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Farias BO, Montenegro KS, Nascimento APA, Magaldi M, Gonçalves-Brito AS, Flores C, Moreira TC, Neves FPG, Bianco K, Clementino MM. First Report of a Wastewater Treatment-Adapted Enterococcus faecalis ST21 Harboring vanA Gene in Brazil. Curr Microbiol 2023; 80:313. [PMID: 37542533 DOI: 10.1007/s00284-023-03418-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/07/2023]
Abstract
Enterococcus faecalis has emerged as an important opportunistic pathogen due to its increasing resistance to antimicrobials, mainly to vancomycin, which leads substantial cases of therapeutic failures. Wastewater treatment plants (WWTP), in turn, are considered hotpots in the spread of antimicrobial resistance according to One Health perspective. In this study, we present the first report of a vancomycin-resistant E. faecalis strain recovered from treated effluent in Brazil. For this purpose, the whole-genome sequencing (WGS) was carried out aiming to elucidate its molecular mechanisms of antimicrobial resistance and its phylogenetic relationships amongst strains from other sources and countries. According to Multilocus Sequence Typing (MLST) analysis this strain belongs to ST21. The WGS pointed the presence of vanA operon, multiple antibiotic resistance and virulence genes, and a significant pathogenic potential for humans. The phylogenomic analysis of E. faecalis 6805 was performed with ST21 representatives from the PubMLST database, including the E. faecalis IE81 strain from clinical sample in Brazil, which had its genome sequenced in this study. Our results demonstrated a strain showing resistance to vancomycin in treated effluent. To the best of our knowledge, this is an unprecedented report of vanA-carrying E. faecalis ST21. Furthermore, it is the first description of a vanA-harboring strain of this species from environmental sample in Brazil. Our data highlight the role of WWTP in the spread of AMR, since these environments are favorable for the selection of multidrug-resistant pathogens and the treated effluents, carrying antibiotic resistance genes, are directed to receiving water bodies.
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Affiliation(s)
- Beatriz O Farias
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ, 4365, Brazil
| | - Kaylanne S Montenegro
- Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Ana Paula A Nascimento
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Mariana Magaldi
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Andressa S Gonçalves-Brito
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ, 4365, Brazil
| | - Claudia Flores
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Thais C Moreira
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Felipe P G Neves
- Departamento de Microbiologia E Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Alameda Barros Terra, S/N. São Domingos, Niterói, RJ, 24020-150, Brazil
| | - Kayo Bianco
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil.
- Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ, 4365, Brazil.
- COVID-19 Monitoring Network in Wastewater, São Paulo, Brazil.
| | - Maysa M Clementino
- Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ, 4365, Brazil
- COVID-19 Monitoring Network in Wastewater, São Paulo, Brazil
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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Shobo CO, Amoako DG, Allam M, Ismail A, Essack SY, Bester LA. A Genomic Snapshot of Antibiotic-Resistant Enterococcus faecalis within Public Hospital Environments in South Africa. Glob Health Epidemiol Genom 2023; 2023:6639983. [PMID: 37342729 PMCID: PMC10279497 DOI: 10.1155/2023/6639983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.
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Affiliation(s)
- Christiana O. Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- School of Laboratory Medicine and Medical Science, Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, UAE
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A. Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
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Loyola-Cruz MÁ, Gonzalez-Avila LU, Martínez-Trejo A, Saldaña-Padilla A, Hernández-Cortez C, Bello-López JM, Castro-Escarpulli G. ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic. Pathogens 2023; 12:pathogens12050743. [PMID: 37242413 DOI: 10.3390/pathogens12050743] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.
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Affiliation(s)
- Miguel Ángel Loyola-Cruz
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Luis Uriel Gonzalez-Avila
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Arturo Martínez-Trejo
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
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Ribeiro J, Silva V, Monteiro A, Vieira-Pinto M, Igrejas G, Reis FS, Barros L, Poeta P. Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli. Animals (Basel) 2023; 13:1362. [PMID: 37106925 PMCID: PMC10135345 DOI: 10.3390/ani13081362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.
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Affiliation(s)
- Jessica Ribeiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Madalena Vieira-Pinto
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Veterinary Science, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filipa S. Reis
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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Kesim B, Ülger ST, Aslan G, Cudal H, Üstün Y, Küçük MÖ. Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections. Clin Oral Investig 2023; 27:995-1004. [PMID: 36723715 DOI: 10.1007/s00784-023-04882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 01/24/2023] [Indexed: 02/02/2023]
Abstract
OBJECTIVES To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm. MATERIALS AND METHODS Root canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0. RESULTS Within the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group. CONCLUSIONS A few taxa were differentially abundant within either the PEI or SEI group. CLINICAL RELEVANCE Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections.
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Affiliation(s)
- Bertan Kesim
- Department of Endodontics, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey. .,Kuzey Çevreyolu Erkilet Dere Mah, Nuh Naci Yazgan Üniversitesi Yerleşkesi, Kocasinan, Kayseri, Turkey.
