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Bak YS, Park JY, Kim JB, Cho SH. Molecular characterization and antibiotic resistance of Staphylococcus aureus strains isolated from patients with diarrhea in Korea between the years 2007 and 2022. Food Sci Biotechnol 2024; 33:1965-1974. [PMID: 38752118 PMCID: PMC11091020 DOI: 10.1007/s10068-023-01478-9] [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: 08/20/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 05/18/2024] Open
Abstract
To investigate the molecular characteristics and antibiotic resistance of Staphylococcus aureus isolates from patients with diarrhea in Korea, 327 S. aureus strains were collected between 2007 and 2022. The presence of staphylococcal enterotoxin (SE) and toxic shock syndrome toxin-1 (TSST-1) genes in S. aureus isolates was determined by PCR. The highest expression of the TSST-1 gene was found in the GIMNO type (43.1% of GIMNO type). GIMNO type (Type I) refers to each staphylococcal enterotoxin (SE) gene gene (initials of genes): G = seg; I = sei; M = selm; N = seln; O = selo. Moreover, Type I isolates showed a significantly higher resistance to most antibiotics. A total of 195 GIMNO-type S. aureus strains were analyzed using multilocus sequence typing (MLST), and 18 unique sequence types (STs) were identified. The most frequent sequence type was ST72 (36.9%), followed by ST5 (22.1%) and ST30 (16.9%). Interestingly, ST72 strains showed a higher prevalence of MRSA than the other STs. In conclusion, our results were the first reported for S. aureus strains in Korea, which significantly expanded S. aureus genotype information for the surveillance of pathogenic S. aureus and may provide important epidemiological information to resolve several infectious diseases caused by S. aureus. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01478-9.
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Affiliation(s)
- Young-Seok Bak
- Department of Emergency Medical Services, Sun Moon University, Asan-si, Chungcheongnam-do 31460 Korea
| | - Jun-Young Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jung-Beom Kim
- Department of Food Science and Technology, Suncheon National University, Suncheon, 57922 Korea
| | - Seung-Hak Cho
- Department of Emergency Medical Services, Sun Moon University, Asan-si, Chungcheongnam-do 31460 Korea
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Cheongju, Republic of Korea
- Division of Bacterial Disease Research, Center for Infectious Disease Research, Korea National Institute of Health, Heungdeok-Gu, Cheongju, 363-951 Republic of Korea
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2
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Lossouarn J, Beurrier E, Bouteau A, Moncaut E, Sir Silmane M, Portalier H, Zouari A, Cattoir V, Serror P, Petit MA. The virtue of training: extending phage host spectra against vancomycin-resistant Enterococcus faecium strains using the Appelmans method. Antimicrob Agents Chemother 2024; 68:e0143923. [PMID: 38591854 DOI: 10.1128/aac.01439-23] [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: 11/02/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elsa Beurrier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Astrid Bouteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Maria Sir Silmane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Heïdi Portalier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
- Université de Rennes, INSERM, UMR_S1230 BRM, Rennes, France
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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3
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Xu W, Fang Y, Zhu K. Enterococci facilitate polymicrobial infections. Trends Microbiol 2024; 32:162-177. [PMID: 37550091 DOI: 10.1016/j.tim.2023.07.010] [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: 04/18/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/09/2023]
Abstract
Enterococci are ubiquitous members of the gut microbiota in human beings and animals and are among the most important nosocomial organisms. Due to their opportunistic pathogenicity, enterococci are referred to as pathobionts and play decisive roles in a diverse array of polymicrobial infections. Enterococci can promote the colonization, pathogenesis, and persistence of various pathogens, compromise the efficacy of drugs, and pose a severe threat to public health. Most current treatments tend to focus on the sole pathogenic bacteria, with insufficient attention to the driving role of enterococci. In this review, we summarize the characteristics of enterococci in infections, the factors facilitating their outgrowth, as well as the sites and types of enterococci-associated polymicrobial infections. We present an overview of the underlying mechanisms of enterococci-mediated pathogenesis in polymicrobial infections. Furthermore, we discuss alternative strategies and potential intervention approaches to restrict such infections, shedding light on the discovery and development of new therapies against polymicrobial infections.
