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Ramos B, Cunha MV. Genomic epidemiology of Staphylococcus aureus from the Iberian Peninsula highlights the expansion of livestock associated-CC398 towards wildlife. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173027. [PMID: 38729368 DOI: 10.1016/j.scitotenv.2024.173027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/04/2024] [Accepted: 05/04/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990-2022 period and a subset of CC398 strains representing the 2008-2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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2
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Yebra G, Mrochen D, Fischer S, Pfaff F, Ulrich RG, Pritchett-Corning K, Holtfreter S, Fitzgerald JR. Bacteriophage-driven emergence and expansion of Staphylococcus aureus in rodent populations. PLoS Pathog 2024; 20:e1012378. [PMID: 39047021 DOI: 10.1371/journal.ppat.1012378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/05/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Human activities such as agriculturalization and domestication have led to the emergence of many new pathogens via host-switching events between humans, domesticated and wild animals. Staphylococcus aureus is a multi-host opportunistic pathogen with a global healthcare and economic burden. Recently, it was discovered that laboratory and wild rodents can be colonised and infected with S. aureus, but the origins and zoonotic potential of rodent S. aureus is unknown. In order to trace their evolutionary history, we employed a dataset of 1249 S. aureus genome sequences including 393 of isolates from rodents and other small mammals (including newly determined sequences for 305 isolates from 7 countries). Among laboratory mouse populations, we identified multiple widespread rodent-specific S. aureus clones that likely originated in humans. Phylogeographic analysis of the most common murine lineage CC88 suggests that it emerged in the 1980s in laboratory mouse facilities most likely in North America, from where it spread to institutions around the world, via the distribution of mice for research. In contrast, wild rodents (mice, voles, squirrels) were colonized with a unique complement of S. aureus lineages that are widely disseminated across Europe. In order to investigate the molecular basis for S. aureus adaptation to rodent hosts, genome-wide association analysis was carried out revealing a unique complement of bacteriophages associated with a rodent host ecology. Of note, we identified novel prophages and pathogenicity islands in rodent-derived S. aureus that conferred the potential for coagulation of rodent plasma, a key phenotype of abscess formation and persistence. Our findings highlight the remarkable capacity of S. aureus to expand into new host populations, driven by the acquisition of genes promoting survival in new host-species.
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Affiliation(s)
- Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel Mrochen
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Fischer
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Kathleen Pritchett-Corning
- Charles River, Research and Professional Services, Wilmington, Massachusetts, United States of America
- Office of Animal Resources, Harvard University Faculty of Arts and Sciences, Cambridge, Massachusetts, United States of America
| | - Silva Holtfreter
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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3
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Silva V, Ribeiro J, Teixeira P, Pinto P, Vieira-Pinto M, Poeta P, Caniça M, Igrejas G. Genetic Complexity of CC5 Staphylococcus aureus Isolates Associated with Sternal Bursitis in Chickens: Antimicrobial Resistance, Virulence, Plasmids, and Biofilm Formation. Pathogens 2024; 13:519. [PMID: 38921816 PMCID: PMC11206601 DOI: 10.3390/pathogens13060519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/09/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Sternal bursitis, a common inflammatory condition in poultry, poses significant challenges to both animal welfare and public health. This study aimed to investigate the prevalence, antimicrobial resistance, and genetic characteristics of Staphylococcus aureus isolates associated with sternal bursitis in chickens. Ninety-eight samples were collected from affected chickens, and 24 S. aureus isolates were identified. Antimicrobial susceptibility testing revealed resistance to multiple agents, with a notable prevalence of aminoglycoside resistance genes. Whole genome sequencing elucidated the genetic diversity and virulence profiles of the isolates, highlighting the predominance of clonal complex 5 (CC5) strains. Additionally, biofilm formation assays demonstrated moderate biofilm production capacity among the isolates. These findings underscore the importance of vigilant monitoring and targeted interventions to mitigate the impact of sternal bursitis in poultry production systems.
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Affiliation(s)
- Vanessa Silva
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Jessica Ribeiro
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Pedro Teixeira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Pedro Pinto
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Madalena Vieira-Pinto
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
| | - Gilberto Igrejas
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ARXIV 2024:arXiv:2403.03688v1. [PMID: 38495572 PMCID: PMC10942477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
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5
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Chen F, Yin Y, Chen H, Wang R, Wang S, Wang H. Global genetic diversity and Asian clades evolution: a phylogeographic study of Staphylococcus aureus sequence type 5. Antimicrob Agents Chemother 2024; 68:e0117523. [PMID: 38259089 PMCID: PMC10916392 DOI: 10.1128/aac.01175-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus sequence type (ST) 5 has spread worldwide; however, phylogeographic studies on the evolution of global phylogenetic and Asian clades of ST5 are lacking. This study included 368 ST5 genome sequences, including 111 newly generated sequences. Primary phylogenetic analysis suggested that there are five clades, and geographical clustering of ST5 methicillin-resistant S. aureus (MRSA) was linked to the acquisition of S. aureus pathogenicity islands (SaPIs; enterotoxin gene island) and integration of the prophage φSa3. The most recent common ancestor of global S. aureus ST5 dates back to the mid-1940s, coinciding with the clinical introduction of penicillin. Bayesian phylogeographic inference allowed to ancestrally trace the Asian ST5 MRSA clade to Japan, which may have spread to major cities in China and Korea in the 1990s. Based on a pan-genome-wide association study, the emergence of Asian ST5 clades was attributed to the gain of prophages, SaPIs, and plasmids, as well as the coevolution of resistance genes. Clade IV displayed greater genomic diversity than the Asian MRSA clades. Collectively, our study provides in-depth insights into the global evolution of S. aureus ST5 mainly in China and the United States and reveals that different S. aureus ST5 clades have arisen independently in different parts of the world, with limited geographic dispersal across continents.
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Affiliation(s)
- Fengning Chen
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
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Lenchenko E, Sachivkina N, Petrukhina O, Petukhov N, Zharov A, Zhabo N, Avdonina M. Anatomical, pathological, and histological features of experimental respiratory infection of birds by biofilm-forming bacteria Staphylococcus aureus. Vet World 2024; 17:612-619. [PMID: 38680142 PMCID: PMC11045526 DOI: 10.14202/vetworld.2024.612-619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/20/2024] [Indexed: 05/01/2024] Open
Abstract
Background and Aim The pathogenesis of staphylococcal infections is mediated by virulence factors, such as enzymes, toxins, and biofilms, which increase the resistance of microorganisms to host immune system evasion. Testing and searching for standardized multi-level algorithms for the indication and differentiation of biofilms at the early stages of diagnosis will contribute to the development of preventive measures to control the critical points of technology and manage dangerous risk factors for the spread of infectious diseases. This research aimed to study the main stages of Staphylococcus aureus biofilm formation in in vitro experiments and to analyze the dynamics of respiratory syndrome development in chickens infected with these bacteria. Materials and Methods Experimental reproduction of the infectious process was performed using laboratory models: 10-day-old White Leghorn chickens (n = 20). Before the experiments, the birds were divided into two groups according to the principle of analogs: Group I (control, n = 10): the birds were intranasally inoculated with 0.5 cm3 of 0.9% NaCl solution; Group II (experiment, n = 10): the birds were intranasally inoculated with a suspension of S. aureus bacteria, 0.5 cm3, concentration 1 billion/cm3. Results Colonization of individual areas of the substrate under study in vitro occurred gradually from the sedimentation and adhesion of single motile planktonic cells to the attachment stage of microcolony development. Staining preparations with gentian violet due to the "metachromosia" property of this dye are a quick and fairly simple way to differentiate cells and the intercellular matrix of biofilms. Fixation with vapors of glutaraldehyde and osmium tetroxide preserves the natural architecture of biofilms under optical and scanning electron microscopy. Pure cultures of S. aureus microorganisms were isolated from the blood, lungs, small intestine, liver, kidneys, and spleen after 5-10 days during experimental infection of chickens. Clinical signs of respiratory syndrome developed within 5-6 days after infection. Acute and subacute serous-fibrinous airsacculitis, characterized by edema and thickening of the membranes of the air sacs and the presence of turbid, watery, foamy contents in the cavity, was the most characteristic pathomorphological sign. The signs of acute congestive hyperemia and one-sided serous-fibrinous pneumonia developed with significant thickening of fibrinous deposits. In Garder's gland, there was an increase in the number of secretory sections, indicating hypersecretion of the glands. In the lymphoid follicles of Meckel's diverticulum, leukocytes, usually lymphocytes, and pseudoeosinophils were detected. Conclusions Hydration and heteromorphism of the internal environment of biofilms determine the localization of differentiated cells in a three-dimensional matrix for protection against adverse factors. The most characteristic pathomorphological sign was the development of acute and subacute serous-fibrinous airsacculitis when reproducing the infectious process in susceptible models. There was a significant thickening of fibrinous deposits and signs of acute congestive hyperemia and one or two serous-fibrinous pneumonia developed.
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Affiliation(s)
- Ekaterina Lenchenko
- Department of Veterinary Medicine, Russian Biotechnological University (BIOTECH University), 125080, Moscow, Russia
| | - Nadezhda Sachivkina
- Department of Veterinary Medicine, Agrarian Technological Institute, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Olesya Petrukhina
- Department of Veterinary Medicine, Agrarian Technological Institute, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Nikolay Petukhov
- Department of Technosphere Security, Agrarian Technological Institute, Peoples’ Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Andrey Zharov
- Department of Technosphere Security, Agrarian Technological Institute, Peoples’ Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Natallia Zhabo
- Department of Foreign Languages, Institute of Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Marina Avdonina
- Department of Linguistics and Intercultural Communication of the Faculty of Distance Learning and Part-Time Education of Moscow State Linguistic University, 119034 Moscow, Russia
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Cuny C, Layer-Nicolaou F, Werner G, Witte W. A look at staphylococci from the one health perspective. Int J Med Microbiol 2024; 314:151604. [PMID: 38367509 DOI: 10.1016/j.ijmm.2024.151604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.