| | - Seda Tezcan Ülger
- Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Gönül Aslan
- Department of Medical Microbiology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Hamza Cudal
- Department of Endodontics, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey
| | - Yakup Üstün
- Department of Endodontics, Faculty of Dentistry, Erciyes University, Kayseri, Turkey
| | - Mustafa Öner Küçük
- Department of Microbiology, Faculty of Dentistry, Nuh Naci Yazgan University, Kayseri, Turkey
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Yoshino Y. Enterococcus casseliflavus Infection: A Review of Clinical Features and Treatment. Infect Drug Resist 2023; 16:363-368. [PMID: 36714353 PMCID: PMC9879772 DOI: 10.2147/idr.s398739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Some Enterococcus species, including Enterococcus faecalis and E. faecium, are increasingly becoming a common cause of nosocomial infections, accounting for the majority of human enterococcal infections, while other species, such as E. casseliflavus, have also been shown to be pathogenic to humans due to the increase in immunocompromised patients. These infections vary widely in their mode of transmission, symptoms, and other characteristics. Treatment is difficult in some cases because enterococci are resistant to numerous antimicrobial agents. Enterococcus faecalis and E. faecium are the best-known opportunistic pathogens, but others, including E. casseliflavus, occasionally cause opportunistic infections. This review summarizes the clinical features of E. casseliflavus infections and discusses effective therapeutic strategies. Bacteremia was the most common form of E. casseliflavus infections. Because E. casseliflavus carries the VanC gene, which confers resistance to vancomycin, less resistant drugs such as ampicillin were found more effective in treating the bacteremia. The second most common form of E. casseliflavus infection was trauma-induced endophthalmitis. This was commonly reported in active young to middle-aged patients. Vitreoretinal surgery and local or systemic administration of sensitive antimicrobial agents seem to be key to successful treatment. Other conditions such as infective endocarditis, meningitis, peritonitis, and pyothorax have also been reported as forms of E. casseliflavus infection. This review clarifies the clinical features of E. casseliflavus infection and provides important insights into its treatment.
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Affiliation(s)
- Yusuke Yoshino
- Teikyo University, School of Medicine, Department of Microbiology and Immunology, Tokyo, Japan,Correspondence: Yusuke Yoshino, Teikyo University, School of Medicine, Department of Microbiology and Immunology, 2-11-1, Kaga, Itabashi, Tokyo, 173-8605, Japan, Tel +81-3-3964-1211, Email
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Wardal E, Żabicka D, Hryniewicz W, Sadowy E. VanA-Enterococcus faecalis in Poland: hospital population clonal structure and vanA mobilome. Eur J Clin Microbiol Infect Dis 2022; 41:1245-1261. [PMID: 36057762 PMCID: PMC9489580 DOI: 10.1007/s10096-022-04479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/18/2022] [Indexed: 11/03/2022]
Abstract
The aim of our study was to characterize the epidemiological situation concerning nosocomial vancomycin-resistant Enterococcus faecalis of VanA-phenotype (VREfs-VanA) in Poland by investigating their clonal relationships and the vanA-associated mobilome. One-hundred twenty-five clinical isolates of VREfs-VanA collected between 2004 and 2016 were studied by phenotypic assays, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), PCR detection of plasmid-specific genes, and Tn1546 structure and localization mapping. Selected isolates were subjected to PFGE-S1, Southern hybridization, genomic sequencing and conjugation experiments. The majority of isolates (97.6%) belonged to clonal complexes CC2 and CC87 of E. faecalis. All isolates were resistant to vancomycin and teicoplanin, and resistance to ciprofloxacin and aminoglycosides (high level) was very prevalent in this group. VanA phenotype was associated with 16 types of Tn1546, carrying insertion sequences IS1216, ISEfa4, IS1251 and IS1542, located on repUS1pVEF1, rep1pIP501, rep2pRE25, rep9pAD1/pTEF2/pCF10 and rep6pS86 replicons. The most common Tn1546 B- and BB-type transposons, harbouring one or two copies of IS1216, were inserted between rep18ap200B and repUS1pVEF1 genes and located on ~ 20 kb and 150-200 kb plasmids. VREfs-VanA in Poland represent a polyclonal group, indicating a number of acquisitions of the vanA determinant. The repUS1pVEF1-vanA plasmids, unique for Poland, were the main factor beyond the acquisition of vancomycin resistance by E. faecalis, circulating in Polish hospitals.
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Affiliation(s)
- Ewa Wardal
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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Correa FEL, Zanella RC, Cassiolato AP, Paiva AD, Okura MH, Conceição N, Oliveira AG. Penicillin-resistant, ampicillin-susceptible Enterococcus faecalis isolates are uncommon in non-clinical sources. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:230-238. [PMID: 35060343 DOI: 10.1111/1758-2229.13043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
This study aimed to investigate whether penicillin-resistant, ampicillin-susceptible E. faecalis (PRASEF) isolates are disseminated in non-clinical sources, and to compare the molecular characteristics and antimicrobial resistance (AMR) profile of clinical and non-clinical E. faecalis isolates. Non-clinical samples (n = 280) were collected and 101 E. faecalis isolates were recovered from food (n = 18), faeces of healthy animals (n = 24), water (n = 28) and sewage (n = 31). PRASEF (n = 68) and penicillin-susceptible, ampicillin-susceptible E. faecalis (n = 77) isolates of clinical origin were also evaluated. A significant variety of AMR profiles was observed among non-clinical isolates according to the source. No food isolate exhibited a multidrug resistance (MDR) phenotype different from those of isolates from animal faeces (50.0%) and sewage (38.7%). Overall, the MDR phenotype was more frequent among clinical (56.6%) than non-clinical isolates (22.8%) (p < 0.01). Non-clinical PRASEF isolates (n = 3) were only recovered from hospital sewage. Note that representative clinical and non-clinical PRASEF isolates were grouped in pulsotype A, and belonged to CC9 (clonal complex). In conclusion, E. faecalis isolates exhibiting the unusual penicillin-resistant but ampicillin-susceptible phenotype appeared to be restricted to the hospital environment. Our findings highlight the ability of PRASEF isolates to survive in sewage, which could enable these hospital-adapted lineages to spread to new ecological niches.
