence identity with S. aureus intact (ST20130943_p1 and UTSW_ MRSA_55_ip3) and incomplete prophages (SA3_LAU_ip3 and MRSA_FKTN_ip4); other modules showed little nucleotide sequence similarity. Ortholog and phylogenetic analyses revealed a common gene pool shared between the prophages and lytic Siphoviridae phages. Moreover, most shared sequences existed within intact (43428/137294, 31.6%) and incomplete prophages (41248/137294, 30.0%). Therefore, the maintenance or loss of functional modules in intact and incomplete prophages is key to balance the costs and benefits of large prophages harboring various AMR and VF genes in the bacterial host. The shared identical functional modules between S. aureus lytic phages and prophages are likely to result in the exchange, acquisition, and loss of functional modules, and therefore contribute to their genetic diversity. Moreover, constant recombination events within prophages globally were responsible for the coevolution of lytic phages and their bacterial hosts.
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Affiliation(s)
- Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xuechao Xu
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yeiling Han
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Aiping Deng
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenwen Zhang
- Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
- *Correspondence: Zhenquan Yang,
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Guoqiang Zhu,
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 09/14/2022] [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
| | | | - 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
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7
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Zhou W, Wen H, Li Y, Gao Y, Zheng X, Yuan L, Zhu G, Yang Z. Whole-Genome Analysis Reveals That Bacteriophages Promote Environmental Adaptation of Staphylococcus aureus via Gene Exchange, Acquisition, and Loss. Viruses 2022; 14:v14061199. [PMID: 35746669 PMCID: PMC9230882 DOI: 10.3390/v14061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 12/12/2022] Open
Abstract
The study of bacteriophages is experiencing a resurgence owing to their antibacterial efficacy, lack of side effects, and low production cost. Nonetheless, the interactions between Staphylococcus aureus bacteriophages and their hosts remain unexplored. In this study, whole-genome sequences of 188 S. aureus bacteriophages—20 Podoviridae, 56 Herelleviridae, and 112 Siphoviridae—were obtained from the National Center for Biotechnology Information (NCBI, USA) genome database. A phylogenetic tree was constructed to estimate their genetic relatedness using single-nucleotide polymorphism analysis. Comparative analysis was performed to investigate the structural diversity and ortholog groups in the subdividing clusters. Mosaic structures and gene content were compared in relation to phylogeny. Phylogenetic analysis revealed that the bacteriophages could be distinguished into three lineages (I–III), including nine subdividing clusters and seven singletons. The subdividing clusters shared similar mosaic structures and core ortholog clusters, including the genes involved in bacteriophage morphogenesis and DNA packaging. Notably, several functional modules of bacteriophages 187 and 2368A shared more than 95% nucleotide sequence identity with prophages in the S. aureus strain RJ1267 and the Staphylococcus pseudintermedius strain SP_11306_4, whereas other modules exhibited little nucleotide sequence similarity. Moreover, the cluster phages shared similar types of holins, lysins, and DNA packaging genes and harbored diverse genes associated with DNA replication and virulence. The data suggested that the genetic diversity of S. aureus bacteriophages was likely due to gene replacement, acquisition, and loss among staphylococcal phages, which may have crossed species barriers. Moreover, frequent module exchanges likely occurred exclusively among the subdividing cluster phages. We hypothesize that during evolution, the S. aureus phages enhanced their DNA replication in host cells and the adaptive environment of their host.
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Affiliation(s)
- Wenyuan Zhou
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225001, China;
| | - Hua Wen
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Yajie Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Yajun Gao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Xiangfeng Zheng
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225001, China;
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China; (W.Z.); (H.W.); (Y.L.); (Y.G.); (X.Z.); (L.Y.)
- Correspondence: ; Tel./Fax: +86-(514)-87978096
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Kwiatkowski P, Masiuk H, Pruss A, Łopusiewicz Ł, Sienkiewicz M, Wojciechowska-Koszko I, Roszkowska P, Bania J, Guenther S, Dołęgowska B. Clonal Diversity, Antimicrobial Susceptibility and Presence of Genes Encoding Virulence Factors in Staphylococcus aureus Strains Isolated from Cut Wound Infections. Curr Microbiol 2022; 79:144. [PMID: 35325311 DOI: 10.1007/s00284-022-02835-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
The aim of the study was to evaluate the clonal relatedness and antimicrobial susceptibility in 52 Staphylococcus aureus strains isolated from cut wound infections in non-related community patients and to determine the presence of selected virulence genes. To analyse the clonal relatedness of investigated strains, pulsed-field gel electrophoresis (PFGE) of macrorestricted DNA fragments was conducted. Antimicrobial susceptibility testing was performed using the AST-P644 card in the VITEK 2 Compact system. All strains were tested for the presence of selected virulence genes using Single and Multiplex PCR. All isolates were classified into 15 PFGE genotypes and seven unique patterns. The vast majority of investigated S. aureus strains were susceptible to all tested antimicrobial agents. Among examined S. aureus strains, 24 combinations of virulence factors were identified. 62.5% of S. aureus strains contained various egc types, alone or together with other staphylococcal enterotoxin genes. A high percentage (86.5%) of isolates harboured superantigen genes. The most frequent enterotoxin gene identified was encoding for sep. All S. aureus strains were classified as agr-positive, and the most frequent agr gene was agr-1. Our results indicate that all examined strains isolated from cut wound infections demonstrated high clonal diversity, diversified gene distribution and good susceptibility to antimicrobial agents.