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Affiliation(s)
- Christiane Cuny
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.
| | - Franziska Layer-Nicolaou
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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Park JM, Kim JH, Kim G, Sim HJ, Ahn SM, Choi KS, Kwon HJ. Rapid Antibacterial Activity Assessment of Chimeric Lysins. Int J Mol Sci 2024; 25:2430. [PMID: 38397110 PMCID: PMC10888538 DOI: 10.3390/ijms25042430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024] Open
Abstract
Various chimeric lysins have been developed as efficacious antibiotics against multidrug-resistant bacteria, but direct comparisons of their antibacterial activities have been difficult due to the preparation of multiple recombinant chimeric lysins. Previously, we reported an Escherichia coli cell-free expression method to better screen chimeric lysins against Staphylococcus aureus, but we still needed to increase the amounts of expressed proteins enough to be able to detect them non-isotopically for quantity comparisons. In this study, we improved the previous cell-free expression system by adding a previously reported artificial T7 terminator and reversing the different nucleotides between the T7 promoter and start codon to those of the T7 phage. The new method increased the expressed amount of chimeric lysins enough for us to detect them using Western blotting. Therefore, the qualitative comparison of activity between different chimeric lysins has become possible via the adjustment of the number of variables between samples without protein purification. We applied this method to select more active chimeric lysins derived from our previously reported chimeric lysin (ALS2). Finally, we compared the antibacterial activities of our selected chimeric lysins with reported chimeric lysins (ClyC and ClyO) and lysostaphin and determined the rank orders of antibacterial activities on different Staphylococcus aureus strains in our experimental conditions.
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Affiliation(s)
- Jin-Mi Park
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Jun-Hyun Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Gun Kim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hun-Ju Sim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun-Min Ahn
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
| | - Kang-Seuk Choi
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
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Saei HD, McClure JA, Kashif A, Chen S, Conly JM, Zhang K. The Role of Prophage ϕSa3 in the Adaption of Staphylococcus aureus ST398 Sublineages from Human to Animal Hosts. Antibiotics (Basel) 2024; 13:112. [PMID: 38391498 PMCID: PMC10886223 DOI: 10.3390/antibiotics13020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
Staphylococcus aureus sequence type (ST) 398 is a lineage affecting both humans and livestock worldwide. However, the mechanisms underlying its clonal evolution are still not clearly elucidated. We applied whole-genome sequencing (WGS) typing to 45 S. aureus strains from China and Canada between 2005 and 2014, in order to gain insight into their evolutionary pathway. Based on WGS phylogenetic analysis, 42 isolates were assigned to the human-associated clade (I/II-GOI) and 3 isolates to livestock-associated clade (IIa). Phylogeny of ϕSa3 sequences revealed five phage groups (Groups 1-5), with Group 1 carrying ϕSa3-Group 1 (ϕSa3-G1), Group 2 carrying ϕSa3-G2, Group 3 carrying ϕSa3-G3, Group 4 carrying ϕSa3-G4 and Group 5 lacking ϕSa3. ϕSa3-G1 was only found in strains that accounted for the most ancestral human clade I, while ϕSa3-G2, ϕSa3-G3 and ϕSa3-G4 were found restricted to sublineages within clade II-GOI. Some isolates of clade II-GOI were also found to be ϕSa3-negative or resistant to methicillin which are unusual characteristics for human-adapted isolates. This study demonstrated a strong association between phylogenetic grouping and phage type, suggesting an important role of ϕSa3 prophage in the evolution of human-adapted ST398 subclones. In addition, our results suggest that this subclone slowly began to adapt to animal hosts by losing ϕSa3 and acquiring methicillin resistance, which was observed in some strains of human-associated clade II-GOI, an intermediate human to livestock transmission clade.
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Affiliation(s)
- Habib Dastmalchi Saei
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia 5756151818, Iran
| | - Jo-Ann McClure
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Precision Laboratories/University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ayesha Kashif
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
| | - Sidong Chen
- Department of Epidemiology, Public Health College, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - John M Conly
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Precision Laboratories/University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
| | - Kunyan Zhang
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Precision Laboratories/University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Medicine, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB T2N 4N1, Canada
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Monecke S, Braun SD, Collatz M, Diezel C, Müller E, Reinicke M, Cabal Rosel A, Feßler AT, Hanke D, Loncaric I, Schwarz S, Cortez de Jäckel S, Ruppitsch W, Gavier-Widén D, Hotzel H, Ehricht R. Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl. Microorganisms 2024; 12:96. [PMID: 38257923 PMCID: PMC10821479 DOI: 10.3390/microorganisms12010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain's genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying "bird-specific" virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.
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Affiliation(s)
- Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Maximillian Collatz
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Adriana Cabal Rosel
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection, Medicine School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria
| | - Dolores Gavier-Widén
- Department of Pathology and Wildlife Disease, National Veterinary Institute (SVA), 75189 Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), 75007 Uppsala, Sweden
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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11
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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12
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Ha EJ, Hong SM, Kim SJ, Ahn SM, Kim HW, Choi KS, Kwon HJ. Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli. Antibiotics (Basel) 2023; 12:1714. [PMID: 38136748 PMCID: PMC10740950 DOI: 10.3390/antibiotics12121714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.
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Affiliation(s)
- Eun-Jin Ha
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Sun-Min Ahn
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Ho-Won Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Republic of Korea
- GeNiner Inc., Seoul 08826, Republic of Korea
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13
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Abrudan MI, Shamanna V, Prasanna A, Underwood A, Argimón S, Nagaraj G, Di Gregorio S, Govindan V, Vasanth A, Dharmavaram S, Kekre M, Aanensen DM, Ravikumar KL. Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India. mSphere 2023; 8:e0018523. [PMID: 37698417 PMCID: PMC10597471 DOI: 10.1128/msphere.00185-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/13/2023] [Indexed: 09/13/2023] Open
Abstract
Staphylococcus aureus is a major pathogen in India causing community and nosocomial infections, but little is known about its molecular epidemiology and mechanisms of resistance in hospital settings. Here, we use whole-genome sequencing (WGS) to characterize 478 S. aureus clinical isolates (393 methicillin-resistant Staphylococcus aureus (MRSA) and 85 methicilin-sensitive Staphylococcus aureus (MSSA) collected from 17 sentinel sites across India between 2014 and 2019. Sequencing results confirmed that sequence type 22 (ST22) (142 isolates, 29.7%), ST239 (74 isolates, 15.48%), and ST772 (67 isolates, 14%) were the most common clones. An in-depth analysis of 175 clonal complex (CC) 22 Indian isolates identified two novel ST22 MRSA lineages, both Panton-Valentine leukocidin+, both resistant to fluoroquinolones and aminoglycosides, and one harboring the the gene for toxic shock syndrome toxin 1 (tst). A temporal analysis of 1797 CC22 global isolates from 14 different studies showed that the two Indian ST22 lineages shared a common ancestor in 1984 (95% highest posterior density [HPD]: 1982-1986), as well as evidence of transmission to other parts of the world. Moreover, the study also gives a comprehensive view of ST2371, a sublineage of CC22, as a new emerging lineage in India and describes it in relationship with the other Indian ST22 isolates. In addition, the retrospective identification of a putative outbreak of multidrug-resistant (MDR) ST239 from a single hospital in Bangalore that persisted over a period of 3 years highlights the need for the implementation of routine surveillance and simple infection prevention and control measures to reduce these outbreaks. To our knowledge, this is the first WGS study that characterized CC22 in India and showed that the Indian clones are distinct from the EMRSA-15 clone. Thus, with the improved resolution afforded by WGS, this study substantially contributed to our understanding of the global population of MRSA. IMPORTANCE The study conducted in India between 2014 and 2019 presents novel insights into the prevalence of MRSA in the region. Previous studies have characterized two dominant clones of MRSA in India, ST772 and ST239, using whole-genome sequencing. However, this study is the first to describe the third dominant clone, ST22, using the same approach. The ST22 Indian isolates were analyzed in-depth, leading to the discovery of two new sublineages of hospital-acquired Staphylococcus aureus in India, both carrying antimicrobial resistance genes and mutations, which limit treatment options for patients. One of the newly characterized sublineages, second Indian cluster, carries the tsst-1 virulence gene, increasing the risk of severe infections. The geographic spread of the two novel lineages, both within India and internationally, could pose a global public health threat. The study also sheds light on ST2371 in India, a single-locus variant of ST22. The identification of a putative outbreak of MDR ST239 in a single hospital in Bangalore emphasizes the need for routine surveillance and simple infection prevention and control measures to reduce these outbreaks. Overall, this study significantly contributes to our understanding of the global population of MRSA, thanks to the improved resolution afforded by WGS.
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Affiliation(s)
- Monica I. Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Department of Biotechnology, NMAM Institute of Technology, Nitte (Deemed to be University), Mangalore, India
| | - Akshatha Prasanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sabrina Di Gregorio
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Ashwini Vasanth
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sravani Dharmavaram
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - K. L. Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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14
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Banaszkiewicz S, Tabiś A, Wałecki B, Łyżwińska K, Bystroń J, Bania J. spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar. MICROBIAL ECOLOGY 2023; 86:2184-2191. [PMID: 37156959 PMCID: PMC10497643 DOI: 10.1007/s00248-023-02236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.
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Affiliation(s)
- Sylwia Banaszkiewicz
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Tabiś
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Wałecki
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Karolina Łyżwińska
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jarosław Bystroń
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
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15
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Zang X, Pascoe B, Mourkas E, Kong K, Jiao X, Sheppard SK, Huang J. Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations. Microb Genom 2023; 9:001121. [PMID: 37877958 PMCID: PMC10634442 DOI: 10.1099/mgen.0.001121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Non-human primates share recent common ancestry with humans and exhibit comparable disease symptoms. Here, we explored the transmission potential of enteric bacterial pathogens in monkeys exhibiting symptoms of recurrent diarrhoea in a biomedical research facility in China. The common zoonotic bacterium Campylobacter jejuni was isolated from macaques (Macaca mulatta and Macaca fascicularis) and compared to isolates from humans and agricultural animals in Asia. Among the monkeys sampled, 5 % (44/973) tested positive for C. jejuni, 11 % (5/44) of which displayed diarrhoeal symptoms. Genomic analysis of monkey isolates, and 1254 genomes from various sources in Asia, were used to identify the most likely source of human infection. Monkey and human isolates shared high average nucleotide identity, common MLST clonal complexes and clustered together on a phylogeny. Furthermore, the profiles of putative antimicrobial resistance genes were similar between monkeys and humans. Taken together these findings suggest that housed macaques became infected with C. jejuni either directly from humans or via a common contamination source.