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Affiliation(s)
- Fábio Ederson Lopes Correa
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | | | | | - Aline Dias Paiva
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Monica Hitomi Okura
- Instituto de Ciências Tecnológicas e Exatas, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Natália Conceição
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia de Rondônia, Colorado do Oeste, Rondônia, Brazil
| | - Adriana Gonçalves Oliveira
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
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10
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Baldinelli F, Broglia A, Kohnle L, Alvarez J. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus faecalis in poultry. EFSA J 2022; 20:e07127. [PMID: 35228848 PMCID: PMC8859914 DOI: 10.2903/j.efsa.2022.7127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecalis (E. faecalis) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. faecalis can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 1-10% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-66% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. faecalis according to Article 8 criteria are mostly birds of the orders Galliformes and Anseriformes, but also mammals and reptiles can serve as reservoirs.
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11
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Lazzaro LM, Cassisi M, Stefani S, Campanile F. Impact of PBP4 Alterations on β-Lactam Resistance and Ceftobiprole Non-Susceptibility Among Enterococcus faecalis Clinical Isolates. Front Cell Infect Microbiol 2022; 11:816657. [PMID: 35127564 PMCID: PMC8811369 DOI: 10.3389/fcimb.2021.816657] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Penicillin-resistance among Enterococcus faecalis clinical isolates has been recently associated with overexpression or aminoacidic substitutions in low-affinity PBP4. Ceftobiprole (BPR), a new-generation cephalosporin, is a therapeutic option against E. faecalis. Here, we present evidence that pbp4 gene sequence alterations may influence the expression level of the gene and ceftobiprole binding to PBP4 in E. faecalis clinical isolates showing remarkable MDR-phenotypes, and how this could interfere with BPR in vitro antibacterial and bactericidal activity. Seven E. faecalis strains from bloodstream infections were analyzed for their antibiotic and β-lactam resistance. BPR bactericidal activity was assessed by time-kill analysis; pbp4 genes were sequenced and pbp4 relative expression levels of transcription were performed by RT-qPCR. Five penicillin-resistant ampicillin-susceptible (PRAS) isolates were detected, 4 of which were also BPR non-susceptible (BPR-NS). In the time-kill experiments, BPR exposure resulted in a potent bactericidal activity (3-5 log10 reduction) at the different concentrations tested. pbp4 gene sequence analysis revealed some mutations that may account for the changes in PBP4 affinity and MIC increase in the 4 BPR-NS strains (MICs 4-16 mg/L): the deletion of an adenine (delA) in the promoter region in all PRAS/BPR-NS strains; 12 different amino acid substitutions, 7 of which were next to the PBP catalytic-sites. The most significant were: T418A, located 6 amino acids (aa) upstream of the catalytic-serine included in the 424STFK427motif I; L475Q, 7 aa upstream of the 482SDN484motif II; V606A and the novel Y605H, 13/14 aa upstream of the 619KTGT622motif III. Taken together, our data showed that elevated BPR MICs were attributable to increased transcription of pbp4 - associated with a single upstream adenine deletion and PBP4 alterations in the catalytic-site motifs - which might interfere with the formation of the BPR/PBP4 complex. pbp4 molecular alterations may account for the changes in PBP4 affinity and MIC increase, without affecting BPR cidal activity. Indeed, our in vitro dynamic analysis by time-kill assays showed that BPR exerted a bactericidal activity against E. faecalis clinical isolates, despite their MDR phenotypes.
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Affiliation(s)
| | | | | | - Floriana Campanile
- Section of Microbiology, Department of Biomedical and Biotechnological Sciences (BIOMETEC), Microbiologia Medica Molecolare e Antibiotico Resistenza (MMARLab), University of Catania, Catania, Italy
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12
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Conwell M, Dooley J, Naughton PJ. Enterococcal biofilm - a nidus for antibiotic resistance transfer? J Appl Microbiol 2022; 132:3444-3460. [PMID: 34990042 PMCID: PMC9306868 DOI: 10.1111/jam.15441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/03/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022]
Abstract
Enterococci, important agents of hospital acquired infection, are listed on the WHO list of multi-drug resistant pathogens commonly encountered in hospital acquired infections are now of increasing importance, due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilm such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilm and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.
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Affiliation(s)
- M Conwell
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - Jsg Dooley
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - P J Naughton
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
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13
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Clinical characteristics and outcome of patients with enterococcal liver abscess. Sci Rep 2021; 11:22265. [PMID: 34782684 PMCID: PMC8593075 DOI: 10.1038/s41598-021-01620-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/25/2021] [Indexed: 11/08/2022] Open
Abstract
Epidemiology of bacteria isolated from pyogenic liver abscesses change, and an increase in enterococci has been reported in European hospitals. The aim of this study was to investigate the clinical characteristics and outcome of enterococcal PLA. We performed a retrospective analysis of patients with microbiologically confirmed PLA at three German university centers. Indicators of enterococcal PLA were determined using binary logistic regression, and survival analysis was performed using Kaplan-Meier statistics and Cox regression analysis. Enterococci were isolated in 51/133 (38%) patients with PLA. Patients with enterococcal PLA had smaller abscess diameter (4.8 vs. 6.7 cm, p = 0.03) than patients with non-enterococcal PLA, but had more frequent polymicrobial culture results. In univariate logistic regression analysis, alcohol abuse (OR 3.94, 95% CI 1.24-12.49, p = 0.02), hepatobiliary malignancies (OR 3.90, 95% CI 1.86-8.18, p < 0.001) and cirrhosis (OR 6.36, 95% CI 1.27-31.96, p = 0.02) were associated with enterococcal PLA. Patients with enterococcal PLA had a higher mortality than patients with non-enterococcal PLA (hazard ratio 2.92; 95% confidence interval 1.09-7.80; p = 0.03), which remained elevated even after excluding patients with hepatobiliary malignancies, cirrhosis, and transplant recipients in a sensitivity analysis. The increased mortality was associated with non-fecal enterococci but not in patients with Enterococcus faecalis. In this retrospective, multicenter study, enterococcal PLA was common and indicated an increased risk of mortality, underscoring the need for close clinical monitoring and appropriate treatment protocols in these patients.