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Affiliation(s)
- Paweł Kwiatkowski
- Department of Diagnostic Immunology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland.
| | - Helena Masiuk
- Department of Medical Microbiology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland
| | - Agata Pruss
- Department of Laboratory Medicine, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland
| | - Łukasz Łopusiewicz
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology Szczecin, Klemensa Janickiego 35, 71-270, Szczecin, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostic, Medical University of Lodz, Muszynskiego 1, 90-151, Lodz, Poland
| | - Iwona Wojciechowska-Koszko
- Department of Diagnostic Immunology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland
| | - Paulina Roszkowska
- Department of Diagnostic Immunology, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wroclaw University of Environmental and Life Sciences, C.K. Norwida 31, 50-375, Wroclaw, Poland
| | - Sebastian Guenther
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489, Greifswald, Germany
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Powstancow Wielkopolskich 72, 70-111, Szczecin, Poland
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9
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Humphrey S, Fillol-Salom A, Quiles-Puchalt N, Ibarra-Chávez R, Haag AF, Chen J, Penadés JR. Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements. Nat Commun 2021; 12:6509. [PMID: 34750368 PMCID: PMC8575950 DOI: 10.1038/s41467-021-26004-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/03/2021] [Indexed: 12/02/2022] Open
Abstract
It is commonly assumed that the horizontal transfer of most bacterial chromosomal genes is limited, in contrast to the frequent transfer observed for typical mobile genetic elements. However, this view has been recently challenged by the discovery of lateral transduction in Staphylococcus aureus, where temperate phages can drive the transfer of large chromosomal regions at extremely high frequencies. Here, we analyse previously published as well as new datasets to compare horizontal gene transfer rates mediated by different mechanisms in S. aureus and Salmonella enterica. We find that the horizontal transfer of core chromosomal genes via lateral transduction can be more efficient than the transfer of classical mobile genetic elements via conjugation or generalized transduction. These results raise questions about our definition of mobile genetic elements, and the potential roles played by lateral transduction in bacterial evolution.
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Affiliation(s)
- Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, Bldg. 1, DK2100, Copenhagen, Denmark
| | - Andreas F Haag
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, Valencia, 46113, Spain.
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10
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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11
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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12
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Najafi Olya Z, Najar-Peerayeh S, Yadegar A, Bakhshi B. Clonal diversity and genomic characterization of Panton-valentine Leukocidin (PVL)-positive Staphylococcus aureus in Tehran, Iran. BMC Infect Dis 2021; 21:372. [PMID: 33882854 PMCID: PMC8058961 DOI: 10.1186/s12879-021-06060-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 04/08/2021] [Indexed: 11/25/2022] Open
Abstract
Background Some Staphylococcus aureus strains produce Panton-Valentine leukocidin (PVL), a bi-component pore-forming toxin, which causes leukocyte lysis and tissue necrosis. Currently, there is very limited information on the molecular epidemiology of PVL-encoding S. aureus strains in Iran. This study aimed to determine the molecular epidemiology and genetic background of PVL-positive S. aureus clinical strains isolated from Iranian patients. Methods A total of 28 PVL-positive S. aureus strains were detected from 600 S. aureus isolates between February 2015 and March 2018 from different hospitals in Tehran, Iran. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Molecular genotyping was performed using SCCmec and accessory gene regulator (agr) typing, PVL haplotyping, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Results The highest antibiotic resistance rate was found to be against erythromycin (57.1%), followed by ciprofloxacin (42.8%) and clindamycin (35.7%). Moreover, 19 (67.9%) out of 28 S. aureus isolates were identified as MRSA, including CA-MRSA (14/19, 73.7%) and HA-MRSA (5/19, 26.3%). SCCmec type IVa was detected as the predominant type (10/19, 52.6%), followed by type III (5/19, 26.3%) and type V (4/19, 21.1%). The agr type I was identified as the most common type (14/28, 50%), and H and R haplotype groups were observed at frequencies of 67.9 and 32.1%, respectively. Among H variants, the predominant variant was H2 (78/9%). The isolates encompassed 21 different sequence types (STs), including 16 new STs (ST5147 to ST5162). Based on eBURST analysis, the isolates were clustered into five CCs, including CC30, CC22, CC1, CC8, and CC5 (ST5160), and nine singletons. PFGE typing showed that 24 isolates were clustered into A (4 pulsotypes), B (9 pulsotypes), and C (11 pulsotypes) clusters. Conclusions A high prevalence of PVL-positive CA-MRSA strains was detected in Iran. The majority of PVL-positive isolates were of H (mostly H2) variant, while R variant was harbored by 100% of PVL-positive MRSA strains. Also, CC8, CC22, and CC30 were identified as the dominant clones among PVL-encoding S. aureus strains. This study promotes a better understanding of the molecular epidemiology and evolution of PVL-positive S. aureus strains in Iran.
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Affiliation(s)
- Zahra Najafi Olya
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Jalal-Ale-Ahmad Ave, Tehran, 14117-13116, Iran
| | - Shahin Najar-Peerayeh
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Jalal-Ale-Ahmad Ave, Tehran, 14117-13116, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bita Bakhshi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Jalal-Ale-Ahmad Ave, Tehran, 14117-13116, Iran.
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13
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Genome Sequencing of a Historic Staphylococcus aureus Collection Reveals New Enterotoxin Genes and Sheds Light on the Evolution and Genomic Organization of This Key Virulence Gene Family. J Bacteriol 2021; 203:JB.00587-20. [PMID: 33649144 DOI: 10.1128/jb.00587-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/16/2021] [Indexed: 01/09/2023] Open
Abstract
We take advantage of a historic collection of 133 Staphylococcus aureus strains accessioned between 1924 and 2016, whose genomes have been long-read sequenced as part of a major National Collection of Type Cultures (NCTC) initiative, to conduct a gene family-wide computational analysis of enterotoxin genes. We identify two novel staphylococcal enterotoxin (pseudo)genes (sel29p and sel30), the former of which has not been observed in any contemporary strain to date. We provide further information on five additional enterotoxin genes or gene variants that either have recently entered the literature or for which the nomenclature or description is currently unclear (selz, sel26, sel27, sel28, and ses-2p). An examination of over 11,000 RefSeq genomes in search of wider support for these seven (pseudo)genes led to the identification of an additional three novel enterotoxin gene family members (sel31, sel32, and sel33) plus two new variants (seh-2p and ses-3p). We cast light on the genomic distribution of the enterotoxin genes, further defining their arrangement in gene clusters. Finally, we show that cooccurrence of enterotoxin genes is prevalent, with individual NCTC strains possessing as many as 18 enterotoxin genes and pseudogenes, and that clonal complex membership rather than time of isolation is the key factor in determining enterotoxin load.IMPORTANCE Staphylococcus aureus strains pose a significant health risk to both human and animal populations. Key among this species' virulence factors is the staphylococcal enterotoxin gene family. Certain enterotoxin forms can induce a potentially life-threatening immune response, while others are implicated in less fatal though often severe conditions such as food poisoning. Genetic characterization of staphylococcal enterotoxin gene family members has steadily accumulated over recent decades, with over 20 genes now established in the literature. Despite the current wealth of knowledge on this important gene family, questions remain about the presence of additional enterotoxin genes and the genomic composition of family members. This study further expands knowledge of the staphylococcal enterotoxins while shedding light on their evolution over the last century.