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Affiliation(s)
- Xiaoqi Zang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ke Kong
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
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16
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Yu S, Zhou Y, Feng D, Jiang Q, Li T, Jiang G, Zhou Z, Li H. Whole genome sequence-based characterization of virulence and antimicrobial resistance gene profiles of Staphylococcus aureus isolated from food poisoning incidents in eastern China. Front Microbiol 2023; 14:1225472. [PMID: 37795294 PMCID: PMC10546991 DOI: 10.3389/fmicb.2023.1225472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Staphylococcus aureus is an opportunistic foodborne pathogen occasionally isolated from diarrhea patients. In recent years, increasing studies have reported the detection of S. aureus in food poisoning incidents due to food contamination in the North and South of China. However, the epidemiology and genetic characteristics of S. aureus from food poisoning incidents in Eastern China remain unknown. The present study examined the genetic characteristics, antimicrobial resistance, and virulent factors of multidrug-resistant S. aureus isolated from 22 food poisoning incidents reported by the hospitals and health centers in Eastern China from 2011 to 2021. A total of 117 resistant and enterotoxigenic S. aureus isolates were collected and sequenced, among which 20 isolates were identified as methicillin resistant. Genetic analysis revealed 19 distinct CC/ST types, with CC6, CC22, CC59, CC88, and CC398 being the most frequent variants in methicillin-resistant S. aureus (MRSA). A considerable shift in CC types from CC1 to CC398 between 2011 and 2021 was observed in this study, indicating that CC398 may be the main epidemic strain circulating in the current food poisoning incidents. Additionally, genes for enterotoxins were detected in 55 isolates, with a prevalence of 27.8% (27/97) for methicillin-sensitive variants and 35.0% (7/20) for MRSA. The scn gene was detected in 59.0% of the isolates, demonstrating diverse contaminations of S. aureus among livestock-to-human transmission. Of the 117 isolates, only ten isolates displayed multi-drug resistance (MDR) to penicillin, tetracycline, and macrolides. None of the 117 foodborne S. aureus isolates tested positive for vanA in this study. Together, the present study provided phylogenetic characteristics of S. aureus from food poisoning incidents that emerged in Eastern China from 2011 to 2021. Our results suggested that these diarrhea episodes were hypotonic and merely transient low-MDR infections, however, further research for continued surveillance given the detection of virulence and antimicrobial resistance determinants is required to elucidate the genomic characteristics of pathogenic S. aureus in food poisoning incidents in the context of public health.
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17
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Souza SSR, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Multi-host infection and phylogenetically diverse lineages shape the recombination and gene pool dynamics of Staphylococcus aureus. BMC Microbiol 2023; 23:235. [PMID: 37626313 PMCID: PMC10463932 DOI: 10.1186/s12866-023-02985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States. RESULTS Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages. CONCLUSIONS Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S. aureus colonization, infection, and transmission across the One Health continuum.
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Affiliation(s)
- Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Spencer A Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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18
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Matuszewska M, Dabrowska A, Murray GGR, Kett SM, Vick AJA, Banister SC, Pantoja Munoz L, Cunningham P, Welch JJ, Holmes MA, Weinert LA. Absence of Staphylococcus aureus in Wild Populations of Fish Supports a Spillover Hypothesis. Microbiol Spectr 2023; 11:e0485822. [PMID: 37341608 PMCID: PMC10434045 DOI: 10.1128/spectrum.04858-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus is a human commensal and opportunistic pathogen that also infects other animals. In humans and livestock, where S. aureus is most studied, strains are specialized for different host species. Recent studies have also found S. aureus in diverse wild animals. However, it remains unclear whether these isolates are also specialized for their hosts or whether their presence is due to repeated spillovers from source populations. This study focuses on S. aureus in fish, testing the spillover hypothesis in two ways. First, we examined 12 S. aureus isolates obtained from the internal and external organs of a farmed fish. While all isolates were from clonal complex 45, genomic diversity indicates repeated acquisition. The presence of a φSa3 prophage containing human immune evasion genes suggests that the source was originally human. Second, we tested for S. aureus in wild fish that were isolated from likely sources. In particular, we sampled 123 brown trout and their environment at 16 sites in the remote Scottish Highlands with variable levels of exposure to humans, birds, and livestock. This screen found no S. aureus infection in any of the wild populations or their environment. Together, these results support that the presence of S. aureus in fish and aquaculture is due to spillover from humans rather than specialization. Given the trends of increasing fish consumption, a better understanding of the dynamics of S. aureus spillover in aquaculture will mitigate future risks to fish and human health. IMPORTANCE Staphylococcus aureus is a human and livestock commensal but also an important pathogen responsible for high human mortality rates and economic losses in farming. Recent studies show that S. aureus is common in wild animals, including fish. However, we do not know whether these animals are part of the normal host range of S. aureus or whether infection is due to repeated spillover events from true S. aureus hosts. Answering this question has implications for public health and conservation. We find support for the spillover hypothesis by combining genome sequencing of S. aureus isolates from farmed fish and screens for S. aureus in isolated wild populations. The results imply that fish are unlikely to be a source of novel emergent S. aureus strains but highlight the prominence of the spillover of antibiotic-resistant bacteria from humans and livestock. This may affect both future fish disease potential and the risk of human food poisoning.
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Affiliation(s)
- Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alicja Dabrowska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Gemma G. R. Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London
| | - Steve M. Kett
- Department of Natural Sciences, Middlesex University London, London, United Kingdom
| | - Andy J. A. Vick
- RAL Space (UKRI-STFC), Harwell Campus, Didcot, Oxfordshire, United Kingdom
| | - Sofie C. Banister
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Peter Cunningham
- Wester Ross Fisheries Trust, Harbour Centre, Gairloch, Wester Ross, United Kingdom
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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19
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Rhoads DD, Pummil J, Ekesi NS, Alrubaye AAK. Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis. PLoS One 2023; 18:e0283914. [PMID: 37406030 DOI: 10.1371/journal.pone.0283914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.
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Affiliation(s)
- Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
| | - Jeff Pummil
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR, United States of America
| | - Nnamdi S Ekesi
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, United States of America
| | - Adnan A K Alrubaye
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
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20
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Choppa VSR, Kim WK. A Review on Pathophysiology, and Molecular Mechanisms of Bacterial Chondronecrosis and Osteomyelitis in Commercial Broilers. Biomolecules 2023; 13:1032. [PMID: 37509068 PMCID: PMC10377700 DOI: 10.3390/biom13071032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Modern day broilers have a great genetic potential to gain heavy bodyweights with a huge metabolic demand prior to their fully mature ages. Moreover, this made the broilers prone to opportunistic pathogens which may enter the locomotory organs under stress causing bacterial chondronecrosis and osteomyelitis (BCO). Such pathogenic colonization is further accelerated by microfractures and clefts that are formed in the bones due to rapid growth rate of the broilers along with ischemia of blood vessels. Furthermore, there are several pathways which alter bone homeostasis like acute phase response, and intrinsic and extrinsic cell death pathways. In contrast, all the affected birds may not exhibit clinical lameness even with the presence of lameness associated factors causing infection. Although Staphylococcus, E. coli, and Enterococcus are considered as common bacterial pathogens involved in BCO, but there exist several other non-culturable bacteria. Any deviation from maintaining a homeostatic environment in the gut might lead to bacterial translocation through blood followed by proliferation of pathogenic bacteria in respective organs including bones. It is important to alleviate dysbiosis of the blood which is analogous to dysbiosis in the gut. This can be achieved by supplementing pro, pre, and synbiotics which helps in providing a eubiotic environment abating the bacterial translocation that was studied to the incidence of BCO. This review focused on potential and novel biomarkers, pathophysiological mechanism, the economic significance of BCO, immune mechanisms, and miscellaneous factors causing BCO. In addition, the role of gut microbiomes along with their diversity and cell culture models from compact bones of chicken in better understanding of BCO were explored.
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Affiliation(s)
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA 30602, USA
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21
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Magoch M, McEwen AG, Napolitano V, Władyka B, Dubin G. Crystal Structure of Staphopain C from Staphylococcus aureus. Molecules 2023; 28:molecules28114407. [PMID: 37298883 DOI: 10.3390/molecules28114407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Staphylococcus aureus is a common opportunistic pathogen of humans and livestock that causes a wide variety of infections. The success of S. aureus as a pathogen depends on the production of an array of virulence factors including cysteine proteases (staphopains)-major secreted proteases of certain strains of the bacterium. Here, we report the three-dimensional structure of staphopain C (ScpA2) of S. aureus, which shows the typical papain-like fold and uncovers a detailed molecular description of the active site. Because the protein is involved in the pathogenesis of a chicken disease, our work provides the foundation for inhibitor design and potential antimicrobial strategies against this pathogen.
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Affiliation(s)
- Malgorzata Magoch
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Alastair G McEwen
- CNRS, INSERM, Université de Strasbourg, IGBMC UMR 7104-UMR-S 1258, F-67400 Illkirch, France
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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22
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Burgold-Voigt S, Monecke S, Busch A, Bocklisch H, Braun SD, Diezel C, Hotzel H, Liebler-Tenorio EM, Müller E, Reinicke M, Reissig A, Ruppelt-Lorz A, Ehricht R. Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger ( Meles meles). Pathogens 2023; 12:pathogens12050704. [PMID: 37242375 DOI: 10.3390/pathogens12050704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.
