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Li G, Wu M, Xiao Y, Tong Y, Li S, Qian H, Zhao T. Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101309. [PMID: 39146704 DOI: 10.1016/j.cbd.2024.101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.
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Affiliation(s)
- Guannan Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 402760, PR China.
| | - Meihong Wu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 402760, PR China
| | - Yi Xiao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 402760, PR China
| | - Yujie Tong
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 402760, PR China
| | - Sheng Li
- Chongqing Academy of Chinese Materia Medica, Chongqing College of Traditional Chinese Medicine, Chongqing 402760, PR China
| | - Heying Qian
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China
| | - Tianfu Zhao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 402760, PR China.
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2
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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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3
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Roer L, Kaya H, Tedim AP, Novais C, Coque TM, Aarestrup FM, Peixe L, Hasman H, Hammerum AM, Freitas AR. VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data. Microbiol Spectr 2024; 12:e0372423. [PMID: 38329344 PMCID: PMC10913372 DOI: 10.1128/spectrum.03724-23] [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: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Luísa Peixe
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana R. Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - On behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
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Kim DH, Kim SA, Jo NG, Bae JH, Nguyen MT, Jo YM, Han NS. Phenotypic and genomic analyses of bacteriocin-producing probiotic Enterococcus faecium EFEL8600 isolated from Korean soy-meju. Front Microbiol 2023; 14:1237442. [PMID: 37731927 PMCID: PMC10507247 DOI: 10.3389/fmicb.2023.1237442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
Enterococcus faecium is a prevalent species found in fermented soybean products, known for its contributions to flavor development and inhibition of pathogenic microorganisms during fermentation. This study aims to provide comprehensive phenotypic and genomic evidence supporting the probiotic characteristics of E. faecium EFEL8600, a bacteriocin-producing strain isolated from Korean soy-meju. Phenotypic analysis revealed that EFEL8600 produced a peptide with inhibitory activity against Listeria monocytogenes, estimated to be 4.6 kDa, corresponding to the size of enterocins P or Q. Furthermore, EFEL8600 exhibited probiotic traits, such as resilience in gastrointestinal conditions, antioxidant and anti-inflammatory activities, and protection of the intestinal barrier. Safety assessments demonstrated no hemolytic and bile salt deconjugation activities. Genomic analysis revealed the presence of several genes associated with probiotic characteristics and bacteriocin production, while few deleterious genes with a low likelihood of expression or transferring were detected. Overall, this study highlights E. faecium EFEL8600 as a potent anti-listeria probiotic strain suitable for use as a starter culture in soymilk fermentation, providing potential health benefits to consumers.
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Affiliation(s)
| | | | | | | | | | | | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Republic of Korea
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5
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Lin PY, Chan SY, Stern A, Chen PH, Yang HC. Epidemiological profiles and pathogenicity of Vancomycin-resistant Enterococcus faecium clinical isolates in Taiwan. PeerJ 2023; 11:e14859. [PMID: 36855433 PMCID: PMC9968458 DOI: 10.7717/peerj.14859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023] Open
Abstract
The emerging Vancomycin-resistant Enterococcus faecium (VRE-fm) is an opportunistic pathogen causing nosocomial infections. The identification of VRE-fm is important for successful prevention and control in healthcare settings. VRE-fm clinical isolates obtained from regional hospitals in northern Taiwan were characterized for antimicrobial susceptibility, virulence genes and biofilm production. Most isolates exhibited multi-drug resistance and carried the virulence genes, esp and hyl. While all isolates produce biofilms, those isolates that carried esp exhibited greater biofilm production. Isolates with different virulence gene carriages were examined for pathogenicity by using a nematode model, Caenorhabditis elegans, for determining microbial-host interactions. The survival assay showed that C. elegans was susceptible to Linezolid-resistant VRE-fm isolates with hyl. Combining the molecular epidemiological profiles regarding pathogenesis in C. elegans can serve as a guide for physicians in limiting opportunistic infections caused by VRE-fm.
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Affiliation(s)
- Pei-Yun Lin
- Department of Laboratory, Taipei City Hospital, Yang-Ming Branch, Taipei, Taiwan
| | - Shang-Yih Chan
- Department of Internal Medicine, Taipei City Hospital, Yang-Ming Branch, Taipei, Taiwan,Department of Exercise and Health Sciences, University of Taipei, Taipei, Taiwan,Department of Health Care Management, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Arnold Stern
- Grossman School of Medicine, New York University, New York, USA
| | - Po-Hsiang Chen
- Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Hung-Chi Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
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6
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Ohkusu K. Enterococcus faecium 129 BIO 3B is classified as Enterococcus lactis 129 BIO 3B. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 42:180-185. [PMID: 37404571 PMCID: PMC10315194 DOI: 10.12938/bmfh.2022-088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 07/06/2023]
Abstract
Enterococcus faecium 129 BIO 3B is a lactic acid bacterium that has been safely used as a probiotic product for over 100 years. Recently, concerns about its safety have arisen because some species of E. faecium belong to the vancomycin-resistant enterococci. The groups of E. faecium with less pathogenic potential have been split into a separate species (Enterococcus lactis). In this study, I investigated the phylogenetic classification and safety of E. faecium 129 BIO 3B as well as E. faecium 129 BIO 3B-R, which is naturally resistant to ampicillin. Mass spectrometry and basic local alignment search tool analysis using specific gene regions failed to differentiate 3B and 3B-R into E. faecium or E. lactis. However, multilocus sequence typing successfully identified 3B and 3B-R as the same sequence types as E. lactis. Overall genome relatedness indices showed that 3B and 3B-R have high degrees of homology with E. lactis. Gene amplification was confirmed for 3B and 3B-R with E. lactis species-specific primers. The minimum inhibitory concentration of ampicillin was confirmed to be 2 µg/mL for 3B, which is within the safety standard for E. faecium set by the European Food Safety Authority. Based on the above results, E. faecium 129 BIO 3B and E. faecium 129 BIO 3B-R were classified as E. lactis. The absence of pathogenic genes except for fms21 in this study demonstrates that these bacteria are safe for use as probiotics.
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Affiliation(s)
- Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, 6-1-1 Shinjuku-ku, Shinjuku, Tokyo 160-8402, Japan
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7
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Maechler F, Weber A, Schwengers O, Schwab F, Denkel L, Behnke M, Gastmeier P, Kola A. Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microb Genom 2023; 9:mgen000937. [PMID: 36748706 PMCID: PMC9973845 DOI: 10.1099/mgen.0.000937] [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: 07/04/2022] [Accepted: 11/22/2022] [Indexed: 01/31/2023] Open
Abstract
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates). SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.