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14
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Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
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15
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Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft JU, Hobman JL, Stekel DJ. A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiol Ecol 2020; 96:5850753. [PMID: 32490523 DOI: 10.1093/femsec/fiaa100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/02/2020] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a major global challenge. Of particular concern are mobilizable elements that can transfer resistance genes between bacteria, leading to pathogens with new combinations of resistance. To date, mathematical models have largely focussed on transfer of resistance by plasmids, with fewer studies on transfer by bacteriophages. We aim to understand how best to model transfer of resistance by transduction by lytic phages. We show that models of lytic bacteriophage infection with empirically derived realistic phage parameters lead to low numbers of bacteria, which, in low population or localised environments, lead to extinction of bacteria and phage. Models that include antagonistic co-evolution of phage and bacteria produce more realistic results. Furthermore, because of these low numbers, stochastic dynamics are shown to be important, especially to spread of resistance. When resistance is introduced, resistance can sometimes be fixed, and at other times die out, with the probability of each outcome sensitive to bacterial and phage parameters. Specifically, that outcome most strongly depends on the baseline death rate of bacteria, with phage-mediated spread favoured in benign environments with low mortality over more hostile environments. We conclude that larger-scale models should consider spatial compartmentalisation and heterogeneous microenviroments, while encompassing stochasticity and co-evolution.
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Affiliation(s)
- Sankalp Arya
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Henry Todman
- School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michelle Baker
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.,School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Steven Hooton
- Division of Food Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jan-Ulrich Kreft
- School of Biosciences & Institute of Microbiology and Infection & Centre for Computational Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jon L Hobman
- Division of Food Science, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Dov J Stekel
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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16
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Rossi CC, Pereira MF, Giambiagi-deMarval M. Underrated Staphylococcus species and their role in antimicrobial resistance spreading. Genet Mol Biol 2020; 43:e20190065. [PMID: 32052827 PMCID: PMC7198029 DOI: 10.1590/1678-4685-gmb-2019-0065] [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: 02/26/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023] Open
Abstract
The increasing threat of antimicrobial resistance has shed light on the interconnection between humans, animals, the environment, and their roles in the exchange and spreading of resistance genes. In this review, we present evidences that show that Staphylococcus species, usually referred to as harmless or opportunistic pathogens, represent a threat to human and animal health for acting as reservoirs of antimicrobial resistance genes. The capacity of genetic exchange between isolates of different sources and species of the Staphylococcus genus is discussed with emphasis on mobile genetic elements, the contribution of biofilm formation, and evidences obtained either experimentally or through genome analyses. We also discuss the involvement of CRISPR-Cas systems in the limitation of horizontal gene transfer and its suitability as a molecular clock to describe the history of genetic exchange between staphylococci.
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Affiliation(s)
- Ciro César Rossi
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Laboratório de Microbiologia Molecular, Rio de Janeiro, RJ, Brazil
| | | | - Marcia Giambiagi-deMarval
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Laboratório de Microbiologia Molecular, Rio de Janeiro, RJ, Brazil
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17
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Kläui AJ, Boss R, Graber HU. Characterization and Comparative Analysis of the Staphylococcus aureus Genomic Island vSaβ: an In Silico Approach. J Bacteriol 2019; 201:e00777-18. [PMID: 31451542 PMCID: PMC6805111 DOI: 10.1128/jb.00777-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/25/2019] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus is a widespread opportunistic pathogen to humans and animals. Of its genome, 20 to 25% varies between strains and consists of phages, pathogenicity islands, transposons, and genomic islands. S. aureus harbors up to three genomic islands, vSaα, vSaβ, and vSaγ. The vSaβ region of S. aureus can encode a number of virulence-associated factors, such as serine proteases, leukocidins, enterotoxins, bacteriocins, or a hyaluronate lyase. In this study, the vSaβ regions of 103 clinically relevant S. aureus strains were characterized in silico and compared to the three predefined vSaβ types. We here suggest a superordinate system of 15 different vSaβ types, of which 12 were newly defined. Each vSaβ type has a distinct structure with a distinct set of genes, which are both highly conserved. Between the different types, gene content and composition vary substantially. Based on our data, a strain's vSaβ type is strongly coupled with its clonal complex, suggesting that vSaβ was acquired in an ancestral S. aureus strain, arguably by phage mediation, before differentiation into clonal complexes. In addition, we addressed the issue of ambiguous nomenclature in the serine protease gene cluster and propose a novel, phylogeny-based nomenclature of the cluster contained in the vSaβ region.IMPORTANCE With the rapid increase of available sequencing data on clinically relevant bacterial species such as S. aureus, the genomic basis of clinical phenotypes can be investigated in much more detail, allowing a much deeper understanding of the mechanisms involved in disease. We characterized in detail the S. aureus genomic island vSaβ and defined a superordinate system to categorize S. aureus strains based on their vSaβ type, providing information about the strains' virulence-associated genes and clinical potential.