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14
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Cattoir V. The multifaceted lifestyle of enterococci: genetic diversity, ecology and risks for public health. Curr Opin Microbiol 2021; 65:73-80. [PMID: 34768106 DOI: 10.1016/j.mib.2021.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022]
Abstract
Enterococci are long-standing members of the gastrointestinal tract of humans and many animals and they are also ubiquitously distributed in natural environments. Classically as harmless bacteria, two main species (namely Enterococcus faecalis and Enterococcus faecium) have become a leading cause of human infections, especially in hospital settings, with the worldwide spread of multidrug-resistant isolates, especially vancomycin-resistant enterococci. In this review, it will be summarized what is known about genetic diversity and ecology of enterococci with a focus on E. faecalis and E. faecium from human and non-human habitats and related risks for public health.
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Affiliation(s)
- Vincent Cattoir
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, Rennes, France; CNR de la Résistance aux Antibiotiques (Laboratoire Associé 'Entérocoques'), Rennes, France; Unité Inserm U1230, Université de Rennes 1, Rennes, France.
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15
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Stępień-Pyśniak D, Hauschild T, Dec M, Marek A, Brzeski M, Kosikowska U. Antimicrobial resistance and genetic diversity of Enterococcus faecalis from yolk sac infections in broiler chicks. Poult Sci 2021; 100:101491. [PMID: 34695638 PMCID: PMC8554262 DOI: 10.1016/j.psj.2021.101491] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/03/2022] Open
Abstract
Despite restrictions on the use of antibiotics in poultry, the percentage of multidrug resistant bacteria, isolated from both adult birds and chicks, remains high. These bacteria can spread between countries via hatching eggs or chicks. Antibiotic resistant bacteria can also pose a threat to hatchery and farm workers or to consumers of poultry. The aim of the study was to perform a phenotypic and genotypic analysis of the drug resistance of E. faecalis isolates from yolk sac infections in broiler chicks from Poland and the Netherlands and to determine their genetic diversity. The tests revealed resistance to antibiotics from category D, that is, tetracycline (69.7%); category C – lincomycin (98.7%), erythromycin (51.3%), aminoglycosides (high-level streptomycin and kanamycin resistance – 10.5% and 3.95%, respectively), and chloramphenicol (7.9%); and category B – ciprofloxacin (25% with resistance or intermediate resistance). No resistance to penicillin, ampicillin, high-level gentamicin, tigecycline, or linezolid was noted. Various combinations of the erm(B), tet(M), tet(L), tet(O), ant(6)-Ia, aph(3′)-IIIa, ant(4′)-Ia, cat, and msr(A/B) genes were detected in all isolates (irrespective of the drug-resistance phenotype). Among isolates that carried the tet(M) and/or the tet(L) gene, 28% also had the Int-Tn gene, in contrast with isolates possessing tet(O). There were 28 sequence types and 43 PFGE restriction patterns. About 60% of isolates were of sequences types ST59, ST16, ST116, ST282, ST36, and ST82. Nine new sequence types were shown (ST836-ST844). In conclusion, broiler chicks can be a source of drug-resistant sequence types of E. faecalis that are potentially hazardous for people and animals. Restrictive programs for antibiotic use in broiler breeding flocks should be developed to decrease drug resistance in day-old chicks and reduce economic losses during rearing.
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Affiliation(s)
- Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, 20-612 Poland.
| | - Tomasz Hauschild
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, Białystok, 15-245 Poland
| | - Marta Dec
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, 20-612 Poland
| | - Agnieszka Marek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, 20-612 Poland
| | - Michał Brzeski
- Veterinary Cabinet - Brzeski and partners, Giżycko, 11-500 Poland
| | - Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Medical University in Lublin, Lublin, 20-093 Poland
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16
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Sadowy E. Mobile genetic elements beyond the VanB-resistance dissemination among hospital-associated enterococci and other Gram-positive bacteria. Plasmid 2021; 114:102558. [PMID: 33472048 DOI: 10.1016/j.plasmid.2021.102558] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022]
Abstract
An increasing resistance to vancomycin among clinically relevant enterococci, such as Enterococcus faecalis and Enterococcus faecium is a cause of a great concern, as it seriously limits treatment options. The vanB operon is one of most common determinants of this type of resistance. Genes constituting the operon are located in conjugative transposons, such as Tn1549-type transposons or, more rarely, in ICEEfaV583-type structures. Such elements show differences in structure and size, and reside in various sites of bacterial chromosome or, in the case of Tn1549-type transposons, are also occasionally associated with plasmids of divergent replicon types. While conjugative transposition contributes to the acquisition of Tn1549-type transposons from anaerobic gut commensals by enterococci, chromosomal recombination and conjugal transfer of plasmids appear to represent main mechanisms responsible for horizontal dissemination of vanB determinants among hospital E. faecalis and E. faecium. This review focuses on diversity of genetic elements harbouring vanB determinants in hospital-associated strains of E. faecium and E. faecalis, the mechanisms beyond vanB spread in populations of these bacteria, and provides an overview of the vanB-MGE distribution among other enterococci and Gram-positive bacteria as potential reservoirs of vanB genes.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland.