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Affiliation(s)
- Wenjiao Xu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Engineering Research Center of Animal Innovative Drugs and Safety Evaluation, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yuwen Fang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Engineering Research Center of Animal Innovative Drugs and Safety Evaluation, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kui Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; Engineering Research Center of Animal Innovative Drugs and Safety Evaluation, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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4
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Kirsch JM, Ely S, Stellfox ME, Hullahalli K, Luong P, Palmer KL, Van Tyne D, Duerkop BA. Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci. PLoS Pathog 2023; 19:e1011424. [PMID: 37267422 PMCID: PMC10266640 DOI: 10.1371/journal.ppat.1011424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/14/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
Insertion sequences (IS) are simple transposons implicated in the genome evolution of diverse pathogenic bacterial species. Enterococci have emerged as important human intestinal pathogens with newly adapted virulence potential and antibiotic resistance. These genetic features arose in tandem with large-scale genome evolution mediated by mobile elements. Pathoadaptation in enterococci is thought to be mediated in part by the IS element IS256 through gene inactivation and recombination events. However, the regulation of IS256 and the mechanisms controlling its activation are not well understood. Here, we adapt an IS256-specfic deep sequencing method to describe how chronic lytic phage infection drives widespread diversification of IS256 in E. faecalis and how antibiotic exposure is associated with IS256 diversification in E. faecium during a clinical human infection. We show through comparative genomics that IS256 is primarily found in hospital-adapted enterococcal isolates. Analyses of IS256 transposase gene levels reveal that IS256 mobility is regulated at the transcriptional level by multiple mechanisms in E. faecalis, indicating tight control of IS256 activation in the absence of selective pressure. Our findings reveal that stressors such as phages and antibiotic exposure drives rapid genome-scale transposition in the enterococci. IS256 diversification can therefore explain how selective pressures mediate evolution of the enterococcal genome, ultimately leading to the emergence of dominant nosocomial lineages that threaten human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Shannon Ely
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Madison E. Stellfox
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Karthik Hullahalli
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Phat Luong
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado–Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America
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Weltzer ML, Wall D. Social Diversification Driven by Mobile Genetic Elements. Genes (Basel) 2023; 14:648. [PMID: 36980919 PMCID: PMC10047993 DOI: 10.3390/genes14030648] [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: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
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Affiliation(s)
- Michael L Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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Pchelin IM, Tkachev PV, Azarov DV, Gorshkov AN, Drachko DO, Zlatogursky VV, Dmitriev AV, Goncharov AE. A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences. Viruses 2023; 15:216. [PMID: 36680256 PMCID: PMC9865981 DOI: 10.3390/v15010216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.
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Affiliation(s)
- Ivan M. Pchelin
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia
| | - Pavel V. Tkachev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia
| | - Daniil V. Azarov
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia
| | - Andrey N. Gorshkov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia
- Laboratory of Pathomorphology, Almazov National Research Centre, 197341 Saint Petersburg, Russia
| | - Daria O. Drachko
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, 199034 Saint Petersburg, Russia
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 199034 Saint Petersburg, Russia
| | - Vasily V. Zlatogursky
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 199034 Saint Petersburg, Russia
| | - Alexander V. Dmitriev
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia
| | - Artemiy E. Goncharov
- Scientific and Educational Center “Molecular Bases of Interaction of Microorganisms and Human” of the WCRC “Center for Personalized Medicine”, Institute of Experimental Medicine, 197022 Saint Petersburg, Russia
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7
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Rossi A, Morlino MS, Gaspari M, Basile A, Kougias P, Treu L, Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. MICROBIOME 2022; 10:125. [PMID: 35965344 PMCID: PMC9377139 DOI: 10.1186/s40168-022-01316-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. RESULTS The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. CONCLUSIONS Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
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Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Gaspari
- Department of Hydraulics, Soil Science and Agricultural Engineering, Faculty of Agriculture, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation Demeter, Thermi, 57001, Thessaloniki, Greece
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
- CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
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Krause AL, Stinear TP, Monk IR. Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions. FEMS Microbiol Rev 2022; 46:6650352. [PMID: 35883217 PMCID: PMC9779914 DOI: 10.1093/femsre/fuac036] [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: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.
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Affiliation(s)
- Alexandra L Krause
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Ian R Monk
- Corresponding author: Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia. E-mail:
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Zaidi SEZ, Zaheer R, Barbieri R, Cook SR, Hannon SJ, Booker CW, Church D, Van Domselaar G, Zovoilis A, McAllister TA. Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum. Front Microbiol 2022; 13:859990. [PMID: 35832805 PMCID: PMC9271880 DOI: 10.3389/fmicb.2022.859990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.
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Affiliation(s)
- Sani-e-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- University of Lethbridge, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Ruth Barbieri
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shaun R. Cook
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | | | - Deirdre Church
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Calgary Laboratory Services, Calgary, AB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- *Correspondence: Tim A. McAllister,
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