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Affiliation(s)
- Sindy Burgold-Voigt
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Anne Busch
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital, 07747 Jena, Germany
| | - Herbert Bocklisch
- Thuringian State Authority for Food-Safety and Consumer Protection (TLLV), 99947 Bad Langensalza, Germany
| | - Sascha D Braun
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Bacterial Infections and Zoonoses, 07751 Jena, Germany
| | | | - Elke Müller
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Martin Reinicke
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Annett Reissig
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Virology, Dresden University Hospital, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz-Institute of Photonic Technology (Leibniz-IPHT), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University, 07743 Jena, Germany
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23
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Park JM, Ko DS, Kim HS, Kim NH, Kim EK, Roh YH, Kim D, Kim JH, Choi KS, Kwon HJ. Rapid Screening and Comparison of Chimeric Lysins for Antibacterial Activity against Staphylococcus aureus Strains. Antibiotics (Basel) 2023; 12:antibiotics12040667. [PMID: 37107029 PMCID: PMC10135017 DOI: 10.3390/antibiotics12040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Chimeric lysins composed of various combinations of cell wall-lysing (enzymatic) and cell-wall-binding (CWB) domains of endolysins, autolysins, and bacteriocins have been developed as alternatives to or adjuvants of conventional antibiotics. The screening of multiple chimeric lysin candidates for activity via E. coli expression is not cost effective, and we previously reported on a simple cell-free expression system as an alternative. In this study, we sufficiently improved upon this cell-free expression system for use in screening activity via a turbidity reduction test, which is more appropriate than a colony reduction test when applied in multiple screening. Using the improved protocol, we screened and compared the antibacterial activity of chimeric lysin candidates and verified the relatively strong activity associated with the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain of secretory antigen SsaA-like protein (ALS2). ALS2 expressed in E. coli showed two major bands, and the smaller one (subprotein) was shown to be expressed by an innate downstream promoter and start codon (ATG). The introduction of synonymous mutations in the promoter resulted in clearly reduced expression of the subprotein, whereas missense mutations in the start codon abolished antibacterial activity as well as subprotein production. Interestingly, most of the S. aureus strains responsible for bovine mastitis were susceptible to ALS2, but those from human and chicken were less susceptible. Thus, the simple and rapid screening method can be applied to select functional chimeric lysins and define mutations affecting antibacterial activity, and ALS2 may be useful in itself and as a lead molecule to control bovine mastitis.
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Affiliation(s)
- Jin-Mi Park
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Dae-Sung Ko
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Hee-Soo Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Nam-Hyung Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
| | - Eun-Kyoung Kim
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Young-Hye Roh
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, College of Veterinary Medicine, Seoul National University, Pyeongchang-gun 25354, Republic of Korea
| | - Jae-Hong Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Kang-Seuk Choi
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.)
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute for Veterinary Science, College of Veterinary Medicine, BK21 for Veterinary Science, Seoul 08826, Republic of Korea
- Correspondence: (K.-S.C.); (H.-J.K.); Tel.: +82-2-880-1266 (K.-S.C. & H.-J.K.)
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24
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Martínez-Seijas C, Mascarós P, Lizana V, Martí-Marco A, Arnau-Bonachera A, Chillida-Martínez E, Cardells J, Selva L, Viana D, Corpa JM. Genomic Characterization of Staphylococcus aureus in Wildlife. Animals (Basel) 2023; 13:ani13061064. [PMID: 36978605 PMCID: PMC10044652 DOI: 10.3390/ani13061064] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Staphylococcus aureus is an opportunistic multi-host pathogen that threatens both human and animal health. Animals can act as a reservoir of S. aureus for humans, but very little is known about wild animals’ epidemiological role. Therefore, in this study, we performed a genomic characterization of S. aureus isolates from wildlife, hunters, and their auxiliary hunting animals of Eastern Spain. Of 20 different species, 242 wild animals were examined, of which 28.1% were S. aureus carriers. The common genet, the Iberian ibex, and the European hedgehog were the species with the highest S. aureus carriage. We identified 30 different sequence types (STs), including lineages associated with wild animals such as ST49 and ST581, multispecies lineages such as ST130, ST398, and ST425, and lineages commonly isolated from humans, including ST1 and ST5. The hunters and the single positive ferret shared ST5, ST398, or ST425 with wild animals. In wildlife isolates, the highest resistance levels were found for penicillin (32.8%). For virulence factors, 26.2% of them carried superantigens, while 14.8% harbored the immune evasion cluster (IEC), which indicates probable human origin. Our findings suggest that wild animals are a reservoir of clinically relevant genes and lineages that could have the potential to be transmitted to humans. These data support the notion that wildlife surveillance is necessary to better understand the epidemiology of S. aureus as a pathogen that circulates among humans, animals, and the environment.
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Affiliation(s)
- Carmen Martínez-Seijas
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Patricia Mascarós
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Víctor Lizana
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Alba Martí-Marco
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Alberto Arnau-Bonachera
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Eva Chillida-Martínez
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - Jesús Cardells
- Servicio de Análisis, Investigación, Gestión de Animales Silvestres (SAIGAS), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Wildlife Ecology & Health Group (WE&H), Universitat Autònoma de Barcelona (UAB), Edifici V, Travessera dels Turons, Bellaterra, 08193 Barcelona, Spain
| | - Laura Selva
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
| | - David Viana
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (D.V.); (J.M.C.); Tel.: +34-961-369-000 (D.V. & J.M.C.)
| | - Juan M. Corpa
- Biomedical Research Institute, PASAPTA-Pathology Group, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (D.V.); (J.M.C.); Tel.: +34-961-369-000 (D.V. & J.M.C.)
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25
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Grossar D, Haynes E, Budge GE, Parejo M, Gauthier L, Charrière JD, Chapuisat M, Dietemann V. Population genetic diversity and dynamics of the honey bee brood pathogen Melissococcus plutonius in a region with high prevalence. J Invertebr Pathol 2023; 196:107867. [PMID: 36503887 PMCID: PMC9885493 DOI: 10.1016/j.jip.2022.107867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
European foulbrood (EFB) is a honey bee brood disease caused by the bacterium Melissococcus plutonius. Large-scale EFB outbreaks have been reported in several countries in recent decades, which entail costly sanitation measures of affected apiaries to restrict the spread of this contagious pathogen. To mitigate its impact, a better understanding of the population dynamics of the etiological agent is required. We here used multi-locus sequence typing (MLST) to infer the genetic diversity and geographical distribution of 160 M. plutonius isolates collected from EFB symptomatic honey bee colonies seven years apart. Isolates belonged to three clonal complexes (CCs) known worldwide and to 12 sequence types (STs), of which five were novel. Phylogenetic and clustering analyses showed that some of these novel sequence types have likely evolved locally during a period of outbreak, but most disappeared again. We further screened the isolates for melissotoxin A (mtxA), a putative virulence gene. The prevalence of STs in which mtxA was frequent increased over time, suggesting that this gene promotes spread. Despite the increased frequency of this gene in the population, the total number of cases decreased, which could be due to stricter control measures implemented before the second sampling period. Our results provide a better understanding of M. plutonius population dynamics and help identify knowledge gaps that limit efficient control of this emerging disease.
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Affiliation(s)
- Daniela Grossar
- Swiss Bee Research Center, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; Department of Ecology and Evolution, Biophore, UNIL-Sorge, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Edward Haynes
- Bee health laboratory, Fera Science Ltd, Sand Hutton, York, YO41 1LZ, the United Kingdom of Great Britain and Northern Ireland; Fera Department of Biology, University of York, York, the United Kingdom of Great Britain and Northern Ireland
| | - Giles E Budge
- Bee health laboratory, Fera Science Ltd, Sand Hutton, York, YO41 1LZ, the United Kingdom of Great Britain and Northern Ireland; School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, the United Kingdom of Great Britain and Northern Ireland
| | - Melanie Parejo
- Swiss Bee Research Center, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, 48940, Spain
| | - Laurent Gauthier
- Swiss Bee Research Center, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland
| | - Jean-Daniel Charrière
- Swiss Bee Research Center, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland
| | - Michel Chapuisat
- Department of Ecology and Evolution, Biophore, UNIL-Sorge, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Dietemann
- Swiss Bee Research Center, Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; Department of Ecology and Evolution, Biophore, UNIL-Sorge, University of Lausanne, 1015 Lausanne, Switzerland
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Jenkins CL, Bean HD. Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection. Pathogens 2023; 12:pathogens12020181. [PMID: 36839453 PMCID: PMC9963134 DOI: 10.3390/pathogens12020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.
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Affiliation(s)
- Carrie L. Jenkins
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Heather D. Bean
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287, USA
- Correspondence:
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Shoaib M, Aqib AI, Muzammil I, Majeed N, Bhutta ZA, Kulyar MFEA, Fatima M, Zaheer CNF, Muneer A, Murtaza M, Kashif M, Shafqat F, Pu W. MRSA compendium of epidemiology, transmission, pathophysiology, treatment, and prevention within one health framework. Front Microbiol 2023; 13:1067284. [PMID: 36704547 PMCID: PMC9871788 DOI: 10.3389/fmicb.2022.1067284] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Staphylococcus aureus is recognized as commensal as well as opportunistic pathogen of humans and animals. Methicillin resistant strain of S. aureus (MRSA) has emerged as a major pathogen in hospitals, community and veterinary settings that compromises the public health and livestock production. MRSA basically emerged from MSSA after acquiring SCCmec element through gene transfer containing mecA gene responsible for encoding PBP-2α. This protein renders the MRSA resistant to most of the β-lactam antibiotics. Due to the continuous increasing prevalence and transmission of MRSA in hospitals, community and veterinary settings posing a major threat to public health. Furthermore, high pathogenicity of MRSA due to a number of virulence factors produced by S. aureus along with antibiotic resistance help to breach the immunity of host and responsible for causing severe infections in humans and animals. The clinical manifestations of MRSA consist of skin and soft tissues infection to bacteremia, septicemia, toxic shock, and scalded skin syndrome. Moreover, due to the increasing resistance of MRSA to number of antibiotics, there is need to approach alternatives ways to overcome economic as well as human losses. This review is going to discuss various aspects of MRSA starting from emergence, transmission, epidemiology, pathophysiology, disease patterns in hosts, novel treatment, and control strategies.