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17
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Fioriti S, Simoni S, Caucci S, Morroni G, Ponzio E, Coccitto SN, Brescini L, Cirioni O, Menzo S, Biavasco F, Giovanetti E, Brenciani A, Vignaroli C. Trend of clinical vancomycin-resistant enterococci isolated in a regional Italian hospital from 2001 to 2018. Braz J Microbiol 2020; 51:1607-1613. [PMID: 32783169 PMCID: PMC7688800 DOI: 10.1007/s42770-020-00360-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022] Open
Abstract
A retrospective study of the epidemiology of vancomycin-resistant enterococci (VRE) in a regional hospital of central Italy in 2001-2018 demonstrated an increased VRE prevalence since 2016. A total of 113 VRE isolates, 89 E. faecium (VREfm) and 24 E. faecalis (VREfs), were collected in the study period. All strains showed high-level resistance to vancomycin; 107 also showed teicoplanin resistance. Altogether, 84 VREfm and 20 VREfs carried vanA, whereas 5 VREfm and 1 VREfs carried vanB. MLST analysis documented that 89 VREfm isolates mainly belonged to ST78, ST80, and ST117. Most strains were isolated from 2001 to 2007, ST78 being the predominant clone. VREfm re-emerged in 2016 with a prevalence of the ST80 lineage. Most VREfs were isolated from 2001 to 2006; although they belonged to 7 different STs, there was a prevalence of ST88 and ST6. Notably, ST88 was sporadically recovered throughout the study period. The increasing rate of VREfm isolation from 2016 to 2018 may be related to the influx of new successful clones and to the renewed and widespread use of vancomycin. Improved infection control measures in hospital wards should be adopted to limit the spread of new epidemic VRE strains.
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Affiliation(s)
- Simona Fioriti
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Elisa Ponzio
- Section of Hygiene of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Lucia Brescini
- Infectious Diseases Clinic of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Oscar Cirioni
- Infectious Diseases Clinic of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy.
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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18
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Shiadeh SMJ, Azimi L, Azimi T, Pourmohammad A, Goudarzi M, Chaboki BG, Hashemi A. Upregulation of efrAB efflux pump among Enterococcus faecalis ST480, ST847 in Iran. Acta Microbiol Immunol Hung 2020; 67:187-192. [PMID: 32986605 DOI: 10.1556/030.2020.01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022]
Abstract
Antibiotic resistance and especially multiresistance in Enterococci, is a serious public health issue especially in infections of immunocompromised patients. EfrAB is a heterodimeric multidrug ATP-binding cassette (ABC) transporter that causes endogenous resistance to antimicrobials including fluoroquinolones in Enterococcus spp. The aim of this study was to seek the gene expression rate and role of efrAB efflux pump in ciprofloxacin resistant Enterococcus faecalis and Multilocus Sequence Typing (MLST) of multiresistant isolates. Phenotypic and genotyping identification of 80 E. faecalis isolates were performed. Minimum inhibitory concentrations (MICs) to ciprofloxacin (CIP) were measured with and without carbonylcyanide 3-chlorophenylhydrazone (CCCP) by broth microdilution. After DNA extraction and sequencing for detection of efrA and efrB genes, the efrAB efflux positive isolates that were resistant to ciprofloxacin and showed decrease of ciprofloxacin MIC range were identified. Isolates that exhibited decrease in ciprofloxacin MIC range from two to ten folds were assessed for biofilm formation and finally, the expression levels of efrB, efrA genes were measured by quantitative Real-Time PCR (qRT-PCR). High rates of resistance to tetracycline and minocycline and low rates of resistance to the most antibiotics used in this study were detected. The results in this study indicated that the incidence of Multiple drug resistance (MDR) was 23.7% and all isolates that were resistant to ciprofloxacin revealed several degrees of overexpression in efrA and efrB genes. Our study found two ST480 and one ST847 in E. faecalis isolates. In conclusion, despite of low frequency of resistance to the most antibiotics and MDRs in our region, we found one ST480 isolate with resistance to eight antibiotics that also exists in other parts of the world.
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Affiliation(s)
| | - Leila Azimi
- 2Pediatric Infections Research Center, Mofid Children's Hospital, Shahid Beheshti, University of Medical Sciences, Tehran, Iran
| | - Taher Azimi
- 3Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Pourmohammad
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahare Gholami Chaboki
- 4Department of Biostatistics, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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19
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Rao C, Dhawan B, Vishnubhatla S, Kapil A, Das B, Sood S. Emergence of high-risk multidrug-resistant Enterococcus faecalis CC2 (ST181) and CC87 (ST28) causing healthcare-associated infections in India. INFECTION GENETICS AND EVOLUTION 2020; 85:104519. [PMID: 32877660 DOI: 10.1016/j.meegid.2020.104519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
High-risk hospital-associated multidrug-resistant (MDR) Enterococcus faecalis clonal complexes (CCs) such as CC2 and CC87 are enriched with virulence determinants that help to accumulate, colonize, and cause serious nosocomial infections. The aim of this study was to establish the epidemiology and clonal composition of 134 clinical E. faecalis isolates and to link molecular typing data with antimicrobial resistance and virulence determinants. All isolates were identified by conventional methods and confirmed by polymerase chain reaction (PCR) (16srRNA gene and ddl genes of E. faecalis/ E. faecium) in 5-years. Disc diffusion test was performed on all strains. We screened all E. faecalis for aac(6')-aph(2″), vanA, and vanB resistance genes, and aggregation substance-asa1, cytolysin-cylA, collagen-binding protein-ace, enterococcal surface protein-esp, gelatinase-gelE, and hyaluronidase-hyl virulence genes by PCR. Representative isolates of E. faecalis were characterized by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Out of 539 patients with enterococcal infections, 134 (24.9%) had E. faecalis infections, 366 (67.9%) had E. faecium infections, and 39 (7.2%) had infections due to other enterococcal species. Of the 134 isolates, 79.1% and 61.9% isolates were high-level gentamicin resistant (HLGR) and MDR. In multivariate analysis, independent predictor for infection due to MDR E. faecalis strains was a surgical intervention (OR 2.41, 95% CI 1.17-4.96, P = 0·017). Overall, the observed rate of in-hospital mortality was 11.9%. The gelE, asa1, ace, cylA, esp and hyl genes were detected in 87.3%, 78.4%, 54.5%, 53.7%, 36.6% and 3.0%, respectively in E. faecalis isolates. The asaI, cylA, and gelE genes were significantly correlated with MDR E. faecalis. The PFGE analysis showed 28 clones with four major clones. MLST analysis revealed two sequence types-ST28 (CC87) and ST181 (CC2). This is the first Indian report on the emergence of the high-risk hospital-associated worldwide-disseminated ST28 (CC87) and ST181 (CC2), which have enriched with multiple virulence determinants and resistance to antibiotics, paticularly ampicillin. This report indicates serious health concern and calls for on-going surveillance, close monitoring, and improved infection control procedures to stop further spread of these isolates.