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Affiliation(s)
- Anita J Kläui
- Food Microbial Systems, Agroscope, Bern, Switzerland
| | - Renate Boss
- Risk Assessment Division, Federal Food Safety and Veterinary Office, Bern, Switzerland
| | - Hans U Graber
- Food Microbial Systems, Agroscope, Bern, Switzerland
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18
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Ko DS, Kim D, Kim EK, Kim JH, Kwon HJ. Evolution of a major bovine mastitic genotype (rpoB sequence type 10-2) of Staphylococcus aureus in cows. J Microbiol 2019; 57:587-596. [PMID: 30982119 DOI: 10.1007/s12275-019-8699-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/31/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
Staphylococcus aureus is the major pathogen leading to bovine mastitis globally while livestock-associated methicillin resistant S. aureus (LA-MRSA) has become a potential threat to public health. MRSA from bovine mastitis is not common but a methicillin susceptible S. aureus (MSSA) genotype, rpoB sequence type (RST)10-2 (RST10-2), is prevalent in Korea. To date, many genomic sequences from S. aureus have been elucidated, but the complete genome sequences of RST10-2 MSSA from bovine mastitis has never been reported. In this study, we determined the complete genome sequence of two RST10-2 MSSA that differ from each other in staphylococcal protein A and molecular prophage types [PMB64-1 (t2489/ mPPT0) and PMB81-4 (t127/mPPT1-2-3)] and conducted a comparative genomics study. The genomic sequences of PMB64-1 and PMB81-4 were more homologous to the representative human RST10-2 strains (MSSA476, MW2 etc.) compared to other RSTs. Most of them shared five common pseudogenes, along with high amino acid identity of four variable virulence genes that were identified in this study. However, PMB64-1 and PMB81-4 acquired different strainspecific pseudogenes and mobile genetic elements than the human strains. The unique pseudogene profile and high identity of the virulence genes were verified in RST10-2 field strains from bovine mastitis. Thus, bovine mastitic RST10-2 MSSA may have an evolutionary relationship with the human RST10-2 community-associated (CA) MSSA and CA-MRSA strains but may have adapted to cows.
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Affiliation(s)
- Dae-Sung Ko
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea.,Laboratory of Avian Diseases, Seoul National University, Seoul, 08826, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eun-Kyung Kim
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Avian Diseases, Seoul National University, Seoul, 08826, Republic of Korea.,The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Department of Farm Animal Medicine, Seoul National University, Seoul, 08826, Republic of Korea. .,The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
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19
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20
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Renard A, Barbera L, Courtier-Martinez L, Dos Santos S, Valentin AS, Mereghetti L, Quentin R, van der Mee-Marquet NL. phiD12-Like Livestock-Associated Prophages Are Associated With Novel Subpopulations of Streptococcus agalactiae Infecting Neonates. Front Cell Infect Microbiol 2019; 9:166. [PMID: 31192160 PMCID: PMC6546898 DOI: 10.3389/fcimb.2019.00166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/03/2019] [Indexed: 01/14/2023] Open
Abstract
Group B Streptococcus (GBS) is a major cause of invasive disease in neonates worldwide. Monitoring data have revealed a continuing trend toward an increase in neonatal GBS infections, despite the introduction of preventive measures. We investigated this trend, by performing the first ever characterization of the prophage content for 106 GBS strains causing neonatal infections between 2002 and 2018. We determined whether the genome of each strain harbored prophages, and identified the insertion site of each of the prophages identified. We found that 71.7% of the strains carried at least one prophage, and that prophages genetically similar to livestock-associated phiD12, carrying genes potentially involved in GBS pathogenesis (e.g., genes encoding putative virulence factors and factors involved in biofilm formation, bacterial persistence, or adaptation to challenging environments) predominated. The phiD12-like prophages were (1) associated with CC17 and 1 strains (p = 0.002), (2) more frequent among strains recovered during the 2011–2018 period than among those from 2002–2010 (p < 0.001), and (3) located at two major insertion sites close to bacterial genes involved in host adaptation and colonization. Our data provide evidence for a recent increase in lysogeny in GBS, characterized by the acquisition, within the genome, of genetic features typical of animal-associated mobile genetic elements by GBS strains causing neonatal infection. We suggest that lysogeny and phiD12-like prophage genetic elements may have conferred an advantage on GBS strains for adaptation to or colonization of the maternal vaginal tract, or for pathogenicity, and that these factors are currently playing a key role in the increasing ability of GBS strains to infect neonates.
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Affiliation(s)
- Adélaïde Renard
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France
| | - Laurie Barbera
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France
| | - Luka Courtier-Martinez
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France
| | - Sandra Dos Santos
- Cellule Régionale d'Epidémiologie Nosocomiale, Centre d'Appui pour la Prévention des Infections Associées aux Soins CPias Centre val de Loire, Service de Bactériologie et Hygiène, Centre Hospitalier Universitaire, Tours, France
| | - Anne-Sophie Valentin
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France
| | - Laurent Mereghetti
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France.,Cellule Régionale d'Epidémiologie Nosocomiale, Centre d'Appui pour la Prévention des Infections Associées aux Soins CPias Centre val de Loire, Service de Bactériologie et Hygiène, Centre Hospitalier Universitaire, Tours, France
| | - Roland Quentin
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France
| | - Nathalie L van der Mee-Marquet
- Bactéries et Risque Materno-Foetal, UMR 1282, Infectiologie Santé Publique, Université de Tours, Tours, France.,Cellule Régionale d'Epidémiologie Nosocomiale, Centre d'Appui pour la Prévention des Infections Associées aux Soins CPias Centre val de Loire, Service de Bactériologie et Hygiène, Centre Hospitalier Universitaire, Tours, France
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21
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Founou LL, Founou RC, Allam M, Ismail A, Finyom Djoko C, Essack SY. Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa. Zoonoses Public Health 2019; 66:512-525. [PMID: 31124311 DOI: 10.1111/zph.12586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/28/2019] [Accepted: 05/05/2019] [Indexed: 01/16/2023]
Abstract
Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo-assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCCmec and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCCmec Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (n = 1/13; 0.07%) compared with South Africa (n = 4/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (spa-type t011) and harboured the type Vc SCCmec and several plasmids. Our study shows that the livestock-associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.