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Affiliation(s)
- Muhammad Shoaib
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Iqra Muzammil
- Department of Medicine, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Noreen Majeed
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Mahreen Fatima
- Faculty of Biosciences, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | | | - Afshan Muneer
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Maheen Murtaza
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Kashif
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Furqan Shafqat
- Department of Microbiology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project, Gansu Province/Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture and Rural Affairs/Lanzhou Institute of Husbandry and Pharmaceutical Sciences of the Chinese Academy of Agricultural Sciences, Lanzhou, China
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28
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Igbinosa EO, Beshiru A, Igbinosa IH, Ogofure AG, Ekundayo TC, Okoh AI. Prevalence, multiple antibiotic resistance and virulence profile of methicillin-resistant Staphylococcus aureus (MRSA) in retail poultry meat from Edo, Nigeria. Front Cell Infect Microbiol 2023; 13:1122059. [PMID: 36936767 PMCID: PMC10017849 DOI: 10.3389/fcimb.2023.1122059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Staphylococcus aureus causes staphylococcal food poisoning and several difficult-to-treat infections. The occurrence and dissemination of methicillin-resistance S. aureus (MRSA) in Nigeria is crucial and well documented in hospitals. However, findings on MRSA from meat in the country are yet to be adequately reported. The current study determined the prevalence, virulence profile and antibiogram characteristics of MRSA from a raw chicken product from retail outlets within Edo. Methods A total of 368 poultry meat samples were assessed for MRSA using a standard culture-based approach and characterized further using a molecular method. The antimicrobial susceptibility profile of the isolates was determined using the disc diffusion method. The biofilm profile of the isolates was assayed via the crystal violet microtitre-plate method. Virulence and antimicrobial resistance genes were screened using polymerase chain reaction via specific primers. Results Of the samples tested, 110 (29.9%) were positive for MRSA. All the isolates were positive for deoxyribonuclease (DNase), coagulase and beta-hemolysis production. Biofilm profile revealed 27 (24.55%) weak biofilm formers, 18 (16.36%) moderate biofilm formers, and 39 (35.45%) strong biofilm formers. The isolates harboured 2 and ≤17 virulence genes. Enterotoxin gene profiling revealed that 100 (90.9%) isolates harboured one or more genes. Resistance against the tested antibiotics followed the order: tetracycline 64(58.2%), ciprofloxacin 71(64.6%), trimethoprim 71(64.6%) and rifampin 103(93.6%). A total of 89 isolates were multidrug-resistant, while 3 isolates were resistant to all 22 antibiotics tested. The isolates harboured antimicrobial-resistant determinants such as methicillin-resistant gene (mecA), tetracycline resistance genes (tetK, tetL), erythromycin resistance genes (ermA, ermC), trimethoprim resistance gene (dfrK). All the staphylococcal cassette chromosome mec (SCCmec) IVa and SCCmec V positive isolates harboured the Panton-Valentine Leukocidin Gene (PVL). Conclusion In conclusion, S. aureus was resistant to commonly used antibiotics; a concern to public health concerning the transmission of these pathogens after consuming these highlight the significance of antimicrobial and enterotoxigenic monitoring of S. aureus in food chains.
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Affiliation(s)
- Etinosa O. Igbinosa
- Applied Microbial Processes and Environmental Health Research Group, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
- Stellenosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Etinosa O. Igbinosa,
| | - Abeni Beshiru
- Applied Microbial Processes and Environmental Health Research Group, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
- Stellenosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- Department of Microbiology, College of Natural and Applied Sciences, Western Delta University, Oghara, Nigeria
| | - Isoken H. Igbinosa
- Applied Microbial Processes and Environmental Health Research Group, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
- Department of Environmental Management and Toxicology, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| | - Abraham G. Ogofure
- Applied Microbial Processes and Environmental Health Research Group, Faculty of Life Sciences, University of Benin, Benin City, Nigeria
| | - Temitope C. Ekundayo
- South African Medical Research Council (SAMRC) Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa
- Department of Microbiology, University of Medical Sciences, Ondo City, Ondo, Nigeria
| | - Anthony I. Okoh
- South African Medical Research Council (SAMRC) Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa
- Department of Environmental Health Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
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Zhao S, Hu I, Lou J, Chong MK, Cao L, He D, Zee BC, Wang MH. The mechanism shaping the logistic growth of mutation proportion in epidemics at population scale. Infect Dis Model 2022; 8:107-121. [PMID: 36632179 PMCID: PMC9811219 DOI: 10.1016/j.idm.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
Virus evolution is a common process of pathogen adaption to host population and environment. Frequently, a small but important fraction of virus mutations are reported to contribute to higher risks of host infection, which is one of the major determinants of infectious diseases outbreaks at population scale. The key mutations contributing to transmission advantage of a genetic variant often grow and reach fixation rapidly. Based on classic epidemiology theories of disease transmission, we proposed a mechanistic explanation of the process that between-host transmission advantage may shape the observed logistic curve of the mutation proportion in population. The logistic growth of mutation is further generalized by incorporating time-varying selective pressure to account for impacts of external factors on pathogen adaptiveness. The proposed model is implemented in real-world data of COVID-19 to capture the emerging trends and changing dynamics of the B.1.1.7 strains of SARS-CoV-2 in England. The model characterizes and establishes the underlying theoretical mechanism that shapes the logistic growth of mutation in population.
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Affiliation(s)
- Shi Zhao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Inchi Hu
- Department of Information Systems, Business Statistics and Operations Management, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China
| | - Marc K.C. Chong
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Benny C.Y. Zee
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China
| | - Maggie H. Wang
- JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China,CUHK Shenzhen Research Institute, Shenzhen, China,Corresponding author. JC School of Public Health and Primary Care, Chinese University of Hong Kong, Hong Kong, China.
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30
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Regressive evolution of an effector following a host jump in the Irish potato famine pathogen lineage. PLoS Pathog 2022; 18:e1010918. [DOI: 10.1371/journal.ppat.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 11/08/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
In order to infect a new host species, the pathogen must evolve to enhance infection and transmission in the novel environment. Although we often think of evolution as a process of accumulation, it is also a process of loss. Here, we document an example of regressive evolution of an effector activity in the Irish potato famine pathogen (Phytophthora infestans) lineage, providing evidence that a key sequence motif in the effector PexRD54 has degenerated following a host jump. We began by looking at PexRD54 and PexRD54-like sequences from across Phytophthora species. We found that PexRD54 emerged in the common ancestor of Phytophthora clade 1b and 1c species, and further sequence analysis showed that a key functional motif, the C-terminal ATG8-interacting motif (AIM), was also acquired at this point in the lineage. A closer analysis showed that the P. mirabilis PexRD54 (PmPexRD54) AIM is atypical, the otherwise-conserved central residue mutated from a glutamate to a lysine. We aimed to determine whether this PmPexRD54 AIM polymorphism represented an adaptation to the Mirabilis jalapa host environment. We began by characterizing the M. jalapa ATG8 family, finding that they have a unique evolutionary history compared to previously characterized ATG8s. Then, using co-immunoprecipitation and isothermal titration calorimetry assays, we showed that both full-length PmPexRD54 and the PmPexRD54 AIM peptide bind weakly to the M. jalapa ATG8s. Through a combination of binding assays and structural modelling, we showed that the identity of the residue at the position of the PmPexRD54 AIM polymorphism can underpin high-affinity binding to plant ATG8s. Finally, we conclude that the functionality of the PexRD54 AIM was lost in the P. mirabilis lineage, perhaps owing to as-yet-unknown selection pressure on this effector in the new host environment.
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31
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Chaguza C, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. CELL GENOMICS 2022; 2:100194. [PMID: 36465278 PMCID: PMC9718559 DOI: 10.1016/j.xgen.2022.100194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA,Corresponding author
| | | | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA,Corresponding author
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El-Deeb W, Cave R, Fayez M, Alhumam N, Quadri S, Mkrtchyan HV. Methicillin Resistant Staphylococci Isolated from Goats and Their Farm Environments in Saudi Arabia Genotypically Linked to Known Human Clinical Isolates: a Pilot Study. Microbiol Spectr 2022; 10:e0038722. [PMID: 35913203 PMCID: PMC9431424 DOI: 10.1128/spectrum.00387-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/09/2022] [Indexed: 11/20/2022] Open
Abstract
We conducted a pilot whole genome sequencing (WGS) study to characterize the genotypes of nine methicillin resistant staphylococci (MRS) isolates recovered from goats and their farm environments in Eastern Province, Saudi Arabia, between November 2019 to August 2020. Seven out of nine isolates were methicillin resistant Staphylococcus aureus (MRSA), and two were methicillin resistant Staphylococcus epidermidis (MRSE). All MRSA isolates possessed genotypes previously identified to infect humans, including isolates harboring ST6-SCCmec IV-t304 (n = 4), ST5-SCCmec VI- t688 (n = 2) and ST5-SCCmec V-t311 (n = 1). 2 MRSA isolates possessed plasmids that were genetically similar to those identified in S. aureus isolates recovered from humans and poultry. In contrast, plasmids found in three MRSA isolates and one MRSE isolate were genetically similar to those recovered from humans. All MRSA isolates harbored the host innate modulate genes sak and scn previously associated with human infections. The genotypes of MRSE isolates were determined as ST35, a well-known zoonotic sequence type and ST153, which has been associated with humans. However, the MRSE isolates were untypeable due to extra ccr complexes identified in their SCCmec elements. Moreover, we identified in ST153 isolate SCCmec element also harbored the Arginine Catabolic Mobile Element (ACME) IV. All MRS isolates were phenotypically resistant to trimethoprim-sulfamethoxazole, an antibiotic for the decolonization of MRS. Three isolates carried antibiotic resistance genes in their SCCmec elements that were not previously described, including those encoding fusidic acid resistance (fusC) and trimethoprim resistance (dfrC) incorporated in the MRSA SCCmec VI. IMPORTANCE Our findings demonstrate a possible cross-transmission of methicillin resistant staphylococci between goats and their local environments and between goats and humans. Due to ever increasing resistance to multiple antibiotics, the burden of MRS has a significant impact on livestock farming, public health, and the economy worldwide. This study highlights that implementing a holistic approach to whole genome sequencing surveillance in livestock and farm environments would aid our understanding of the transmission of methicillin resistant staphylococci and, most importantly, allow us to implement appropriate infection control and hygiene practices.