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Affiliation(s)
- Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Luisa Denkel
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Behnke
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité – Universitätsmedizin Berlin, Berlin, Germany
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Distinction between Enterococcus faecium and Enterococcus lactis by a gluP PCR-Based Assay for Accurate Identification and Diagnostics. Microbiol Spectr 2022; 10:e0326822. [PMID: 36453910 PMCID: PMC9769498 DOI: 10.1128/spectrum.03268-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
It was recently proposed that Enterococcus faecium colonizing the human gut (previous clade B) actually corresponds to Enterococcus lactis. Our goals were to develop a PCR assay to rapidly differentiate these species and to discuss the main phenotypic and genotypic differences from a clinical perspective. The pan-genome of 512 genomes of E. faecium and E. lactis strains was analyzed to assess diversity in genes between the two species. Sequences were aligned to find the best candidate gene for designing species-specific primers, and their accuracy was tested with a collection of 382 enterococci. E. lactis isolates from clinical origins were further characterized by whole-genome sequencing (Illumina). Pan-genome analysis resulted in 12 gene variants, with gene gluP (rhomboid protease) being selected as the candidate for species differentiation. The nucleotide sequence of gluP diverged by 90 to 92% between sets, which allowed species identification through PCR with 100% specificity and no cross-reactivity. E. lactis strains were greatly pan-susceptible and not host specific. Hospital E. lactis isolates were susceptible to clinically relevant antibiotics, lacked infection-associated virulence markers, and were associated with patients presenting risk factors for enhanced bacterial translocation. Here, we propose a PCR-based assay using gluP for easy routine differentiation between E. faecium and E. lactis that could be implemented in different public health contexts. We further suggest that E. lactis, a dominant human gut species, can cross the gut barrier in severely ill, immunodeficient, and surgical patients. Knowing that bacterial translocation may be a sepsis promoter, the relevance of infections caused by E. lactis strains, even if they are pan-susceptible, should be explored. IMPORTANCE Enterococcus faecium is a WHO priority pathogen that causes severe and hard-to-treat human infections. It was recently proposed that E. faecium colonizing the human gut (previous clade B) actually corresponds to Enterococcus lactis; therefore, some of the human infections occurring globally are being misidentified. In this work, we developed a PCR-based rapid identification method for the differentiation of E. faecium and E. lactis and discussed the main phenotypic and genotypic differences of these species from a clinical perspective. We identified the gluP gene as the best candidate, based on the phylogenomic analysis of 512 published pan-genomes, and validated the PCR assay with a comprehensive collection of 382 enterococci obtained from different sources. Further detailed analysis of clinical E. lactis strains showed that they are highly susceptible to antibiotics and lack the typical virulence markers of E. faecium but are able to cause severe human infections in immunosuppressed patients, possibly in part due to gut barrier translocation.
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Quintela-Baluja M, Jobling K, Graham DW, Tabraiz S, Shamurad B, Alnakip M, Böhme K, Barros-Velázquez J, Carrera M, Calo-Mata P. Rapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs. Int J Mol Sci 2022; 23:ijms232213830. [PMID: 36430310 PMCID: PMC9697693 DOI: 10.3390/ijms232213830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry.
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Affiliation(s)
- Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
- Correspondence:
| | - Kelly Jobling
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David W. Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Shamas Tabraiz
- School of Natural and Applied Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK
| | | | - Mohamed Alnakip
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
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10
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Vasconcellos HVGD, Silva KFB, Montenegro H, Miguel CB, Tizioto P, Agostinho F, Araújo MC, Ribas RM, Silva MVD, Soares SDC, Rodrigues Júnior V, Batistão DWDF, Oliveira CJF, Rodrigues WF. Staphylococcus aureus and Enterococcus faecium isolated from pigeon droppings (Columba livia) in the external environment close to hospitals. Rev Soc Bras Med Trop 2022; 55:e0353. [PMID: 36000617 PMCID: PMC9405951 DOI: 10.1590/0037-8682-0353-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 05/12/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Domestic pigeons carry pathogens in their droppings, posing a potential public health problem. Methods: The phenotypic and genotypic antimicrobial resistances of Staphylococcus aureus and Enterococcus faecium in the feces of urban pigeons near hospitals with intensive care units were measured. Results: Twenty-nine samples showed Enterococcus growth, whereas one was positive for S. aureus. The S. aureus isolate was sensitive to the antibiotics tested via antibiogram, however resistance genes were identified. E. faecium isolates showed phenotypic resistance to gentamicin, erythromycin, and ciprofloxacin. Conclusions: Antimicrobial profiles harmful to health were demonstrated in bacterial pathogens isolated from the external environment of hospitals.
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Affiliation(s)
- Henrique Vieira Gartz de Vasconcellos
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Kerollyn Fernandes Bernardes Silva
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | | | - Camila Botelho Miguel
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | | | - Ferdinando Agostinho
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Marcelo Costa Araújo
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Rosineide Marques Ribas
- Universidade Federal de Uberlândia, Instituto de Ciências Biomédicas, Laboratório de Microbiologia Molecular, Uberlândia, MG, Brasil
| | - Marcos Vinícius da Silva
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Siomar de Castro Soares
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Virmondes Rodrigues Júnior
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Deivid William da Fonseca Batistão
- Universidade Federal de Uberlândia, Instituto de Ciências Biomédicas, Laboratório de Microbiologia Molecular, Uberlândia, MG, Brasil.,Universidade Federal de Uberlândia, Escola de Medicina, Uberlândia, MG, Brasil
| | - Carlo José Freire Oliveira
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
| | - Wellington Francisco Rodrigues
- Universidade Federal do Triângulo Mineiro, Instituto de Ciências Biológicas e Naturais, Laboratório de Imunologia e Bioinformática, Uberaba, MG, Brasil
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11
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Belloso Daza MV, Milani G, Cortimiglia C, Pietta E, Bassi D, Cocconcelli PS. Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. Front Microbiol 2022; 13:894241. [PMID: 35814695 PMCID: PMC9262338 DOI: 10.3389/fmicb.2022.894241] [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: 03/11/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.
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12
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Freitas AR, Tedim AP, Almeida-Santos AC, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Novais C, Peixe L. High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach. Microorganisms 2022; 10:microorganisms10030632. [PMID: 35336207 PMCID: PMC8948916 DOI: 10.3390/microorganisms10030632] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10–12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.
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Affiliation(s)
- Ana R. Freitas
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
| | - Ana P. Tedim
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), 47012 Valladollid, Spain;
| | - Ana C. Almeida-Santos
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Bárbara Duarte
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Houyem Elghaieb
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Mohamed S. Abbassi
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Abdennaceur Hassen
- Laboratory of Treatment and Valorisation of Wastewater, Centre of Research and Water Technologies (CERTE), Technopark of Borj-Cédria, Soliman 8020, Tunisia;
| | - Carla Novais
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
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13
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Ekore DO, Onanga R, Nguema PPM, Lozano C, Kumulungui BS. The Antibiotics Used in Livestock and Their Impact on Resistance in Enterococcus faecium and Enterococcus hirae on Farms in Gabon. Antibiotics (Basel) 2022; 11:224. [PMID: 35203826 PMCID: PMC8868485 DOI: 10.3390/antibiotics11020224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/10/2022] Open
Abstract
The emergence of antibiotic resistance is a major concern around the world. The objective of this study was to investigate the antibiotics used in livestock and their impact on resistance in Enterococcus faecium and Enterococcus hirae on farms in Gabon. A structured questionnaire was used to collect information on the farms. Samples were collected from farms (n = 20) tested for Enterococcus by culture and isolation and were identified using a polymerase chain reaction (PCR) and sequencing. Antibiotic susceptibility was determined by the disc diffusion method on Mueller Hinton agar. The 20 farms included laying hens (6), swine (6), sheep (4) and cattle farms (4). Tetracycline was the most used antibiotic family (91%) and the most used prophylactic method (47%) for the treatment of animals. A total of 555 samples were collected and 515 (93%) Enterococcus spp. isolates of the genus were obtained. The prevalence of E. faecium and E. hirae were 10% and 8%, respectively. The isolates from E. faecium and E. hirae we found were related to clinical and human isolates in the NCBI database. E. faecium and E. hirae isolates showed a high resistance to tetracycline (69% and 65%) and rifampicin (39% and 56%). The tet(M) gene was detected in 65 tetracycline-resistant isolates with a large majority in hens (78% (21/27) and 86% (12/14) in E. faecium and E. hirae, respectively). The consumption of antibiotics favours the emergence of antibiotic resistance in animals in Gabon.