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Affiliation(s)
- Chandrabhan Rao
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Sreenivas Vishnubhatla
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bimal Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
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20
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Gawryszewska I, Żabicka D, Hryniewicz W, Sadowy E. Penicillin-Resistant, Ampicillin-Susceptible Enterococcus faecalis in Polish Hospitals. Microb Drug Resist 2020; 27:291-300. [PMID: 32640911 DOI: 10.1089/mdr.2019.0504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The objective of this study was to characterize Polish penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF), increasingly reported to the National Reference Centre for Susceptibility Testing, Poland, to elucidate the path of emergence of such strains. A total of 136 isolates were examined by antimicrobial susceptibility testing and for the β-lactamase production (cefinase test). The clonality of isolates was established by multilocus sequence typing (MLST) and the penicillin-binding protein pbp4 gene was sequenced to search for putative mutation(s). The presence of pheromone-responsive plasmids was investigated by clumping test and PCR detection of plasmid-specific genes. All Polish PRASEF were multidrug resistant and β-lactamase-negative. MLST assigned isolates mostly to high-risk enterococcal clonal complexes (HIRECCs) 6 (57.4%) and 87 (30.1%), in addition to to CC88 (12.5%). The sequencing of pbp4 revealed mutations upstream of a putative promoter region and amino acid alterations in PBP4, affecting 24 positions and resulting in 30 variants. While production of aggregation substance was observed for 17.6% of isolates, genes of pheromone plasmids were much more commonly detected. However, no conjugal transfer of penicillin resistance was observed. Penicillin resistance in E. faecalis emerges mostly in HiRECCs due to PBP4 overproduction and/or mutations. The acquisition of penicillin resistance by HiRECCs may represent the next step in the evolution of E. faecalis as human nosocomial pathogen.
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Affiliation(s)
- Iwona Gawryszewska
- Department of Molecular Microbiology and National Medicines Institute, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology and National Medicines Institute, Warsaw, Poland
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Prevalence of an Intestinal ST40 Enterococcus faecalis over Other E. faecalis Strains in the Gut Environment of Mice Fed Different High Fat Diets. Int J Mol Sci 2020; 21:ijms21124330. [PMID: 32570702 PMCID: PMC7352901 DOI: 10.3390/ijms21124330] [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: 05/27/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
E. faecalis is a commensal bacterium with specific strains involved in opportunistic and nosocomial infections. Therefore, it is important to know how the strains of this species are selected in the gut. In this study, fifteen E. faecalis strains, isolated over twelve weeks from the faeces of mice fed standard chow or one of three high fat diets enriched with extra virgin olive oil, refined olive oil or butter were subjected to a genetic “Multilocus Sequence Typing” study that revealed the presence of mainly two genotypes, ST9 and ST40, the latter one prevailing at the end of the research. A V3–V5 sequence comparison of the predominant ST40 strain (12B3-5) in a metagenomic study showed that this sequence was the only E. faecalis present in the mouse cohort after twelve weeks. The strain was subjected to a comparative proteomic study with a ST9 strain by 2D electrophoresis and mass spectrometry. After comparing the results with a E. faecalis database, unshared entries were compared and 12B3-5 showed higher antimicrobial production as well as greater protection from environmental factors such as xenobiotics, oxidative stress and metabolite accumulation, which could be the reason for its ability to outcompete other possible rivals in an intestinal niche.
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22
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Saffari F, Darehkordi H, Ahmadrajabi R. Clonal dissemination of high-level gentamicin-resistant isolates of Enterococcus faecalis within a university hospital in southeastern Iran. Wien Med Wochenschr 2020; 171:18-23. [PMID: 31993873 DOI: 10.1007/s10354-019-00716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 10/31/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Combination of a cell wall-active antibiotic with an aminoglycoside confers a synergistic effect in the treatment of some severe enterococcal infections. Unfortunately, with the emergence of enterococci with high-level resistance to aminoglycosides, particularly to gentamicin, the efficacy of the synergistic combinations has decreased. In this study, high-level gentamicin-resistant (HLGR) isolates of enterococci and the diversity of the genes encoding aminoglycoside-modifying enzymes (AMEs) as well as putative clonal dissemination of HLGR isolates were investigated in a university hospital in southeastern Iran. METHODS The minimum inhibitory concentration of gentamicin was determined and HLGR isolates were investigated for AME genes. Genetic similarity between isolates was analyzed using repetitive extragenic palindromic (rep)-Polymerase Chain Reaction (PCR) assay. RESULTS Of 150 Enterococcus isolates, 62 isolates including Enterococcus faecalis (n = 46) and E. faecium (n = 16) were identified as HLGR. The most prevalent AME genes in both species were as follows: aph(3')-IIIa (n = 44), aac(6')-Ie-aph(2')-Ia (n = 36), and ant(4')-Ia (n = 15). The rep-PCR analysis showed clonality among E. faecalis isolates, so that 27 isolates were grouped in seven clusters representing similarity greater than 95%. CONCLUSIONS No link between AME determinants and clusters was found. Clonal spread of HLGR isolates of E. faecalis was found within our hospital. More rigorous recommendations are required to avoid dissemination of such resistant microorganisms in the hospital setting.