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Affiliation(s)
- Wael El-Deeb
- Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Internal Medicine, Infectious Diseases and Fish Diseases, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Rory Cave
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Mahmoud Fayez
- Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Veterinary Serum and Vaccine Research Institute, Ministry of Agriculture, Cairo, Egypt
| | - Naser Alhumam
- Department of Microbiology and parasitology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
| | - Sayed Quadri
- Division of Microbiology and Immunology, Department of Biomedical Sciences, College of Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Kingdom of Saudi Arabia
| | - Hermine V. Mkrtchyan
- School of Biomedical Sciences, University of West London, London, United Kingdom
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Presence of Methicillin Resistant Staphylococcus aureus (MRSA) in Feces of the Small Indian Mongooses (Urva auropunctata) on Saint Kitts and Nevis, West Indies. Antibiotics (Basel) 2022; 11:antibiotics11080990. [PMID: 35892380 PMCID: PMC9331971 DOI: 10.3390/antibiotics11080990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Although, historically, Methicillin-Resistant Staphylococcus aureus (MRSA) was restricted to humans, since 2005 these strains emerged in livestock and wildlife. Therefore, a One Health approach was applied to analyze the diversity and characteristics of S. aureus strains isolated from the invasive species of mongoose (Urva auropunctata) in St. Kitts. Fecal samples collected from these animals (n = 81) were cultured on selective agar. The isolated S. aureus strains were identified using MALDI-TOF and further characterized by whole genome sequence analysis. The fecal microbiome study identified the presence of S. aureus in 5 animals. Both MSSA (n = 3) and MRSA (n = 2) strains were identified. The two MRSA isolated were nearly identical ST5 SCCmec IVa (2B) strains. The two MSSA isolated were a new ST7434, pertaining to clonal complex 30, and the other belonged to ST5, but unrelated to the MRSA ST5. The SCCmec IVa (2B) is, however, the main SCCmec in human MRSA of different STs identified in St Kitts, indicating potential horizontal transmission events. In conclusion, a new type of MSSA, ST7434, was found and MRSA ST5 t002 SCCmec IVa (2B) found its way into wildlife on a small Caribbean Island. Further One Health studies are necessary to determine the role of MRSA in wildlife.
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Clonal distribution and antimicrobial resistance of methicillin-susceptible and -resistant Staphylococcus aureus strains isolated from broiler farms, slaughterhouses, and retail chicken meat. Poult Sci 2022; 101:102070. [PMID: 36041389 PMCID: PMC9449669 DOI: 10.1016/j.psj.2022.102070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/23/2022] Open
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35
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Belhout C, Elgroud R, Butaye P. Methicillin-Resistant Staphylococcus aureus (MRSA) and Other Methicillin-Resistant Staphylococci and Mammaliicoccus (MRNaS) Associated with Animals and Food Products in Arab Countries: A Review. Vet Sci 2022; 9:vetsci9070317. [PMID: 35878334 PMCID: PMC9320237 DOI: 10.3390/vetsci9070317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/11/2022] [Accepted: 06/21/2022] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Staphylococci are present in the microbiota of both humans and animal species, being recognized as the most important opportunistic pathogens. Antimicrobial resistance (AMR) has become a global public health issue presenting a significant risk because it severely limits treatment options. Methicillin resistance in staphylococci (MRS) poses a specific problem as it may cause serious human and animal infections, eventually resulting in death. The increasing observation of MRS in different animal species has raised the concern of their impact on animal health and the potential of zoonotic transmission. The availability of comprehensive data on the ecology and distribution of MRS in animals and food products worldwide is necessary to understand their relevance in the “One Health” domain. However, there is a gap in information in terms of MRS and the Arab countries. Therefore, our study aimed to provide an overview of the situation of MRS in these countries by reviewing the available data on livestock and animal products and making recommendations for the future. Abstract The prevalence of methicillin resistance in staphylococci has been increasing globally and is currently one of the major public health concerns. In particular, treating infections caused by staphylococci with acquired antimicrobial resistance is problematic, as their treatment is more difficult. The resistance is found both in human and animal staphylococcal strains. Methicillin-resistant staphylococci (MRS) have also been increasingly reported in wildlife. In Arab countries, MRS has been detected in food producing animals and food products; however, the risk this poses is somewhat unclear, and still a significant lack of information on the trend and distribution of these pathogens in these countries, which have a specific ecosystem (desert) and traditions (Muslim culture). In this manuscript, we aim to provide an overview of the prevalence and the major MRS clonal lineages circulating in these specific countries and compare to them other situations with different ecosystems and cultures.
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Affiliation(s)
- Chahrazed Belhout
- HASAQ Laboratory, High National Veterinary School, Issad Abbes Avenue, Oued Smar, El Harrach, Algiers 16270, Algeria
- Correspondence:
| | - Rachid Elgroud
- Institute of Veterinary Sciences, University Frères Mentouri Constantine 1, Constantine 25017, Algeria;
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium;
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Graham BD, Selby CM, Forga AJ, Coles ME, Beer LC, Graham LE, Teague KD, Tellez-Isaias G, Hargis BM, Vuong CN. Development of an environmental contamination model to simulate the microbial bloom that occurs in commercial hatch cabinets. Poult Sci 2022; 101:101890. [PMID: 35512499 PMCID: PMC9079238 DOI: 10.1016/j.psj.2022.101890] [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: 01/20/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial blooms that emerge in commercial hatch cabinets consist of apathogenic and pathogenic microorganisms, including Escherichia coli, Enterococcus faecalis, and Aspergillus fumigatus. Objectives of the present study included the development of a multipathogen contamination model to mimic commercial conditions and optimization of sampling methods to quantify bacterial or fungal presence within the hatch cabinet. The pathogen challenge mix (PM) was recreated from select bacterial or fungal isolates recovered from an egg homogenate (EH) derived from the contents of infertile eggs and late embryonic mortalities. Isolates selected for PM included Enterococcus faecalis (∼108 CFU/egg), Staphylococcus aureus (∼107 CFU/egg), Staphylococcus chromogenes (∼107 CFU/egg), Aspergillus fumigatus (∼106 spores/egg), and 2 Escherichia coli (∼108 CFU/egg) isolates. Challenge (100 μL of PM or EH) was administered using a sterile loop to a 28 mm area on the blunt end of the eggshell at day 19 of embryogenesis (DOE). In 3 experiments, microbiological data were collected from environmental hatcher samples (open-agar plate method), fluff samples, postmortem whole-body chick rinse samples, and gastrointestinal tract (GIT) samples to evaluate select bacteria and fungi circulating within the hatch cabinet and colonization of GIT. Cumulative bacterial and fungal recovery from the PM hatching environment from DOE20 to hatch was higher than the nonchallenged group (NC) and EH group at ∼860 and ∼1,730 CFU, respectively. Bacterial recovery from GIT, fluff, and chick rinse samples were similar for the PM and EH group in Exp. 1. However, Aspergillus fumigatus recovery from fluff and chick rinse samples for the PM group was significantly (P < 0.001) higher than the NC and EH group. In Exp. 2 and 3, PM challenge significantly (P < 0.05) increased Gram-negative bacterial recovery from the GIT, fluff and chick rinse samples compared to both the NC and EH group. These data suggest this innovative multispecies environmental contamination model using PM could be utilized to evaluate strategies to mitigate microbial contamination in commercial hatch cabinets in a laboratory setting.
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Affiliation(s)
- B D Graham
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA.
| | - C M Selby
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - A J Forga
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - M E Coles
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - L C Beer
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - L E Graham
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - K D Teague
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - G Tellez-Isaias
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - B M Hargis
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
| | - C N Vuong
- Department of Poultry Science, University of Arkansas Division of Agriculture, Fayetteville, AR 72701, USA
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A bottom-up view of antimicrobial resistance transmission in developing countries. Nat Microbiol 2022; 7:757-765. [PMID: 35637328 DOI: 10.1038/s41564-022-01124-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
Antimicrobial resistance (AMR) is tracked most closely in clinical settings and high-income countries. However, resistant organisms thrive globally and are transmitted to and from healthy humans, animals and the environment, particularly in many low- and middle-income settings. The overall public health and clinical significance of these transmission opportunities remain to be completely clarified. There is thus considerable global interest in promoting a One Health view of AMR to enable a more realistic understanding of its ecology. In reality, AMR surveillance outside hospitals remains insufficient and it has been very challenging to convincingly document transmission at the interfaces between clinical specimens and other niches. In this Review, we describe AMR and its transmission in low- and middle-income-country settings, emphasizing high-risk transmission points such as urban settings and food-animal handling. In urban and food production settings, top-down and infrastructure-dependent interventions against AMR that require strong regulatory oversight are less likely to curtail transmission when used alone and should be combined with bottom-up AMR-containment approaches. We observe that the power of genomics to expose transmission channels and hotspots is largely unharnessed, and that existing and upcoming technological innovations need to be exploited towards containing AMR in low- and middle-income settings.
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Abstract
Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24®] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR. IMPORTANCE Antimicrobial resistance (AMR) represents a considerable burden to health care systems, with the public health community largely in consensus that AMR will be a major cause of death worldwide in the coming decades. Humans carry antibiotic resistance in the microbes that live in and on us, collectively known as the human microbiome. Diet is a powerful method for shaping the human gut microbiome and may be a tractable method for lessening antibiotic resistance, and yet little is known about the relationship between diet and AMR. We examined this relationship in healthy individuals who contained various abundances of antibiotic resistance genes and found that individuals who consumed diverse diets that were high in fiber and low in animal protein had fewer antibiotic resistance genes. Dietary interventions may be useful for lessening the burden of antimicrobial resistance and might ultimately motivate dietary guidelines which will consider how nutrition can reduce the impact of infectious disease.