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Affiliation(s)
- Désiré Otsaghe Ekore
- Centre International de Recherche Médicales de Franceville, Franceville, Gabon; (R.O.); (P.P.M.N.); (C.L.); (B.S.K.)
- Ecole Doctorale Régional d’Afrique Central, Franceville, Gabon
| | - Richard Onanga
- Centre International de Recherche Médicales de Franceville, Franceville, Gabon; (R.O.); (P.P.M.N.); (C.L.); (B.S.K.)
| | - Pierre Phillipe Mbehang Nguema
- Centre International de Recherche Médicales de Franceville, Franceville, Gabon; (R.O.); (P.P.M.N.); (C.L.); (B.S.K.)
- Institut de Recherche en Ecologie Tropical, Libreville, Gabon
| | - Chloé Lozano
- Centre International de Recherche Médicales de Franceville, Franceville, Gabon; (R.O.); (P.P.M.N.); (C.L.); (B.S.K.)
| | - Brice Serge Kumulungui
- Centre International de Recherche Médicales de Franceville, Franceville, Gabon; (R.O.); (P.P.M.N.); (C.L.); (B.S.K.)
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14
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Prieto‐Maradona M, Querol A, Sijtsma L, Evaristo Suarez J, Sundh I, Vlak J, Barizzone F, Hempen M, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 15: suitability of taxonomic units notified to EFSA until September 2021. EFSA J 2022; 20:e07045. [PMID: 35126735 PMCID: PMC8792879 DOI: 10.2903/j.efsa.2022.7045] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a generic pre-evaluation of the safety of biological agents. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. The QPS list was updated in relation to the revised taxonomy of the genus Bacillus, to synonyms of yeast species and for the qualifications 'absence of resistance to antimycotics' and 'only for production purposes'. Lactobacillus cellobiosus has been reclassified as Limosilactobacillus fermentum. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS taxonomic units (TU)s. Of the 70 microorganisms notified to EFSA, 64 were not evaluated: 11 filamentous fungi, one oomycete, one Clostridium butyricum, one Enterococcus faecium, five Escherichia coli, one Streptomyces sp., one Bacillus nakamurai and 43 TUs that already had a QPS status. Six notifications, corresponding to six TUs were evaluated: Paenibacillus lentus was reassessed because an update was requested for the current mandate. Enterococcus lactis synonym Enterococcus xinjiangensis, Aurantiochytrium mangrovei synonym Schizochytrium mangrovei, Schizochytrium aggregatum, Chlamydomonas reinhardtii synonym Chlamydomonas smithii and Haematococcus lacustris synonym Haematococcus pluvialis were assessed for the first time. The following TUs were not recommended for QPS status: P. lentus due to a limited body of knowledge, E. lactis synonym E. xinjiangensis due to potential safety concerns, A. mangrovei synonym S. mangrovei, S. aggregatum and C. reinhardtii synonym C. smithii, due to lack of a body of knowledge on its occurrence in the food and feed chain. H. lacustris synonym H. pluvialis is recommended for QPS status with the qualification 'for production purposes only'.
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15
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Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss MA. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks. Front Microbiol 2021; 12:728356. [PMID: 34646248 PMCID: PMC8503688 DOI: 10.3389/fmicb.2021.728356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.
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Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.,IDbyDNA Inc., Salt Lake City, UT, United States
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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16
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Belloso Daza MV, Cortimiglia C, Bassi D, Cocconcelli PS. Genome-based studies indicate that the Enterococcus faecium Clade B strains belong to Enterococcus lactis species and lack of the hospital infection associated markers. Int J Syst Evol Microbiol 2021; 71. [PMID: 34402778 DOI: 10.1099/ijsem.0.004948] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Enterococcus lactis and the heterotypic synonym Enterococcus xinjiangensis from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. Enterococcus faecium type strain NCTC 7171T was used as the reference genome for determining E. lactis and E. faecium to be separate species. However, this taxonomic classification did not consider the diverse lineages of E. faecium, and the double nature of hospital-associated (clade A) and community-associated (clade B) isolates. Here, we investigated the taxonomic relationship among isolates of E. faecium of different origins and E. lactis, using a genome-based approach. Additional to 16S rRNA gene sequence analysis, we estimated the relatedness among strains and species using phylogenomics based on the core pangenome, multilocus sequence typing, the average nucleotide identity and digital DNA-DNA hybridization. Moreover, following the available safety assessment schemes, we evaluated the virulence profile and the ampicillin resistance of E. lactis and E. faecium clade B strains. Our results confirmed the genetic and evolutionary differences between clade A and the intertwined clade B and E. lactis group. We also confirmed the absence in these strains of virulence gene markers IS16, hylEfm and esp and the lack of the PBP5 allelic profile associated with ampicillin resistance. Taken together, our findings support the reassignment of the strains of E. faecium clade B as E. lactis.
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Affiliation(s)
- Mireya Viviana Belloso Daza
- Dipartimento di Scienze e Tecnologie Alimentari per Una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Claudia Cortimiglia
- Dipartimento di Scienze e Tecnologie Alimentari per Una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Daniela Bassi
- Dipartimento di Scienze e Tecnologie Alimentari per Una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
| | - Pier Sandro Cocconcelli
- Dipartimento di Scienze e Tecnologie Alimentari per Una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy
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17
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Mariam SH. A sampling survey of enterococci within pasteurized, fermented dairy products and their virulence and antibiotic resistance properties. PLoS One 2021; 16:e0254390. [PMID: 34264984 PMCID: PMC8282027 DOI: 10.1371/journal.pone.0254390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 01/17/2023] Open
Abstract
Globally, fermented foods (FFs), which may be traditional or industrially-produced, are major sources of nutrition. In the traditional practice, the fermentation process is driven by communities of virtually uncharacterized microflora indigenous to the food substrate. Some of these flora can have virulent or antibiotic resistance properties, posing risk to consumers. Others, such as Enterococcus faecalis and Enterococcus faecium, may also be found in such foods. Enterococci that harbor antibiotic resistance or virulence factors can cycle among animals, food, humans and the environment, thereby transferring these harmful properties at the gene level to harmless commensals in the food matrix, animals and humans. In this work, several microbial isolates obtained from different FF sources were analyzed for their identity and virulence and/or antibiotic resistance properties. For identification aiming at enterococci, isolates that were Gram-positive and catalase- and oxidase-negative were subjected to multiple tests including for growth in broth containing 6.5% NaCl, growth and hydrolytic activity on medium containing bile-esculin, hemolytic activity on blood agar, and growth at 45°C and survival after incubation at 60°C for 30 min. Furthermore, the isolates were tested for susceptibility/resistance to a select group of antibiotics. Finally, the isolates were molecularly-characterized with respect to species identity and presence of virulence-encoding genes by amplification of target genes. Most sources contained enterococci, in addition to most of them also containing Gram-negative flora. Most of these also harbored virulence factors. Several isolates were also antibiotic-resistant. These results strongly suggest attention should be given to better control presence of such potentially pathogenic species.