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Affiliation(s)
- Luria Leslie Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Food Safety and Environmental Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Raspail Carrel Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Mushal Allam
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Cyrille Finyom Djoko
- Metabiota Inc., Yaoundé, Cameroon.,Centre for Research and Doctoral Training in Life Science, Health and Environment, The Biotechnology Centre, University of Yaoundé I, Yaoundé, Cameroon
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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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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Comprehensive Virulence Gene Profiling of Bovine Non- aureus Staphylococci Based on Whole-Genome Sequencing Data. mSystems 2019; 4:mSystems00098-18. [PMID: 30863792 PMCID: PMC6401416 DOI: 10.1128/msystems.00098-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/15/2019] [Indexed: 12/21/2022] Open
Abstract
Non-aureus staphylococci (NAS) are the most frequently isolated pathogens from milk in dairy cattle worldwide. The virulence factors (VFs) and mechanisms by which these bacteria cause udder infection are not fully known. We determined the distribution and associations of 191 VFs in 25 NAS species and investigated the relationship between VFs and disease. Although the overall number of VFs was not associated with disease severity, increasing numbers of toxin and host immune evasion genes specifically were associated with more severe disease outcomes. These findings suggest that the development of disease and the interactions of VFs with the host are complex and determined by the interplay of genes rather than just the presence of virulence genes. Together, our results provide foundational genetic knowledge to other researchers to design and conduct further experiments, focusing on understanding the synergy between VFs and roles of individual NAS species in IMI and characterizing species-specific effects on udder health. Non-aureus staphylococci (NAS) are the most frequently isolated pathogens from intramammary infection (IMI) in dairy cattle. Virulence factors (VFs) and mechanisms by which NAS cause IMI are not fully known. Herein, we analyzed the distribution of 191 VFs in 441 genomes of 25 NAS species, after classifying VFs into functional categories: adherence (n = 28), exoenzymes (n = 21), immune evasion (n = 20), iron metabolism (n = 29), and toxins (n = 93). In addition to establishing VF gene profiles, associations of VF genes between and among functional categories were computed, revealing distinctive patterns of association among VFs for various NAS species. Associations were also computed for low, medium, and high somatic cell count (SCC) and clinical mastitis (CM) isolates, demonstrating distinctive patterns of associations for low SCC and CM isolates, but no differences between high SCC and CM isolates. To determine whether VF distributions had any association with SCC or CM, various clustering approaches, including complete linkages, Ward clustering, and t-distributed stochastic neighbor embedding, were applied. However, no clustering of isolates representing low SCC, medium SCC, or high SCC or CM was identified. Regression analysis to test for associations with individual VF functional categories demonstrated that each additional toxin and host immune evasion gene increased the odds of having high SCC or CM, although an overall increase in the number of VFs was not associated with increased SCC or occurrence of CM. In conclusion, we established comprehensive VF gene profiling, determined VF gene distributions and associations, calculated pathogenic potentials of all NAS species, and detected no clear link between VF genes and mastitis. IMPORTANCE Non-aureus staphylococci (NAS) are the most frequently isolated pathogens from milk in dairy cattle worldwide. The virulence factors (VFs) and mechanisms by which these bacteria cause udder infection are not fully known. We determined the distribution and associations of 191 VFs in 25 NAS species and investigated the relationship between VFs and disease. Although the overall number of VFs was not associated with disease severity, increasing numbers of toxin and host immune evasion genes specifically were associated with more severe disease outcomes. These findings suggest that the development of disease and the interactions of VFs with the host are complex and determined by the interplay of genes rather than just the presence of virulence genes. Together, our results provide foundational genetic knowledge to other researchers to design and conduct further experiments, focusing on understanding the synergy between VFs and roles of individual NAS species in IMI and characterizing species-specific effects on udder health.
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Chen J, Quiles-Puchalt N, Chiang YN, Bacigalupe R, Fillol-Salom A, Chee MSJ, Fitzgerald JR, Penadés JR. Genome hypermobility by lateral transduction. Science 2018; 362:207-212. [PMID: 30309949 DOI: 10.1126/science.aat5867] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/14/2018] [Indexed: 02/01/2023]
Abstract
Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of Staphylococcus aureus engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program. Here, DNA packaging initiates in situ from integrated prophages, and large metameric spans including several hundred kilobases of the S. aureus genome are packaged in phage heads at very high frequency. In situ replication before DNA packaging creates multiple prophage genomes so that lateral-transducing particles form during normal phage maturation, transforming parts of the S. aureus chromosome into hypermobile regions of gene transfer.
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Affiliation(s)
- John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore.
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Yin Ning Chiang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - Rodrigo Bacigalupe
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Melissa Su Juan Chee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - José R Penadés
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK. .,Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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Genomic mapping of ST85 bla NDM-1 and bla OXA-94 producing Acinetobacter baumannii isolates from Syrian Civil War Victims. Int J Infect Dis 2018; 74:100-108. [PMID: 30053579 DOI: 10.1016/j.ijid.2018.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES The rapid emergence of carbapenem-resistant Acinetobacter baumannii is a global health concern. A comparative genomic analysis was performed on two ST85 A. baumannii strains harboring blaNDM-1 and blaOXA-94 collected in Lebanon from Syrian Civil War victims. METHODS Genome sequencing data of ACMH-6200 and ACMH-6201 were used for in silico extraction of multilocus sequence types (MLST), resistance genes, and virulence factors. Plasmids were genetically mapped in silico and using PCR-based replicon typing (PBRT). The genetic environment of blaNDM-1 and blaOXA-94 was determined, and whole-genome single nucleotide polymorphism (wgSNP) analysis in comparison with 41 publicly available A. baumannii genomes was performed. RESULTS Tn125 carrying blaNDM-1 was truncated by the insertion of ISAba14 downstream of dct, generating ΔTn125. blaOXA-94 was upstream of ISAba13 and ISAba17. Resistance to ceftazidime could be attributed to AmpC cephalosporinase encoded by blaADC-25, and to blaNDM-1 on plasmids. GyrA (S83L) and ParC (S80L) substitutions conferred resistance to fluoroquinolones. wgSNP analysis separated the isolates based on their sequence types. CONCLUSIONS The role of refugees in the transmission of antimicrobial resistance in developing countries is understudied. As such, this study sheds light on the correlation between population mobility and the importation of drug-resistant pathogens. It also highlights the manifold mechanisms underlying antibiotic resistance in A. baumannii.