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Li X, Chen Y, Wang S, Duan X, Zhang F, Guo A, Tao P, Chen H, Li X, Qian P. Exploring the Benefits of Metal Ions in Phage Cocktail for the Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) Infection. Infect Drug Resist 2022; 15:2689-2702. [PMID: 35655790 PMCID: PMC9154003 DOI: 10.2147/idr.s362743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is an important zoonotic pathogen worldwide. Infections due to MRSA are associated with higher mortality rates compared with methicillin-susceptible S. aureus. Meanwhile, bacteriophages have been shown to overcome the emergence of MRSA. Methods Phage PHB22a, PHB25a, PHB38a, and PHB40a were isolated. Here, we evaluated the ability of a phage cocktail containing phages PHB22a, PHB25a, PHB38a, and PHB40a against MRSA S-18 strain in vivo and in vitro. Phage whole-genome sequencing, host-range determination, lytic activity, and biofilm clearance experiments were performed in vitro. Galleria mellonella larvae and a mouse systemic infection model to evaluate the efficacy of phage therapy in vivo. Results The phage cocktail exhibited enhanced antibacterial and anti-biofilm effects compared to the single phage. Phage cocktail contained with Ca2+/Zn2+ significantly reduced the number of viable bacteria (24-h or 48-h biofilm) by more than 0.81-log compared to the phage cocktail alone. Furthermore, we demonstrated that the addition of Ca2+ and Zn2+ phage cocktail could increase the survival rate of G. mellonella larvae infected with S. aureus by 10% compared with phage cocktail alone. This was further confirmed in the mouse model, which showed a 2.64-log reduction of host bacteria S-18, when Ca2+ and Zn2+ were included in the cocktail compared with the phage cocktail alone. Conclusion Our results indicated that phage cocktail supplemented with Ca2+/Zn2+ could effectively remove bacteria in biofilms and mice tissues infected with S. aureus.
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Affiliation(s)
- Xinxin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Yibao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Shuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Xiaochao Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Fenqiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Xiangmin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, People’s Republic of China
- Correspondence: Ping Qian, Tel +86-27-87282608, Fax +86-27-87282608, Email
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Baldinelli F, Broglia A, Kohnle L, Alvarez J. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Staphylococcus aureus in cattle and horses. EFSA J 2022; 20:e07312. [PMID: 35582361 PMCID: PMC9087474 DOI: 10.2903/j.efsa.2022.7312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus (S. aureus) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for cattle and horses in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR S. aureus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (60-90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 1-5%, 5-10% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-90% and 60-90% probability of meeting the criteria, respectively). The animal species to be listed for AMR S. aureus according to Article 8 criteria include mainly mammals, birds, reptiles and fish.
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Shared antibiotic resistance and virulence genes in Staphylococcus aureus from diverse animal hosts. Sci Rep 2022; 12:4413. [PMID: 35292708 PMCID: PMC8924228 DOI: 10.1038/s41598-022-08230-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses an important threat in human and animal health. In this study, we ask whether resistance and virulence genes in S. aureus are homogeneously distributed or constrained by different animal hosts. We carried out whole genome sequencing of 114 S. aureus isolates from ten species of animals sampled from four New England states (USA) in 2017-2019. The majority of the isolates came from cats, cows and dogs. The maximum likelihood phylogenetic tree based on the alignment of 89,143 single nucleotide polymorphisms of 1173 core genes reveal 31 sequence types (STs). The most common STs were ST5, ST8, ST30, ST133 and ST2187. Every genome carried at least eight acquired resistance genes. Genes related to resistance found in all genomes included norA (fluoroquinolone), arlRS (fluoroquinolone), lmrS (multidrug), tet(38) (tetracycline) and mepAR (multidrug and tigecycline resistance). The most common superantigen genes were tsst-1, sea and sec. Acquired antibiotic resistance (n = 10) and superantigen (n = 9) genes of S. aureus were widely shared between S. aureus lineages and between strains from different animal hosts. These analyses provide insights for considering bacterial gene sharing when developing strategies to combat the emergence of high-risk clones in animals.
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Tissot S, Gérard AL, Boutry J, Dujon AM, Russel T, Siddle H, Tasiemski A, Meliani J, Hamede R, Roche B, Ujvari B, Thomas F. Transmissible Cancer Evolution: The Under-Estimated Role of Environmental Factors in the “Perfect Storm” Theory. Pathogens 2022; 11:pathogens11020241. [PMID: 35215185 PMCID: PMC8876101 DOI: 10.3390/pathogens11020241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022] Open
Abstract
Although the true prevalence of transmissible cancers is not known, these atypical malignancies are likely rare in the wild. The reasons behind this rarity are only partially understood, but the “Perfect Storm hypothesis” suggests that transmissible cancers are infrequent because a precise confluence of tumor and host traits is required for their emergence. This explanation is plausible as transmissible cancers, like all emerging pathogens, will need specific biotic and abiotic conditions to be able to not only emerge, but to spread to detectable levels. Because those conditions would be rarely met, transmissible cancers would rarely spread, and thus most of the time disappear, even though they would regularly appear. Thus, further research is needed to identify the most important factors that can facilitate or block the emergence of transmissible cancers and influence their evolution. Such investigations are particularly relevant given that human activities are increasingly encroaching into wild areas, altering ecosystems and their processes, which can influence the conditions needed for the emergence and spread of transmissible cell lines.
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Affiliation(s)
- Sophie Tissot
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Correspondence:
| | - Anne-Lise Gérard
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Justine Boutry
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
| | - Antoine M. Dujon
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Tracey Russel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia;
| | - Hannah Siddle
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK;
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Aurélie Tasiemski
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d’Infection et d’Immunité de Lille, 59000 Lille, France;
| | - Jordan Meliani
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Benjamin Roche
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinariay Zootecnia, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 01030, Mexico
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 32020, Australia; (A.M.D.); (B.U.)
| | - Frédéric Thomas
- CREEC/MIVEGEC, Université de Montpellier, CNRS, IRD, 34394 Montpellier, France; (A.-L.G.); (J.B.); (J.M.); (B.R.); (F.T.)
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Mohammadi Mollaahmadi C, Anzabi Y, Shayegh J. Comparison of the Frequency of Biofilm-Forming Genes ( icaABCD) in Methicillin-Resistant S. aureus Strains Isolated from Human and Livestock. ARCHIVES OF RAZI INSTITUTE 2021; 76:1655-1663. [PMID: 35546969 PMCID: PMC9083861 DOI: 10.22092/ari.2020.351381.1522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/21/2020] [Indexed: 03/08/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) can cause infections in both human and animal groups, which is a serious threat to public health worldwide. Attachment and colonization are the first steps for S. aureus pathogenesis, and biofilm-mediated infections have a significant negative impact on human and animal health. The MRSA can adapt to different environments and give rise to different strains of human and animal MRSA, causing transmissions of the disease between humans and animals. This study aimed to investigate biofilm production in vitro, and the presence of icaABCD genes in MRSA isolates in both human as well as the disease transmission between human and animal strains. In total, 39 human and 35 livestock isolates were evaluated by the Congo Red Agar method. The presence of mecA and icaABCDR genes were assessed by polymerase chain reaction (PCR), and finally, the PCR products were examined by agarose gel electrophoresis. The results showed that the mecA gene frequency in human and animal isolates was 64.1% and 36.1%, respectively, and there was a significant relationship between mecA and icaAD in human isolates. In addition, significant relationships were found between icaA and Rifampicin and also between icaC and Chloramphenicol and Penicillin in human isolates. In animal isolates, there was a significant relationship between mecA and Trimethoprim as well as between icaR and Rifampicin. It was concluded that all operon ica genes were involved in biofilm production, but icaA and icaD genes in MRSA were more closely associated with mecA. Both animal and human strains can be involved in disease transmission, but this conclusion should be made cautiously.
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Affiliation(s)
- C Mohammadi Mollaahmadi
- Faculty of Basic Sciences, Department of Microbiology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Y Anzabi
- Department of Pathobiology, Faculty of Veterinary Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran.,Biotechnology Research Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - J Shayegh
- Department of Veterinary Medicine, Islamic Azad University, Shabestar Branch, Islamic Azad University, Shabestar, Iran
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Liao G, Wu Z, Lv J, Ren Q, Chen W. Investigation of clonal diversity, virulence genes, and antibiotic resistance of Staphylococcus aureus recovered from raw cow milk in southern Xinjiang, China. Folia Microbiol (Praha) 2021; 67:245-252. [PMID: 34735675 DOI: 10.1007/s12223-021-00924-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/21/2021] [Indexed: 10/19/2022]
Abstract
Staphylococcus aureus is an important pathogen of humans and animals. The aim of this study was to characterize 71 of S. aureus isolates from raw cow milk in southern Xinjiang of China, including molecular typing, distribution of virulence genes, and antimicrobial susceptibility. The isolates belonged to 18 sequence types (STs) (including 11 novel STs) and 6 spa types which were divided into five different clonal complexes (CCs), including CC188, CC352, CC22, CC398, and CC5406. The majority of the strains was grouped into multilocus sequence typing (MLST) CC188 (n = 41), t189 (n = 40), and ST5796 (n = 17). Only 30.9, 12.7, 11.3, and 9.9% of the isolates were resistant to erythromycin, clindamycin/norfloxacin, tetracycline, and gentamicin, respectively. Nine of multidrug resistant (MDR) isolates were observed which was associated with CC398-t2876. The adhesion molecules clfa, clfb, and hlb were most frequently detected with the percentage rate of 98.6% (70/71), 98.6% (70/71), and 90.1% (64/71), respectively. The percentage rates of the staphylococcal enterotoxin genes sea, seb, sec, sed, seg, and sei in S. aureus isolates were 5.6, 19.8, 40.8, 1.4, 49.3, and 30.9%, respectively. The see, seh, and sej genes were not found. This study provides data about the occurrence of S. aureus in raw cow milk, revealing high carriage frequency, drug resistance, and population structure of S. aureus. Furthermore, this study suggests that effective hygienic measures be taken when handling dairy cows, in order to prevent spreading MDR strains to human through direct contact and/or consumption of contaminated food.
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Affiliation(s)
- Guanghua Liao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences, Tarim University, Alar, 86-843300, China
| | - Zihao Wu
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences, Tarim University, Alar, 86-843300, China
| | - Junfan Lv
- College of Animal Sciences, Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production & Construction Corps, Tarim University, Alar, 86-843300, China
| | - Qiang Ren
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences, Tarim University, Alar, 86-843300, China
| | - Wei Chen
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Sciences, Tarim University, Alar, 86-843300, China. .,College of Animal Sciences, Key Laboratory of Tarim Animal Husbandry and Science Technology of Xinjiang Production & Construction Corps, Tarim University, Alar, 86-843300, China.