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Affiliation(s)
- Solomon H. Mariam
- Aklilu Lemma Institute of Pathobiology, Armauer Hansen Research Institute, Addis Ababa University, Addis Ababa, Ethiopia
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18
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Eisenberger D, Tuschak C, Werner M, Bogdan C, Bollinger T, Hossain H, Friedrich P, Hussein Z, Pöhlmann C, Würstl B, Nickel S, Lehner-Reindl V, Höller C, Liebl B, Valenza G. Whole-genome analysis of vancomycin-resistant Enterococcus faecium causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavaria, Germany. J Antimicrob Chemother 2021; 75:1398-1404. [PMID: 32083651 DOI: 10.1093/jac/dkaa041] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. METHODS Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. RESULTS Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals: ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. CONCLUSIONS Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages.
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Affiliation(s)
| | | | - Markus Werner
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Bogdan
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Bollinger
- Institut für Laboratoriumsmedizin, Mikrobiologie und Krankenhaushygiene (ILMH), Klinikum Bayreuth GmbH, Bayreuth, Germany
| | - Hamid Hossain
- Institut für Laboratoriumsmedizin und Mikrobiologie, Klinikum St Marien Amberg, Amberg, Germany.,Institut für Laboratoriumsmedizin und Mikrobiologie, Kliniken Nordoberpfalz AG, Weiden, Germany
| | - Petra Friedrich
- Deutsches Beratungszentrum für Hygiene BZH GmbH, Freiburg, Germany
| | - Ziyad Hussein
- Institut für Laboratoriumsdiagnostik und Transfusionsmedizin, DONAUISAR Klinikum, Deggendorf, Germany
| | - Christoph Pöhlmann
- Abteilung für Hygiene und Mikrobiologie, Klinikum Memmingen, Memmingen, Germany
| | - Benjamin Würstl
- Stabsstelle Krankenhaushygiene und Infektionsprävention, München Klinik, München, Germany
| | - Silke Nickel
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | | | | | - Bernhard Liebl
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Giuseppe Valenza
- Bavarian Health and Food Safety Authority, Erlangen, Germany.,Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
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19
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Freitas AR, Tedim AP, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Read A, Alves V, Novais C, Peixe L. Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link. J Antimicrob Chemother 2021; 75:2416-2423. [PMID: 32607549 DOI: 10.1093/jac/dkaa227] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts. METHODS poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives. RESULTS poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30-100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment. CONCLUSIONS poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Antónia Read
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Valquíria Alves
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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20
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Finisterra L, Duarte B, Peixe L, Novais C, Freitas AR. Industrial dog food is a vehicle of multidrug-resistant enterococci carrying virulence genes often linked to human infections. Int J Food Microbiol 2021; 358:109284. [PMID: 34144837 DOI: 10.1016/j.ijfoodmicro.2021.109284] [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: 01/15/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
The increase in the number of pets in recent years has been followed by an exponential growth of the industrial pet food sector, which has been accompanied by new food safety risks, namely antibiotic resistance. The aim of this study was to investigate whether dog food commercially available in Portugal is a reservoir of clinically-relevant antibiotic resistant Enterococcus. Fifty-five samples (25 brands; 22 wet, 14 raw frozen, 8 dry, 7 treats and 4 semi-wet) were collected on 9 commercial surfaces in the Porto region (September 2019 to January 2020). Most samples were obtained from brands that are commercialized worldwide (n = 21/25). Sample (25 g) processing included pre-enrichment and enrichment steps in culture media without/with 3 antibiotics, and then plating into selective media without/with the same antibiotics. Susceptibility was studied for 13 antibiotics (disk diffusion; Etest; microdilution) according to EUCAST/CLSI. Clinically-relevant species (E. faecium and E. faecalis), antibiotic resistance (vanA, vanB, optrA, poxtA) and virulence (e.g. ptsD, esp, sgrA) genes were identified by PCR. Other species of Enterococcus were identified by MALDI-TOF MS. Clonality was established by MLST in selected isolates. Enterococcus (n = 184; 7 species; >85% E. faecium and E. faecalis) were detected in 30 samples (54%) of different types (14 raw, 16 heat treated-7 dry, 6 wet, 3 treats). E. faecium and E. faecalis were more frequent in dry and wet samples, respectively. More than 40% of enterococci recovered were resistant to erythromycin, tetracycline, quinupristin-dalfopristin, streptomycin, gentamicin, chloramphenicol, ampicillin or ciprofloxacin, and to a lesser extent to linezolid (23%; optrA, poxtA) or vancomycin and teicoplanin (2% each; vanA). Multidrug-resistant isolates (31%), including to vancomycin and linezolid, were obtained mostly from raw foods, although also detected in wet samples or treats, and mainly from culture media supplemented with antibiotics. Samples subjected to thermal treatment mostly carried non-MDR isolates. The variety of clones observed included strains previously identified in hospitalized patients (E. faecium ST17/ST80; E. faecalis ST40), farm animals, pets and environmental strains. This study shows that dog food from international brands is a vehicle of clinically-relevant enterococci carrying resistance to last resort antibiotics and relevant virulence genes, thus positioning pet food as an important source of antibiotic resistance spread within the One Health context. The high incidence of Enterococcus in a variety of dog food samples indicates the need to review selection of raw materials, manufacturing and hygiene practices in an emerging food sector growing worldwide.
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Affiliation(s)
- Liliana Finisterra
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG)
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG).
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; Departmento de Ciências, Instituto Universitário de Ciências da Saúde (IUCS), Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), CRL, Gandra, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG).
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21
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Koutsoumanis K, Allende A, Álvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L. Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021; 19:e06651. [PMID: 34178158 PMCID: PMC8210462 DOI: 10.2903/j.efsa.2021.6651] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.
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22
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Revtovich AV, Tjahjono E, Singh KV, Hanson BM, Murray BE, Kirienko NV. Development and Characterization of High-Throughput Caenorhabditis elegans - Enterococcus faecium Infection Model. Front Cell Infect Microbiol 2021; 11:667327. [PMID: 33996637 PMCID: PMC8116795 DOI: 10.3389/fcimb.2021.667327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
The genus Enterococcus includes two Gram-positive pathogens of particular clinical relevance: E. faecalis and E. faecium. Infections with each of these pathogens are becoming more frequent, particularly in the case of hospital-acquired infections. Like most other bacterial species of clinical importance, antimicrobial resistance (and, specifically, multi-drug resistance) is an increasing threat, with both species considered to be of particular importance by the World Health Organization and the US Centers for Disease Control. The threat of antimicrobial resistance is exacerbated by the staggering difference in the speeds of development for the discovery and development of the antimicrobials versus resistance mechanisms. In the search for alternative strategies, modulation of host-pathogen interactions in general, and virulence inhibition in particular, have drawn substantial attention. Unfortunately, these approaches require a fairly comprehensive understanding of virulence determinants. This requirement is complicated by the fact that enterococcal infection models generally require vertebrates, making them slow, expensive, and ethically problematic, particularly when considering the thousands of animals that would be needed for the early stages of experimentation. To address this problem, we developed the first high-throughput C. elegans-E. faecium infection model involving host death. Importantly, this model recapitulates many key aspects of murine peritonitis models, including utilizing similar virulence determinants. Additionally, host death is independent of peroxide production, unlike other E. faecium-C. elegans virulence models, which allows the assessment of other virulence factors. Using this system, we analyzed a panel of lab strains with deletions of targeted virulence factors. Although removal of certain virulence factors (e.g., Δfms15) was sufficient to affect virulence, multiple deletions were generally required to affect pathogenesis, suggesting that host-pathogen interactions are multifactorial. These data were corroborated by genomic analysis of selected isolates with high and low levels of virulence. We anticipate that this platform will be useful for identifying new treatments for E. faecium infection.