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Affiliation(s)
- Fereshteh Saffari
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, end of 22-Bahman Street, Kerman, Iran
| | - Hosein Darehkordi
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, end of 22-Bahman Street, Kerman, Iran
| | - Roya Ahmadrajabi
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, end of 22-Bahman Street, Kerman, Iran.
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23
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Bhardwaj S, Mehta M, Sood S. Enterococci in the oral cavity of periodontitis patients from different urban socioeconomic groups. Dent Res J (Isfahan) 2020. [DOI: 10.4103/1735-3327.280894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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The lytic bacteriophage vB_EfaH_EF1TV, a new member of the Herelleviridae family, disrupts biofilm produced by Enterococcus faecalis clinical strains. J Glob Antimicrob Resist 2019; 21:68-75. [PMID: 31678321 DOI: 10.1016/j.jgar.2019.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES The aim of this study is to characterize a new bacteriophage able to infect Enterococcus faecalis, and to evaluate its ability to disrupt biofilm. METHODS The vB_EfaH_EF1TV (EF1TV) host-range was determined by spot test and efficiency of plating using a collection of 15E. faecalis clinical strains. The phage genome was sequenced with a next generation sequencing approach. Anti-biofilm activity was tested by crystal violet method and confocal laser scanning microscopy. Phage-resistant mutants were selected and sequenced to investigate receptors exploited by phage for infection. RESULTS EF1TV is a newly discoveredE. faecalis phage which belongs to the Herelleviridae family. EF1TV, whose genome is 98% identical to φEF24C, is characterized by a linear dsDNA genome of 143,507 bp with direct terminal repeats of 1,911 bp. The phage is able to infect E. faecalis and shows also the ability to degrade biofilm produced by strains of this species. The results were confirmed by confocal laser scanning microscopy analyzing the biofilm reduction in the same optical field before and after phage infection. CONCLUSIONS The EF1TV phage shows promising features such as an obligatory lytic nature, an anti-biofilm activity and the absence of integration-related proteins, antibiotic resistance determinants and virulence factors, and therefore could be a promising tool for therapeutic applications.
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Fitness Restoration of a Genetically Tractable Enterococcus faecalis V583 Derivative To Study Decoration-Related Phenotypes of the Enterococcal Polysaccharide Antigen. mSphere 2019; 4:4/4/e00310-19. [PMID: 31292230 PMCID: PMC6620374 DOI: 10.1128/msphere.00310-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
E. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle. Commensal and generally harmless in healthy individuals, Enterococcus faecalis causes opportunistic infections in immunocompromised patients. Plasmid-cured E. faecalis strain VE14089, derived from sequenced reference strain V583, is widely used for functional studies due to its improved genetic amenability. Although strain VE14089 has no major DNA rearrangements, with the exception of an ∼20-kb integrated region of pTEF1 plasmid, the strain presented significant growth differences from the V583 reference strain of our collection (renamed VE14002). In the present study, genome sequencing of strain VE14089 identified additional point mutations. Excision of the integrated pTEF1 plasmid region and sequential restoration of wild-type alleles showing nonsilent mutations were performed to obtain the VE18379 reference-derivative strain. Recovery of the growth ability of the restored VE18379 strain at a level similar to that seen with the reference strain points to GreA and Spx as bacterial fitness determinants. Virulence potential in Galleria mellonella and intestinal colonization in mouse demonstrated host adaptation of the VE18379 strain equivalent to VE14002 host adaptation. We further demonstrated that deletion of the 16.8-kb variable region of the epa locus recapitulates the key role of Epa decoration in host adaptation, providing a genetic system to study the role of specific epa-variable regions in host adaptation independently of other genetic variations. IMPORTANCEE. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle.
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26
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León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019; 21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.
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Affiliation(s)
- Ricardo León-Sampedro
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain
| | - Mercedes Rodriguez-Baños
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - María José Pozuelo
- Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain
| | - Carlos Francés-Cuesta
- Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Fernando González Candelas
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
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27
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Lloréns-Villar Y, Tusell F, Canut A, Barrasa H, Corral E, Martín A, Rodríguez-Gascón A. Antibiotic susceptibility trend before and after long-term use of selective digestive decontamination: a 16 year ecological study. J Antimicrob Chemother 2019; 74:2289-2294. [DOI: 10.1093/jac/dkz186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
The aim of this study was to compare antimicrobial susceptibility rates in a Spanish ICU before and after the introduction of selective digestive decontamination (SDD) and also to compare these with susceptibility data from other Spanish ICUs without SDD.