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Ekesi NS, Hasan A, Parveen A, Shwani A, Rhoads DD. Embryo lethality assay as a tool for assessing virulence of isolates from bacterial chondronecrosis with osteomyelitis in broilers. Poult Sci 2021; 100:101455. [PMID: 34607145 PMCID: PMC8496174 DOI: 10.1016/j.psj.2021.101455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022] Open
Abstract
We used an embryo lethality assay (ELA) to assess virulence for different isolates from cases of bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Lameness is among the most significant animal welfare issues in the poultry industry. Bacterial infections are a major cause of lameness and different bacterial species have been obtained from lame broilers. Reliable lab-based assays are required to assess relative virulence of bacteria obtained from lame broilers. ELA has been used to assess lethal dosage of Enterococcus faecalis and Enterococcus cecorum. We hypothesized that ELA could substitute for more laborious and costly assessments of BCO isolate pathogenicity using live birds. We evaluated 2 different levels of bacteria injected into eggs from layer and commercial broiler embryos. Significant findings include 1) Escherichia coli from neighboring farms operated by the same integrator had very different embryo lethality, 2) isolate Staphylococcus agnetis 908 had low virulence in ELA, even though this isolate can induce more than 50% BCO lameness, 3) Enterococcus cecorum 1415 also had low pathogenicity; even though it was recovered from severe bilateral tibial dyschondroplasia, 4) human and chicken BCO isolates of S. aureus had significant pathogenicity, 5) virulence for some isolates was highly variable possibly corresponding with quality of the embryos/fertile eggs used, and 6) ELA pathogenicity was much lower for our BCO isolates than previous reports which may reflect maternal environment. Overall, ELA virulence and BCO virulence are not always concordant indicating that ELA may not be an effective measure for assessing virulence with respect to BCO.
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Affiliation(s)
- Nnamdi S Ekesi
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Amer Hasan
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA; Department of Veterinary Public Health, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Alia Parveen
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Abdulkarim Shwani
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA
| | - Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, USA.
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Crestani C, Forde TL, Lycett SJ, Holmes MA, Fasth C, Persson-Waller K, Zadoks RN. The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? Microb Genom 2021; 7. [PMID: 34486971 PMCID: PMC8715428 DOI: 10.1099/mgen.0.000648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Group B Streptococcus (GBS; Streptococcus agalactiae) is a major neonatal and opportunistic bacterial pathogen of humans and an important cause of mastitis in dairy cattle with significant impacts on food security. Following the introduction of mastitis control programmes in the 1950s, GBS was nearly eradicated from the dairy industry in northern Europe, followed by re-emergence in the 21st century. Here, we sought to explain this re-emergence based on short and long read sequencing of historical (1953–1978; n=44) and contemporary (1997–2012; n=76) bovine GBS isolates. Our data show that a globally distributed bovine-associated lineage of GBS was commonly detected among historical isolates but never among contemporary isolates. By contrast, tetracycline resistance, which is present in all major GBS clones adapted to humans, was commonly and uniquely detected in contemporary bovine isolates. These observations provide evidence for strain replacement and suggest a human origin of newly emerged strains. Three novel GBS plasmids were identified, including two showing >98 % sequence similarity with plasmids from Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis, which co-exist with GBS in the human oropharynx. Our findings support introduction of GBS into the dairy population due to human-to-cattle jumps on multiple occasions and demonstrate that reverse zoonotic transmission can erase successes of animal disease control campaigns.
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Affiliation(s)
- Chiara Crestani
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK
| | - Taya L Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - Charlotta Fasth
- National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | | | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Campus, Glasgow G61 1QH, UK.,Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK.,School of Veterinary Science, University of Sydney, Werombi Road, Camden, NSW 2570, Australia
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47
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Molecular Diversity of Methicillin-Resistant and -Susceptible Staphylococcus aureus Detected in Animals: A Focus on Aquatic Animals. DIVERSITY 2021. [DOI: 10.3390/d13090417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus (S. aureus) are one of the best-known opportunistic pathogens capable of causing different types of infections in animals. Furthermore, it has the ability to acquire resistance to various antibiotics very easily. Methicillin-resistant S. aureus (MRSA) are currently of great concern as they are the leading cause of infections in humans and animals, with a major impact on health and the economy. Several studies already demonstrate that the spread of MRSA is constantly increasing due to its ability to form reservoirs in humans, animals and the environment. In fact, several works have already identified the presence of these bacteria in animals, including domestic animals, farm animals and even wild animals. Furthermore, the incidence of various S. aureus strains in aquatic animals has also been reported by different authors, although it is still a rarely discussed topic. Some of these strains have previously been associated with humans and other animals. Strain 398 is the strain that manages to infect a wider spectrum of hosts, having been identified in several different species. Aside from this strain, many others have yet to be identified. In addition, many of these strains have virulence factors and antibiotic resistance genes that worsen the situation. The present work is a review of studies that intend to investigate the epidemiology of this agent in samples of aquatic animals from different origins, in order to better understand its distribution, prevalence and the molecular lineages associated with these species.
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48
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Ko DS, Kim NH, Kim EK, Ha EJ, Ro YH, Kim D, Choi KS, Kwon HJ. Comparative genomics of bovine mastitis-origin Staphylococcus aureus strains classified into prevalent human genotypes. Res Vet Sci 2021; 139:67-77. [PMID: 34256183 DOI: 10.1016/j.rvsc.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/15/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Humans may serve as a reservoir host of Staphylococcus aureus, resulting in transmission to animals. Previously, we used RNA polymerase beta subunit gene (rpoB)-based genotyping and classified S. aureus strains into rpoB sequence types (RSTs). According to our previous work, the predominant genotypes of S. aureus in humans and cows differ in Korea, but some predominant genotypes (RST4-1 and RST2-1) in humans have been isolated from bovine mastitis. Therefore, it needs to be determined whether some strains of the predominant human genotypes have adapted to or caused occasional infections in cows. We determined the whole genome sequences of 2 bovine mastitis-origin strains, PMB179 (RST4-1) and PMB196 (RST2-1), and performed comparative genomics with the corresponding RST4-1 and RST2-1 S. aureus strains in the NCBI database. We identified 257 and 180 pseudogenes among 131 RST4-1 and 54 RST2-1 strains, respectively, for the comparison of pseudogene profiles. RST4-1 strains shared more common pseudogenes than RST2-1 strains, and some epidemiologically related strains shared common pseudogenes. However, most of the pseudogenes were strain-specific, and diverse pseudogene profiles were apparent in both the RST4-1 and RST2-1 strains. Furthermore, analysis of the mobile genetic elements, virulence genes, and antibiotic resistance genes revealed no molecular markers to differentiate PMB179 and PMB196 from human strains. Interestingly, the collective comparison of RST4-1 or RST2-1 strains revealed cumulative acquisition steps of genomic islands and antibiotic resistance genes. In conclusion, our data support PMB179 and PMB196 causing occasional infections that result in bovine mastitis.
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Affiliation(s)
- Dae-Sung Ko
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Nam-Hyung Kim
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Eun-Kyung Kim
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Eun-Jin Ha
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Young-Hye Ro
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea.
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49
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Host genotype and genetic diversity shape the evolution of a novel bacterial infection. THE ISME JOURNAL 2021; 15:2146-2157. [PMID: 33603148 PMCID: PMC8245636 DOI: 10.1038/s41396-021-00911-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023]
Abstract
Pathogens continue to emerge from increased contact with novel host species. Whilst these hosts can represent distinct environments for pathogens, the impacts of host genetic background on how a pathogen evolves post-emergence are unclear. In a novel interaction, we experimentally evolved a pathogen (Staphylococcus aureus) in populations of wild nematodes (Caenorhabditis elegans) to test whether host genotype and genetic diversity affect pathogen evolution. After ten rounds of selection, we found that pathogen virulence evolved to vary across host genotypes, with differences in host metal ion acquisition detected as a possible driver of increased host exploitation. Diverse host populations selected for the highest levels of pathogen virulence, but infectivity was constrained, unlike in host monocultures. We hypothesise that population heterogeneity might pool together individuals that contribute disproportionately to the spread of infection or to enhanced virulence. The genomes of evolved populations were sequenced, and it was revealed that pathogens selected in distantly-related host genotypes diverged more than those in closely-related host genotypes. S. aureus nevertheless maintained a broad host range. Our study provides unique empirical insight into the evolutionary dynamics that could occur in other novel infections of wildlife and humans.
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50
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Rohmer C, Wolz C. The Role of hlb-Converting Bacteriophages in Staphylococcus aureus Host Adaption. Microb Physiol 2021; 31:109-122. [PMID: 34126612 DOI: 10.1159/000516645] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/17/2021] [Indexed: 11/19/2022]
Abstract
As an opportunistic pathogen of humans and animals, Staphylococcus aureus asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening acute and chronic infections. The evolution of S. aureus resulting from short- and long-term adaptation to diverse hosts is tightly associated with mobile genetic elements. S. aureus strains can carry up to four temperate phages, many of which possess accessory genes encoding staphylococcal virulence factors. More than 90% of human nasal isolates of S. aureus have been shown to carry Sa3int phages, whereas invasive S. aureus isolates tend to lose these phages. Sa3int phages integrate as prophages into the bacterial hlb gene, disrupting the expression of the sphingomyelinase Hlb, an important virulence factor under specific infection conditions. Virulence factors encoded by genes carried by Sa3int phages include staphylokinase, enterotoxins, chemotaxis-inhibitory protein, and staphylococcal complement inhibitor, all of which are highly human specific and probably essential for bacterial survival in the human host. The transmission of S. aureus from humans to animals is strongly correlated with the loss of Sa3int phages, whereas phages are regained once a strain is transmitted from animals to humans. Thus, both the insertion and excision of prophages may confer a fitness advantage to this bacterium. There is also growing evidence that Sa3int phages may perform "active lysogeny," a process during which prophages are temporally excised from the chromosome without forming intact phage particles. The molecular mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unclear. Nevertheless, their regulation is likely fine-tuned to ensure bacterial survival within different hosts.
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Affiliation(s)
- Carina Rohmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 "Controlling Microbes to Fight Infections", Tübingen, Germany
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