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Affiliation(s)
| | - Elissa Tjahjono
- Department of BioSciences, Rice University, Houston, TX, United States
| | - Kavindra V. Singh
- Division of Infectious Diseases, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Blake M. Hanson
- Division of Infectious Diseases, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, TX, United States
| | - Barbara E. Murray
- Division of Infectious Diseases, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
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23
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Deng F, Chen Y, Zhou X, Xiao H, Sun T, Deng Y, Wen J. New Insights into the Virulence Traits and Antibiotic Resistance of Enterococci Isolated from Diverse Probiotic Products. Microorganisms 2021; 9:microorganisms9040726. [PMID: 33807433 PMCID: PMC8065695 DOI: 10.3390/microorganisms9040726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/23/2022] Open
Abstract
The GRAS (generally recognized as safe) status of Enterococcus has not yet been authenticated, but enterococci, as probiotics, have been increasingly applied in human healthcare and animal husbandry, for instance as a dietary supplement, feed additive, or growth promotor. The food chain is the important route for introducing enterococci into the human gut. The pathogenicity of Enterococcus from probiotic products requires investigation. In the study, 110 commercial probiotic products used for human, animal, aquaculture, and plants were examined, among which 36 enterococci were identified, including 31 from Enterococcus faecium, 2 from E. faecalis, 2 from E. casseliflavus, and 1 from E. gallinarum. Strikingly, 28 of the 36 enterococci isolated from probiotics here did not mention the presence of Enterococcus in the labeled ingredients, and no Enterococcus isolates were found from 5 animal probiotics that were labeled with the genus. In total, 35 of the 110 products exhibited hemolysis, including 5 (10.6%) human probiotics, 14 (41.2%) animal probiotics, 8 (57.1%) aquaculture probiotics, and 8 (53.3%) plant probiotics. The detection rates of virulence factors associated with adhesion, antiphagocytosis, exoenzyme, biofilm, and other putative virulence markers (PVM) in 36 enterococci were 94.4%, 91.7%, 5.6%, 94.4% and 8.3%. Twenty-six of the 36 isolated strains exhibited biofilm formation ability, where 25 strains (69.4%) and one (2.8%) were strong and weak biofilm producers, respectively. We analyzed the resistance rates against erythromycin (97%), vancomycin and ciprofloxacin (8%), tetracycline (3%), and high-level aminoglycosides (0%), respectively. High detection rates of msrC/lsaA (86%) and aac(6')-Ii (86%) were observed, followed by vanC (8%), tetM (3%). The Tn5801-tetM-like integrative conjugative element (ICE) was identified in E. gallinarum, exhibiting resistance to tetracycline (64 μg/mL). Seven probiotic E. faecalis and E. faecium, as active ingredients in human probiotics, shared the same STs (sequence types) and were distinct from the STs of other contaminated or mislabeled enterococci, indicating that two particular STs belonged to native probiotic isolates. These findings advocate appropriate assessments of enterococci when used in probiotics.
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Affiliation(s)
- Fengru Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Yunsheng Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Xiaoyu Zhou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Huiying Xiao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Tianyu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Correspondence: (Y.D.); (J.W.)
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; (F.D.); (Y.C.); (X.Z.); (H.X.); (T.S.)
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
- Correspondence: (Y.D.); (J.W.)
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24
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Aun E, Kisand V, Laht M, Telling K, Kalmus P, Väli Ü, Brauer A, Remm M, Tenson T. Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs. Front Microbiol 2021; 12:601490. [PMID: 33841342 PMCID: PMC8032980 DOI: 10.3389/fmicb.2021.601490] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.
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Affiliation(s)
- Erki Aun
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mailis Laht
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kaidi Telling
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Piret Kalmus
- Department of Clinical Veterinary Medicine, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Age Brauer
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
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25
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Janjusevic A, Markovic Denic L, Minic R, Grgurevic A, Cirkovic I. Intestinal carriage of vancomycin-resistant Enterococcus spp. among high-risk patients in university hospitals in Serbia: first surveillance report. Ann Clin Microbiol Antimicrob 2021; 20:18. [PMID: 33743726 PMCID: PMC7981873 DOI: 10.1186/s12941-021-00423-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The screening for intestinal carriage of vancomycin-resistant Enterococcus spp. (VRE) among high risk patients in the Balkan region and molecular epidemiology of VRE is insufficiently investigated, yet it could be of key importance in infection control. The aim of this study was to provide baseline data on VRE intestinal carriage among high-risk patients in Serbian university hospitals, to determine the phenotypic/genotypic profiles of the isolated VRE, to obtain knowledge of local resistance patterns and bridge the gaps in current VRE surveillance. METHODS The VRE reservoir was investigated using stool samples from 268 inpatients. Characterization of isolated VRE stains consisted of BD Phoenix system, genotypic identification, glycopeptide and quinupristin-dalfopristin (Q-D) resistance probing, virulence gene (esp, hyl, efaA, asa1, gelE, cpd) detection and MLVA. Biofilm formation was evaluated by the microtiter plate method. RESULTS VRE carriage prevalence among at-risk patients was 28.7%. All VRE strains were vanA positive multidrug-resistant Enterococcus faecium (VRfm), harboring ermB-1 (38.9%), esp (84%), efaA (71.2%), hyl (54.5%), asa1 (23.4%), gelE and cpd (11.6%) each. Ability of biofilm production was detected in 20.8%. Genetic relatedness of the isolates revealed 13 clusters, heterogeneous picture and 25 unique MTs profiles. CONCLUSION The obtained prevalence of VRE intestinal carriage among high-risk inpatients in Serbia is higher than the European average, with high percentage of multidrug resistance. The emergence of resistance to Q-D is of particular concern. Close monitoring of pattern of resistance and strict adherence to specific guidelines are urgently needed in Serbia.
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Affiliation(s)
- Ana Janjusevic
- Department of Bacteriology, Institute of Virology, Vaccines and Sera “Torlak”, Vojvode Stepe 458, 11152 Belgrade, Serbia
| | - Ljiljana Markovic Denic
- Department of Epidemiology, Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Visegradska 26a, PO Box 20, 11129 Belgrade, Serbia
| | - Rajna Minic
- Department of Bacteriology, Institute of Virology, Vaccines and Sera “Torlak”, Vojvode Stepe 458, 11152 Belgrade, Serbia
| | - Anita Grgurevic
- Department of Epidemiology, Institute of Epidemiology, Faculty of Medicine, University of Belgrade, Visegradska 26a, PO Box 20, 11129 Belgrade, Serbia
| | - Ivana Cirkovic
- Department of Bacteriology, Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotića 1, 11000 Belgrade, Serbia
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26
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Freitas AR, Pereira AP, Novais C, Peixe L. Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? Int J Antimicrob Agents 2020; 57:106227. [PMID: 33207280 DOI: 10.1016/j.ijantimicag.2020.106227] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/26/2020] [Accepted: 11/07/2020] [Indexed: 12/13/2022]
Abstract
Enterococcus faecium is a significant opportunistic human pathogen with a broad host range, including humans, farm animals, pets and wildlife. Specialised subpopulations have globally evolved towards a powerful and convergent adaption to the healthcare environment by acquiring a cocktail of key antimicrobial resistance and virulence genes, enabling them to thrive in the disturbed microbiota of hospitalised patients. These populations can also be found in different community reservoirs, but the relevance of their dispersal in non-human hosts is greatly unknown and is here discussed. This review provides a brief historical overview of what we have been considering E. faecium high-risk clones worldwide alongside the advances in strain typing technologies that have revolutionised our understanding of the genetic evolution of this species over the last three decades.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Ana P Pereira
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal.