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26
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Zhou W, Li X, Osmundson T, Shi L, Ren J, Yan H. WGS analysis of ST9-MRSA-XII isolates from live pigs in China provides insights into transmission among porcine, human and bovine hosts. J Antimicrob Chemother 2018; 73:2652-2661. [DOI: 10.1093/jac/dky245] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/27/2018] [Indexed: 12/21/2022] Open
Affiliation(s)
- Wenyuan Zhou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Xinhui Li
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA
| | - Todd Osmundson
- Department of Biology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, USA
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
- State Key Laboratory of Food Safely Technology for Meat Products, Xiamen, Fujian, China
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - He Yan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- State Key Laboratory of Food Safely Technology for Meat Products, Xiamen, Fujian, China
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27
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Jiang S, Zeng J, Zhou X, Li Y. Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria. J Dent Res 2018; 97:1092-1099. [PMID: 29928825 DOI: 10.1177/0022034518782659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Growing evidence suggests the existence of new antibiotic resistance mechanisms. Recent studies have revealed that quorum-quenching enzymes, such as MacQ, are involved in both antibiotic resistance and cell-cell communication. Furthermore, some small bacterial regulatory RNAs, classified into RNA attenuators and small RNAs, modulate the expression of resistance genes. For example, small RNA sprX, can shape bacterial resistance to glycopeptide antibiotics via specific downregulation of protein SpoVG. Moreover, some bacterial lipocalins capture antibiotics in the extracellular space, contributing to severe multidrug resistance. But this defense mechanism may be influenced by Agr-regulated toxins and liposoluble vitamins. Outer membrane porin proteins and efflux pumps can influence intracellular concentrations of antibiotics. Alterations in target enzymes or antibiotics prevent binding to targets, which act to confer high levels of resistance in respiratory/oral bacteria. As described recently, horizontal gene transfer, including conjugation, transduction and transformation, is common in respiratory/oral microflora. Many conjugative transposons and plasmids discovered to date encode antibiotic resistance proteins and can be transferred from donor bacteria to transient recipient bacteria. New classes of mobile genetic elements are also being identified. For example, nucleic acids that circulate in the bloodstream (circulating nucleic acids) can integrate into the host cell genome by up-regulation of DNA damage and repair pathways. With multidrug resistant bacteria on the rise, new drugs have been developed to combate bacterial antibiotic resistance, such as innate defense regulators, reactive oxygen species and microbial volatile compounds. This review summaries various aspects and mechanisms of antibiotic resistance in the respiratory/oral microbiota. A better understanding of these mechanisms will facilitate minimization of the emergence of antibiotic resistance.
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Affiliation(s)
- S Jiang
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J Zeng
- 2 Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - X Zhou
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Y Li
- 1 State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Hannigan GD, Duhaime MB, Koutra D, Schloss PD. Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. PLoS Comput Biol 2018; 14:e1006099. [PMID: 29668682 PMCID: PMC5927471 DOI: 10.1371/journal.pcbi.1006099] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/30/2018] [Accepted: 03/21/2018] [Indexed: 01/17/2023] Open
Abstract
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. The human microbiome, the collection of microbial communities that colonize the human body, is a crucial component to health and disease. Two major components of the human microbiome are the bacterial and viral communities. These communities have primarily been studied separately using metrics of community composition and diversity. These approaches have failed to capture the complex dynamics of interacting bacteria and phage communities, which frequently share genetic information and work together to maintain ecosystem homestatsis (e.g. kill-the-winner dynamics). Removal of bacteria or phage can disrupt or even collapse those ecosystems. Relationship-based network approaches allow us to capture this interaction information. Using this network-based approach with three independent human cohorts, we were able to present an initial understanding of how phage-bacteria networks differ throughout the human body, so as to provide a baseline for future studies of how and why microbiome networks differ in disease states.
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Affiliation(s)
- Geoffrey D. Hannigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Danai Koutra
- Department of Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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29
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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30
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Lee J, Park N, Park JY, Kaplan BLF, Pruett SB, Park JW, Park YH, Seo KS. Induction of Immunosuppressive CD8 +CD25 +FOXP3 + Regulatory T Cells by Suboptimal Stimulation with Staphylococcal Enterotoxin C1. THE JOURNAL OF IMMUNOLOGY 2017; 200:669-680. [PMID: 29237775 DOI: 10.4049/jimmunol.1602109] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/13/2017] [Indexed: 12/17/2022]
Abstract
Superantigens (SAgs) produced by Staphylococcus aureus at high concentrations induce proliferation of T cells bearing specific TCR Vβ sequences and massive cytokinemia that cause toxic shock syndrome. However, the biological relevance of SAgs produced at very low concentrations during asymptomatic colonization or chronic infections is not understood. In this study, we demonstrate that suboptimal stimulation of human PBMCs with a low concentration (1 ng/ml) of staphylococcal enterotoxin C1, at which half-maximal T cell proliferation was observed, induced CD8+CD25+ T cells expressing markers related to regulatory T cells (Tregs), such as IFN-γ, IL-10, TGF-β, FOXP3, CD28, CTLA4, TNFR2, CD45RO, and HLA-DR. Importantly, these CD8+CD25+ T cells suppressed responder cell proliferation mediated in contact-dependent and soluble factor-dependent manners, involving galectin-1 and granzymes, respectively. In contrast, optimal stimulation of human PBMCs with a high concentration (1 μg/ml) of staphylococcal enterotoxin C1, at which maximal T cell proliferation was observed, also induced similar expression of markers related to Tregs, including FOXP3 in CD8+CD25+ cells, but these T cells were not functionally immunosuppressive. We further demonstrated that SAg-induced TCR Vβ-restricted and MHC class II-restricted expansion of immunosuppressive CD8+CD25+ T cells is independent of CD4+ T cells. Our results suggest that the concentration of SAg strongly affects the functional characteristics of activated T cells, and low concentrations of SAg produced during asymptomatic colonization or chronic S. aureus infection induce immunosuppressive CD8+ Tregs, potentially promoting colonization, propagation, and invasion of S. aureus in the host.
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Affiliation(s)
- Juyeun Lee
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Nogi Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Joo Youn Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Barbara L F Kaplan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Stephen B Pruett
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292; and
| | - Yong Ho Park
- Department of Microbiology, BK21 Program for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, South Korea
| | - Keun Seok Seo
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762;
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31
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Phage-mediated dissemination of virulence factors in pathogenic bacteria facilitated by antibiotic growth promoters in animals: a perspective. Anim Health Res Rev 2017; 18:160-166. [DOI: 10.1017/s1466252317000147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractAddition of sub-therapeutic antibiotics to the feed of food-producing animals for growth promotion and disease prevention has become a common agricultural practice in many countries. The emergence of antibiotic-resistant pathogens is a looming concern associated with the use of antibiotic growth promoters (AGPs) around the world. In addition, some studies have shown that AGPs may not only affect antibiotic resistance but may also stimulate the dissemination of virulence factors via bacteriophages. Although only a few studies are currently available in the literature regarding this topic, in this article we endeavor to provide a perspective about how AGPs would impact the transmission of virulence factors by horizontal gene transfer via phages in a few pathogenic bacterial species significant to livestock production.
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32
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Sansevere EA, Robinson DA. Staphylococci on ICE: Overlooked agents of horizontal gene transfer. Mob Genet Elements 2017; 7:1-10. [PMID: 28932624 DOI: 10.1080/2159256x.2017.1368433] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/19/2022] Open
Abstract
Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.
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Affiliation(s)
- Emily A Sansevere
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
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Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Sci Rep 2017; 7:44929. [PMID: 28322317 PMCID: PMC5359561 DOI: 10.1038/srep44929] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/16/2017] [Indexed: 12/29/2022] Open
Abstract
Discovery of clustered, regularly interspaced, short palindromic repeats and the Cas9 RNA-guided nuclease (CRISPR/Cas9) system provides a new opportunity to create programmable gene-specific antimicrobials that are far less likely to drive resistance than conventional antibiotics. However, the practical therapeutic use of CRISPR/Cas9 is still questionable due to current shortcomings in phage-based delivery systems such as inefficient delivery, narrow host range, and potential transfer of virulence genes by generalized transduction. In this study, we demonstrate genetic engineering strategies to overcome these shortcomings by integrating CRISPR/Cas9 system into a temperate phage genome, removing major virulence genes from the host chromosome, and expanding host specificity of the phage by complementing tail fiber protein. This significantly improved the efficacy and safety of CRISPR/Cas9 antimicrobials to therapeutic levels in both in vitro and in vivo assays. The genetic engineering tools and resources established in this study are expected to provide an efficacious and safe CRISPR/Cas9 antimicrobial, broadly applicable to Staphylococcus aureus.
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34
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Planet PJ, Narechania A, Chen L, Mathema B, Boundy S, Archer G, Kreiswirth B. Architecture of a Species: Phylogenomics of Staphylococcus aureus. Trends Microbiol 2016; 25:153-166. [PMID: 27751626 DOI: 10.1016/j.tim.2016.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022]
Abstract
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
| | - Barun Mathema
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sam Boundy
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gordon Archer
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
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35
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Khan S, Cole N, Hume EB, Garthwaite LL, Nguyen-Khuong T, Walsh BJ, Willcox MD. Identification of pathogenic factors potentially involved in Staphylococcus aureus keratitis using proteomics. Exp Eye Res 2016; 151:171-8. [DOI: 10.1016/j.exer.2016.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 01/11/2023]
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36
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Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing. Appl Environ Microbiol 2016; 82:5910-7. [PMID: 27474712 PMCID: PMC5038045 DOI: 10.1128/aem.01496-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.
IMPORTANCE The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.
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Stubbendieck RM, Vargas-Bautista C, Straight PD. Bacterial Communities: Interactions to Scale. Front Microbiol 2016; 7:1234. [PMID: 27551280 PMCID: PMC4976088 DOI: 10.3389/fmicb.2016.01234] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022] Open
Abstract
In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.
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Affiliation(s)
- Reed M. Stubbendieck
- Interdisciplinary Program in Genetics, Texas A&M University, College StationTX, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTX, USA
| | - Carol Vargas-Bautista
- Department of Plant Pathology and Microbiology, Texas A&M Agrilife Research, WeslacoTX, USA
| | - Paul D. Straight
- Interdisciplinary Program in Genetics, Texas A&M University, College StationTX, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College StationTX, USA
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Hoai TD, Nishiki I, Yoshida T. Properties and genomic analysis of Lactococcus garvieae lysogenic bacteriophage PLgT-1, a new member of Siphoviridae , with homology to Lactococcus lactis phages. Virus Res 2016; 222:13-23. [DOI: 10.1016/j.virusres.2016.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
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Moon BY, Park JY, Robinson DA, Thomas JC, Park YH, Thornton JA, Seo KS. Mobilization of Genomic Islands of Staphylococcus aureus by Temperate Bacteriophage. PLoS One 2016; 11:e0151409. [PMID: 26953931 PMCID: PMC4783081 DOI: 10.1371/journal.pone.0151409] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/26/2016] [Indexed: 01/21/2023] Open
Abstract
The virulence of Staphylococcus aureus, in both human and animal hosts, is largely influenced by the acquisition of mobile genetic elements (MGEs). Most S. aureus strains carry a variety of MGEs, including three genomic islands (νSaα, νSaβ, νSaγ) that are diverse in virulence gene content but conserved within strain lineages. Although the mobilization of pathogenicity islands, phages and plasmids has been well studied, the mobilization of genomic islands is poorly understood. We previously demonstrated the mobilization of νSaβ by the adjacent temperate bacteriophage ϕSaBov from strain RF122. In this study, we demonstrate that ϕSaBov mediates the mobilization of νSaα and νSaγ, which are located remotely from ϕSaBov, mostly to recipient strains belonging to ST151. Phage DNA sequence analysis revealed that chromosomal DNA excision events from RF122 were highly specific to MGEs, suggesting sequence-specific DNA excision and packaging events rather than generalized transduction by a temperate phage. Disruption of the int gene in ϕSaBov did not affect phage DNA excision, packaging, and integration events. However, disruption of the terL gene completely abolished phage DNA packing events, suggesting that the primary function of temperate phage in the transfer of genomic islands is to allow for phage DNA packaging by TerL and that transducing phage particles are the actual vehicle for transfer. These results extend our understanding of the important role of bacteriophage in the horizontal transfer and evolution of genomic islands in S. aureus.