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27
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Elghaieb H, Freitas AR, Abbassi MS, Novais C, Zouari M, Hassen A, Peixe L. Dispersal of linezolid-resistant enterococci carrying poxtA or optrA in retail meat and food-producing animals from Tunisia. J Antimicrob Chemother 2020; 74:2865-2869. [PMID: 31243458 DOI: 10.1093/jac/dkz263] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/02/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES The epidemiology of Enterococcus resistant to priority antibiotics including linezolid has mainly been investigated in developed countries and especially in hospitals. We aimed to evaluate the contribution of different non-human reservoirs for the burden of MDR enterococci in Tunisia, where scarce data are available. METHODS Samples (n = 287) were collected from urban wastewater (n = 57), retail meat (n = 29; poultry/bovine/ovine), milk (n = 89; bovine/ovine), farm animal faeces (n = 80; poultry/bovine/ovine) and pets (n = 32; rabbit/dogs/cats/birds) in different Tunisian regions (2014-17). They were plated onto Slanetz-Bartley agar after pre-enrichment without antibiotics. Standard methods were used for bacterial identification and characterization of antibiotic resistance and virulence genes (PCR), antibiotic susceptibility testing (disc diffusion/broth microdilution; EUCAST/CLSI) and clonality (SmaI-PFGE/MLST). RESULTS All samples carried Enterococcus (n = 377 isolates) resistant to antibiotics considered to be critical or highly important by WHO. Even without antibiotic selection, 38% of Enterococcus faecalis (Efs) and 22% of Enterococcus faecium (Efm) were identified as MDR. Linezolid-resistant isolates (5%; MIC = 8 mg/L) comprised six poxtA-carrying Efm (cow milk), seven optrA-carrying Efs (chicken faeces/meat) and five Efm lacking cfr/optrA/poxtA (poultry/bovine/ovine/wastewater). Clinically relevant Efm clones (clade A1) were identified in animal/meat sources. Ampicillin resistance (1%) was confined to ST18/ST78-like MDR Efm clones from bovine meat/milk samples carrying relevant virulence markers (e.g. ptsD/IS16). CONCLUSIONS This study provides evidence of the contribution of livestock and foodstuffs to the dispersal of acquired linezolid resistance genes including poxtA and optrA. We report the first poxtA-carrying Efm in Tunisia, and for the first time in bovine samples, stressing the urgent need for alternative measures to counteract the spread of linezolid-resistant enterococci globally.
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Affiliation(s)
- Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, Tunis, Tunisia
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | | | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Hammam-Lif, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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28
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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29
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Freitas AR, Novais C, Coque TM, Peixe L. Comment on: Emergence of plasmid-mediated oxazolidinone resistance gene poxtA from CC17 Enterococcus faecium of pig origin. J Antimicrob Chemother 2020; 75:1358-1359. [PMID: 31617898 DOI: 10.1093/jac/dkz432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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30
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Rios R, Reyes J, Carvajal LP, Rincon S, Panesso D, Echeverri AM, Dinh A, Kolokotronis SO, Narechania A, Tran TT, Munita JM, Murray BE, Planet PJ, Arias CA, Diaz L. Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. Sci Rep 2020; 10:5636. [PMID: 32221315 PMCID: PMC7101424 DOI: 10.1038/s41598-020-62371-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America (LATAM). Here, we provide a complete genomic characterization of 55 representative Latin American VREfm recovered from 1998-2015 in 5 countries. The LATAM VREfm population is structured into two main clinical clades without geographical clustering. Using the LATAM genomes, we reconstructed the global population of VREfm by including 285 genomes from 36 countries spanning from 1946 to 2017. In contrast to previous studies, our results show an early branching of animal related isolates and a further split of clinical isolates into two sub-clades within clade A. The overall phylogenomic structure of clade A was highly dependent on recombination (54% of the genome) and the split between clades A and B was estimated to have occurred more than 2,765 years ago. Furthermore, our molecular clock calculations suggest the branching of animal isolates and clinical clades occurred ~502 years ago whereas the split within the clinical clade occurred ~302 years ago (previous studies showed a more recent split between clinical an animal branches around ~74 years ago). By including isolates from Latin America, we present novel insights into the population structure of VREfm and revisit the evolution of these pathogens.
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Affiliation(s)
- Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Lina P Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Diana Panesso
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Aura M Echeverri
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - An Dinh
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Sergios-Orestis Kolokotronis
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Truc T Tran
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Barbara E Murray
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Paul J Planet
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania & Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cesar A Arias
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.,Division of Infectious Diseases, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA.,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia. .,Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. .,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile.
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31
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019). EFSA J 2020; 18:e05966. [PMID: 32874212 PMCID: PMC7448045 DOI: 10.2903/j.efsa.2020.5966] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
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32
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Murray SA, Holbert AC, Norman KN, Lawhon SD, Sawyer JE, Scott HM. Macrolide-susceptible probiotic Enterococcus faecium ST296 exhibits faecal-environmental-oral microbial community cycling among beef cattle in feedlots. Lett Appl Microbiol 2020; 70:274-281. [PMID: 31883125 DOI: 10.1111/lam.13269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Enterococci are included in the United States National Antimicrobial Resistance Monitoring System to track antibiotic resistance among commensal Gram-positive enteric bacteria, largely due to their high abundance in food animals and in retail meat. In the U.S. cattle industry, macrolides are used to prevent and control liver abscesses, which cause significant economic losses. Previous studies have suggested that feeding tylosin and the intensity of the pen environment, both expand and sustain respectively the prevalence of multidrug resistance among enterococci in feedlot cattle. This has led to research into alternative feed supplements and improved stewardship practices. In a randomized controlled trial, we measured the impact of a probiotic and an altered pen environment on antimicrobial resistance among faecal Enterococcus spp. in cattle fed tylosin. Supplementing cattle with an Enterococcus faecium and Saccharomyces cerevisiae-based probiotic yielded the isolation of E. faecium of the probiotic sequence type (ST296) from faecal and environmental samples in treatment groups, as well as from cattle and the manure pack in nearby pens. Of importance, the probiotic strain also was found in a desiccated and milled manure pack sample taken 120 days after the initial trial ended. Phylogenetic and SNP analyses revealed clonal survival and spread compatible with faecal-environmental-oral recycling of the probiotic strain within and among cattle and pens. The increase in prevalence of the ST296 strain occurred concomitant with a decrease in ST240, the dominant sequence type associated with ermB and tet(M) resistance genes in this trial. SIGNIFICANCE AND IMPACT OF THE STUDY: We demonstrate that a macrolide-susceptible probiotic Enterococcus faecium ST296 strain fed to beef cattle becomes fully embedded in the microbial community cycling of bacteria via faecal-environmental-oral transmission within and among feedlot pens. An initial investment in feeding the probiotic is thereby leveraged into expanding numbers of susceptible bacteria in cattle and their environment, even among those cattle fed tylosin.