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Affiliation(s)
- Bo Youn Moon
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
- Department of Microbiology, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul, 151–742, South Korea
| | - Joo Youn Park
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
| | - D. Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216, United States of America
| | - Jonathan C. Thomas
- Department of Biology, University of Bolton, Bolton, Greater Manchester, BL3 5AB United Kingdom
| | - Yong Ho Park
- Department of Microbiology, College of Veterinary Medicine and BK21 Program for Veterinary Science, Seoul National University, Seoul, 151–742, South Korea
| | - Justin A. Thornton
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, United States of America
| | - Keun Seok Seo
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, United States of America
- * E-mail:
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Li X, Gerlach D, Du X, Larsen J, Stegger M, Kühner P, Peschel A, Xia G, Winstel V. An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae. Sci Rep 2015; 5:17219. [PMID: 26596631 PMCID: PMC4667565 DOI: 10.1038/srep17219] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/27/2015] [Indexed: 01/10/2023] Open
Abstract
Many Staphylococcus aureus have lost a major genetic barrier against phage infection, termed clustered regularly interspaced palindromic repeats (CRISPR/cas). Hence, S. aureus strains frequently exchange genetic material via phage-mediated horizontal gene transfer events, but, in turn, are vulnerable in particular to lytic phages. Here, a novel strategy of S. aureus is described, which protects S. aureus against the lytic activity of Podoviridae, a unique family of staphylococcal lytic phages with short, non-contractile tails. Unlike most staphylococcal phages, Podoviridae require a precise wall teichoic acid (WTA) glycosylation pattern for infection. Notably, TarM-mediated WTA α-O-GlcNAcylation prevents infection of Podoviridae while TarS-mediated WTA β-O-GlcNAcylation is required for S. aureus susceptibility to podoviruses. Tracking the evolution of TarM revealed an ancient origin in other staphylococci and vertical inheritance during S. aureus evolution. However, certain phylogenetic branches have lost tarM during evolution, which rendered them podovirus-susceptible. Accordingly, lack of tarM correlates with podovirus susceptibility and can be converted into a podovirus-resistant phenotype upon ectopic expression of tarM indicating that a "glyco-switch" of WTA O-GlcNAcylation can prevent the infection by certain staphylococcal phages. Since lytic staphylococcal phages are considered as anti-S. aureus agents, these data may help to establish valuable strategies for treatment of infections.
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Affiliation(s)
- Xuehua Li
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - David Gerlach
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Jesper Larsen
- Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Marc Stegger
- Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.,Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W Shamrell Blvd, Flagstaff, 86001 Arizona, USA
| | - Petra Kühner
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Guoqing Xia
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany.,Institute of Inflammation &Repair, The University of Manchester, Manchester, United Kingdom
| | - Volker Winstel
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
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Spoor LE, Richardson E, Richards AC, Wilson GJ, Mendonca C, Gupta RK, McAdam PR, Nutbeam-Tuffs S, Black NS, O'Gara JP, Lee CY, Corander J, Ross Fitzgerald J. Recombination-mediated remodelling of host-pathogen interactions during Staphylococcus aureus niche adaptation. Microb Genom 2015; 1:e000036. [PMID: 28348819 PMCID: PMC5320625 DOI: 10.1099/mgen.0.000036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/22/2015] [Indexed: 11/23/2022] Open
Abstract
Large-scale recombination events have led to the emergence of epidemic clones of several major bacterial pathogens. However, the functional impact of the recombination on clonal success is not understood. Here, we identified a novel widespread hybrid clone (ST71) of livestock-associated Staphylococcus aureus that evolved from an ancestor belonging to the major bovine lineage CC97, through multiple large-scale recombination events with other S. aureus lineages occupying the same ruminant niche. The recombination events, affecting a 329 kb region of the chromosome spanning the origin of replication, resulted in allele replacement and loss or gain of an array of genes influencing host–pathogen interactions. Of note, molecular functional analyses revealed that the ST71 hybrid clone has acquired multiple novel pathogenic traits associated with acquired and innate immune evasion and bovine extracellular matrix adherence. These findings provide a paradigm for the impact of large-scale recombination events on the rapid evolution of bacterial pathogens within defined ecological niches.
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Affiliation(s)
- Laura E Spoor
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Emily Richardson
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Amy C Richards
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Gillian J Wilson
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Chriselle Mendonca
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Ravi Kr Gupta
- Department of Microbiology and Immunology, University of Arkansas School for Medical Sciences, Little Rock, Arkansas, USA
| | - Paul R McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Stephen Nutbeam-Tuffs
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Nikki S Black
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Ireland
| | - James P O'Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Ireland
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas School for Medical Sciences, Little Rock, Arkansas, USA
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush, Midlothian, UK
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Koymans KJ, Vrieling M, Gorham RD, van Strijp JAG. Staphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation. Curr Top Microbiol Immunol 2015; 409:441-489. [PMID: 26919864 DOI: 10.1007/82_2015_5017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.
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Affiliation(s)
- Kirsten J Koymans
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Manouk Vrieling
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Ronald D Gorham
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Jos A G van Strijp
- Department of Medical Microbiology, University Medical Center Utrecht, G04-614, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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