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Affiliation(s)
- S A Murray
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - A C Holbert
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - K N Norman
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - S D Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | - J E Sawyer
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - H M Scott
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
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33
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Risks associated with enterococci as probiotics. Food Res Int 2019; 129:108788. [PMID: 32036912 DOI: 10.1016/j.foodres.2019.108788] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/07/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023]
Abstract
Probiotics are naturally occurring microorganisms that confer health benefits by altering host commensal microbiota, modulating immunity, enhancing intestinal barrier function, or altering pain perception. Enterococci are human and animal intestinal commensals that are used as probiotics and in food production. These microorganisms, however, express many virulence traits including cytolysin, proteases, aggregation substance, capsular polysaccharide, enterococcal surface protein, biofilm formation, extracellular superoxide, intestinal translocation, and resistance to innate immunity that can lead to serious hospital-acquired infections. In addition, enterococci are facile in acquiring antibiotic resistance genes to many clinically important antibiotics encoded on a wide variety of conjugative plasmids, transposons, and bacteriophages. The pathogenicity and disease burden caused by enterococci render them poor choices as probiotics. No large, randomized, placebo-controlled clinical trials have demonstrated the safety and efficacy of any enterococcal probiotic. As a result, no enterococcal probiotic has been approved by the United States Food and Drug Administration for the treatment, cure, or amelioration of human disease. In 2007, the European Food Safety Authority concluded that enterococci do not meet the standard for "Qualified Presumption of Safety". Enterococcal strains used or proposed for use as probiotics should be carefully screened for efficacy and safety.
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34
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Dec M, Stępień-Pyśniak D, Gnat S, Fratini F, Urban-Chmiel R, Cerri D, Winiarczyk S, Turchi B. Antibiotic Susceptibility and Virulence Genes in Enterococcus Isolates from Wild Mammals Living in Tuscany, Italy. Microb Drug Resist 2019; 26:505-519. [PMID: 31663834 DOI: 10.1089/mdr.2019.0052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Drug resistance is of great importance to human and animal health, but wild environments are still poorly understood in terms of their function as reservoirs of dangerous microbes and resistance determinants. The aim of the study was to determine the antibiotic susceptibility and virulence factors of Enterococcus bacteria from wildlife in Tuscany, Italy. Of the 36 mammalian fecal samples, 52 isolates were derived and classified as Enterococcus faecium (46% of isolates), Enterococcus hirae (19%), Enterococcus faecalis (13%), Enterococcus gallinarum (8%), Enterococcus casseliflavus (6%), Enterococcus durans (4%), Enterococcus mundtii (2%), and Enterococcus canintestini (2%) using both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and methods based on analysis of genetic material. The isolates tested showed the most frequent resistance to tetracycline (36.5% isolates), ciprofloxacin (36.5%), and erythromycin (25%). Three isolates showed high level of resistance (minimal inhibitory concentration ≥1,024 μg/mL) to vancomycin and teicoplanin, and 15% of the isolates demonstrated multidrug resistance. No isolate resistant to ampicillin, linezolid, or streptomycin was found. Among resistance genes, aac(6)-Ii (50% isolates), msrA/B (48%), msrC (42%), and tetM (31%) were identified most frequently. All E. faecium and E. faecalis isolates were positive for the efaAfm and efaAfs genes, respectively. Other virulence-associated genes, that is, gelE, cylA, asa1, esp, ace, orf1481, ptsD, and sgrA, were found in the majority of E. faecalis and several E. faecium isolates. Multilocus sequence typing analysis performed for selected isolates revealed three new sequence types. The results obtained indicate that wild mammals might act as reservoirs of resistance and virulence determinants that could be transferred between different ecosystems.
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Affiliation(s)
- Marta Dec
- Department of Veterinary Prevention and Avian Diseases and Faculty of Veterinary Medicine, Institute of Biological Bases of Animal Diseases, University of Life Sciences in Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases and Faculty of Veterinary Medicine, Institute of Biological Bases of Animal Diseases, University of Life Sciences in Lublin, Lublin, Poland
| | - Sebastian Gnat
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Institute of Biological Bases of Animal Diseases, University of Life Sciences in Lublin, Lublin, Poland
| | - Filippo Fratini
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases and Faculty of Veterinary Medicine, Institute of Biological Bases of Animal Diseases, University of Life Sciences in Lublin, Lublin, Poland
| | - Domenico Cerri
- Department of Veterinary Science, University of Pisa, Pisa, Italy
| | - Stanisław Winiarczyk
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Barbara Turchi
- Department of Veterinary Science, University of Pisa, Pisa, Italy
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35
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Kerschner H, Cabal A, Hartl R, Machherndl-Spandl S, Allerberger F, Ruppitsch W, Apfalter P. Hospital outbreak caused by linezolid resistant Enterococcus faecium in Upper Austria. Antimicrob Resist Infect Control 2019; 8:150. [PMID: 31516698 PMCID: PMC6732827 DOI: 10.1186/s13756-019-0598-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Enterococcus faecium is part of the human gastrointestinal flora but may act as opportunistic pathogen. Environmental persistence, high colonization capability and diverse intrinsic and acquired resistance mechanisms make it especially successful in nosocomial high-risk settings. In March 2014, an outbreak of Linezolid resistant Enterococcus faecium (LREfm) was observed at the hematooncology department of a tertiary care center in Upper Austria. Methods We report on the outbreak investigation together with the whole genome sequencing (WGS)-based typing results including also non-outbreak LREfm and susceptible isolates. Results The 54 investigated isolates could be divided in six clusters based on cgMLST. Cluster one comprised LREfm isolates of genotype ST117 and CT24, which was identified as the causative clone of the outbreak. In addition, the detection of four other clusters comprising isolates originating from hematooncology patients but also at other hospitals, pointed to LREfm transmission between local healthcare facilities. LREfm patients (n = 36) were typically at risk for acquisition of nosocomial pathogens because of immunosuppression, frequent hospitalization and antibiotic therapies. Seven of these 36 patients developed LREfm infection but were successfully treated. After termination of the initial outbreak, sporadic cases occurred despite a bundle of applied outbreak control interventions. Conclusions WGS proved to be an effective tool to differentiate several LREfm clusters in an outbreak. Active screening for LREfm is important in a high-risk setting such as hematooncology, where multiple introductions are possible and occur despite intensified infection control measures. Electronic supplementary material The online version of this article (10.1186/s13756-019-0598-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Adriana Cabal
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria.,3European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Sigrid Machherndl-Spandl
- Department of Internal Medicine 1, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Franz Allerberger
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Werner Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
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Oravcová V, Peixe L, Coque TM, Novais C, Francia MV, Literák I, Freitas AR. Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids. ENVIRONMENT INTERNATIONAL 2018; 118:125-133. [PMID: 29870913 DOI: 10.1016/j.envint.2018.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The most prevalent type of acquired vancomycin resistance in Enterococcus faecium (VREfm) is encoded by the vanA transposon Tn1546, mainly located on transferable plasmids. vanA plasmids have been characterized in VREfm from a variety of sources but not wild birds. The aim of this study was to analyse the genetic context of VREfm strains recovered from wild corvid birds and to compare their plasmid and strain characteristics with human strains. To achieve that, 75 VREfm isolates, including strains from wild birds recovered during wide surveillance studies performed in Europe, Canada and the United States (2010-2013), and clinical and wastewater strains from Czech Republic, a region lacking data about vanA plasmids, were analysed. Their population structure, presence of major putative virulence markers and characterization of vanA transposons and plasmids were established. VREfm from wild birds were mainly associated with major human lineages (ST18 and ST78) circulating in hospitals worldwide and were enriched in putative virulence markers that are highly associated with clinical E. faecium from human infections. They also carried plasmids of the same families usually found in the clinical setting [RCR, small theta plasmids, RepA_N (pRUM/pLG1) and Inc18]. The clinically widespread IS1251-carrying Tn1546 type "F" was predominant and Tn1546-vanA was mainly located on pRUM/Axe-Txe (USA) and Inc18- or pLG1-like (Europe) plasmids. VREfm from hospitals and wastewaters carried Tn1546-vanA in different plasmid types including mosaic pRUM-Inc18 plasmids, not identified in wild birds. This is the first characterization of vanA plasmids obtained from wild birds. A similar plasmid pool seems to exist in different clonal E. faecium backgrounds of humans and wild birds. The isolation of VREfm strains from wild birds that belong to human E. faecium adapted lineages and carry virulence genes, Tn1546 and plasmid variants widespread in the clinical setting is of concern and highlight their role as potential drivers of the global dissemination of vancomycin resistance.
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Affiliation(s)
- Veronika Oravcová
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, n° 228, 4050-313 Porto, Portugal.
| | - Teresa M Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera Colmenar km 9.1, 28034 Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, n° 228, 4050-313 Porto, Portugal.
| | - Maria V Francia
- Microbiology, Marqués de Valdecilla University Hospital e Instituto de Investigación Marqués de Valdecilla (IDIVAL), Av. Valdecilla, 25, 39008 Santander, Cantabria, Spain.
| | - Ivan Literák
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, n° 228, 4050-313 Porto, Portugal.
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Russo N, Caggia C, Pino A, Coque TM, Arioli S, Randazzo CL. Enterococcus spp. in Ragusano PDO and Pecorino Siciliano cheese types: A snapshot of their antibiotic resistance distribution. Food Chem Toxicol 2018; 120:277-286. [PMID: 30009890 DOI: 10.1016/j.fct.2018.07.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/21/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023]
Abstract
In the present study, 110 enterococci were isolated from two Sicilian cheese types, Ragusano PDO and Pecorino Siciliano. Isolates, firstly identified by MALDI-TOF/MS and a multiplex PCR assay, were tested for susceptibility to the most relevant clinical antibiotics. Clonal relationships among isolates were evaluated by pulsed-field-gel electrophoresis (PFGE) analysis and the presence of vanA and vanB genes, in vancomycin resistant enterococci (VRE), was investigated. Overall, E. faecalis, E. durans (35% for each species) and E. faecium (28%) were the major identified species. Different occurrence between cheese types was revealed. Most isolates from Ragusano PDO cheese were identified as E. durans (46%) and/or E. faecalis (43%), while E. faecium (605) was mainly detected in Pecorino Siciliano cheese. High incidence of resistance (97% of total strains) was detected for rifampicin, erythromycin and ampicillin. Moreover, 83 isolates (75%) exhibited multidrug-resistant phenotypes and the one VRE (vanB) isolate was identified as E. durans. PFGE analysis clustered isolates into 22 genotypes and the presence of the same PFGE types, for both E. durans and E. faecalis, in the two cheese types, suggest the link between enterococci and geographical area of production. Results of present study raise concerns about possible role of dairy enterococci as reservoirs of antibiotic resistance.
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Affiliation(s)
- Nunziatina Russo
- Dipartimento di Agricoltura Alimentazione e Ambiente (Di3A), University of Catania, Italy
| | - Cinzia Caggia
- Dipartimento di Agricoltura Alimentazione e Ambiente (Di3A), University of Catania, Italy.
| | - Alessandra Pino
- Dipartimento di Agricoltura Alimentazione e Ambiente (Di3A), University of Catania, Italy
| | - Teresa M Coque
- Servicio de Microbiología, Istituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER ESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Stefania Arioli
- Department of Food Environmental and Nutritional Science (DeFENS), University of Milan, Italy
| | - Cinzia L Randazzo
- Dipartimento di Agricoltura Alimentazione e Ambiente (Di3A), University of Catania, Italy
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Novais C, Campos J, Freitas AR, Barros M, Silveira E, Coque TM, Antunes P, Peixe L. Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:1102-1112. [PMID: 29996407 DOI: 10.1016/j.scitotenv.2017.12.265] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/18/2017] [Accepted: 12/21/2017] [Indexed: 06/08/2023]
Abstract
The role of European fish farms in the spread of antimicrobial-resistance in the environment and food chain, as well as possible sources of their contamination by clinically relevant antimicrobial-resistance bacteria is scarcely known. This study aimed to assess the contribution of Portuguese rural trout farms on dispersion of Enterococcus with antimicrobial-resistance and putative virulence genes in the environment and food chain, as well as to identify farms contamination sources. We also assessed the presence of Enterococcus with low-levels of antimicrobial-resistance using epidemiological cut-offs (ECOFFs). Enterococcus spp. (n=391) from water/sediment recovered upstream, within and downstream trout tanks, feed, trout (2 aquacultures; no antibiotic use) and marketed trout (8 supermarkets) showed variable resistance to tetracycline, erythromycin, ciprofloxacin, chloramphenicol, quinupristin-dalfopristin, nitrofurantoin or aminoglycosides. Antimicrobial-resistance rates were similar among upstream, within and downstream trout tank samples (P>0.05), positioning water-supplying aquacultures as a source of multidrug-resistant (MDR) strains. Nevertheless, predominance of MDR E. faecium in feed, trout tanks and trout comparing to upstream samples, suggests feed as an additional aquaculture contamination source. The observation of E. faecium and E. faecalis susceptible to ampicillin and gentamicin by clinical breakpoints but with low-levels of resistance to those antimicrobials by ECOFFs breakpoints is of concern, as they might evolve throughout secondary genetic events to resistance levels with human clinical impact. Multiple MDR clones carrying copper tolerance (tcrB/cueO), putative virulence or other genes often associated with clinical strains (e.g. E. faecium with IS16/ptsD/sgrA) were observed, some in distinct samples (e.g. upstream and within trout tanks). They included major human and animal Enterococcus lineages, suggesting human and non-aquatic animal origins. The results highlight the need to define the maximum acceptance level of antimicrobial-resistance genes/bacteria to assess water quality and to monitor antimicrobial-resistance strains on feed, essential requirements to maintain a sustainable aquaculture production.
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Affiliation(s)
- Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal.
| | - Joana Campos
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal.
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal.
| | - Mariana Barros
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal.
| | - Eduarda Silveira
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal; Centro de Investigação Vasco da Gama (CIVG), Escola Universitária Vasco da Gama, Coimbra, Portugal.
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal and Instituto Ramón and Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid. Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal; Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Porto, Portugal.
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Porto, Portugal.
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Freitas AR, Novais C, Duarte B, Pereira AP, Coque TM, Peixe L. High rates of colonisation by ampicillin-resistant enterococci in residents of long-term care facilities in Porto, Portugal. Int J Antimicrob Agents 2018; 51:503-507. [DOI: 10.1016/j.ijantimicag.2017.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 11/15/2022]
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