Methods
We performed a retrospective study in the ICU of the University Hospital of Alava, where SDD was implemented in 2002. The SDD protocol consisted of a 2% mixture of gentamicin, colistin and amphotericin B applied on the buccal mucosa and a suspension of the same drugs in the gastrointestinal tract; additionally, for the first 3 days, systemic ceftriaxone was administered. From 1998 to 2013 we analysed the susceptibility rates for 48 antimicrobial/organism combinations. Interrupted time series using a linear dynamic model with SDD as an intervention was used. Data from other ICUs were obtained from the ENVIN-HELICS national registry.
Results
Only amoxicillin/clavulanic acid against Escherichia coli and Proteus mirabilis, and a high concentration of gentamicin against Enterococcus faecalis, resulted in a significant decrease in the susceptibility rate after the implementation of SDD, with a drop of 20%, 27% and 32%, respectively. Compared with other Spanish ICUs without SDD, the susceptibility rate was higher in the ICU of our hospital in most cases. When it was lower, differences were <10%, except for a high concentration of streptomycin against Enterococcus faecium, for which the difference was 19%.
Conclusions
No relevant changes in the overall susceptibility rate after the implementation of SDD were detected. Susceptibility rates were not lower than those in the Spanish ICUs without SDD.
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Affiliation(s)
- Yanire Lloréns-Villar
- Servicio de Farmacia Hospitalaria, Hospital Universitario de Álava, Vitoria-Gasteiz, Spain
| | - Fernando Tusell
- Departamento de Economía Aplicada III, Facultad de Ciencias Económicas y Empresariales, Universidad del País Vasco UPV/EHU, Bilbao, Spain
| | - Andrés Canut
- Servicio de Microbiología, Hospital Universitario de Álava, Vitoria-Gasteiz, Spain
| | - Helena Barrasa
- Servicio de Medicina Intensiva, Hospital Universitario de Álava, Vitoria-Gasteiz, Spain
| | - Esther Corral
- Servicio de Medicina Intensiva, Hospital Universitario de Álava, Vitoria-Gasteiz, Spain
| | - Alejandro Martín
- Servicio de Medicina Intensiva, Hospital Universitario de Álava, Vitoria-Gasteiz, Spain
| | - Alicia Rodríguez-Gascón
- Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Centro de investigación Lascaray ikergunea, Universidad del País Vasco UPV/EHU, Vitoria, Spain
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Abstract
The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.
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Affiliation(s)
- Mónica García-Solache
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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29
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Comparison of genotypes, antimicrobial resistance and virulence profiles of oral and non oral Enterococcus faecalis from Brazil, Japan and the United Kingdom. J Dent 2019; 84:49-54. [PMID: 30862557 DOI: 10.1016/j.jdent.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES To determine whether phenotypic and genotypic differences amongst isolates ofEnterococcus faecalis relate to geographical and clinical origin. METHODS E. faecalis from primary endodontic infections in Brazilian patients (n = 20), oral infections in UK patients (n = 10), and non-oral infections in Japanese patients (n = 9) were studied. In addition, 20 environmental vancomycin resistant Enterococcus faecalis (VRE) isolates from a UK hospital were analysed. For all isolates, polymerase chain reaction (PCR) was used to detect genes associated with antibiotic resistance and virulence, whilst randomly amplified polymorphic DNA-PCR (RAPD-PCR) was used to produce molecular profiles. RESULTS Gelatinase gene (gelE) was prevalent amongst isolates (77-100%) and for oral isolates, genes of aggregation substances (agg), immune evasion protein (esp), cytolysin (cylB), tetracycline resistance (tetM; tetL) and erythromycin resistance (ermB) were detected to varying extent. Japanese non-oral isolates had a similar genetic profile to oral isolates, but with higher prevalence of ermB and cylB. All VRE isolates were positive for gelE, esp, agg, vanA, ermB and tetM, 95% were positive for cylB and 17% positive for tetL. All isolates were negative for ermA, asa373 vanB, vanC1 and vanC2/3. RAPD-PCR revealed clustering of VRE isolates. CONCLUSIONS RAPD-PCR analysis revealed extensive genetic variability among the tested isolates. Oral isolates carried antibiotic resistance genes for tetracycline and whilst they possessed genes that could contribute to pathogenicity, these were detected at lower incidence compared with non-oral and VRE isolates. RAPD-PCR proved to be a useful approach to elucidate relatedness of disparate isolates.
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Marques C, Belas A, Franco A, Aboim C, Gama LT, Pomba C. Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J Antimicrob Chemother 2019; 73:377-384. [PMID: 29136156 DOI: 10.1093/jac/dkx401] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Objectives To evaluate temporal trends in antimicrobial resistance, over 16 years, in bacteria isolated from dogs and cats with urinary tract infection (UTI) and the clonal lineages of bacteria harbouring critical antimicrobial resistance mechanisms. Methods Antimicrobial susceptibility testing was conducted for 948 bacteria isolated from dogs and cats with UTI (1999-2014). Resistance mechanisms were detected by PCR, namely ESBL/AmpC in third-generation cephalosporin (3GC)-resistant Escherichia coli and Proteus mirabilis, mecA in methicillin-resistant staphylococci, and aac(6')-Ieaph(2″)-Ia and aph(2″)-1d in high-level gentamicin-resistant (HLGR) enterococci. Resistant bacteria were typed by MLST, and temporal trends in E. coli and Enterobacteriaceae antimicrobial resistance were determined by logistic regression. Results Enterobacteriaceae had a significant temporal increase in resistance to amoxicillin/clavulanate, 3GCs, trimethoprim/sulfamethoxazole, fluoroquinolones, gentamicin and tetracycline (P < 0.001). An increase in MDR was also detected (P < 0.0001). 3GC resistance was mainly caused by the presence of blaCTX-M-15 and blaCMY-2 in E. coli and the presence of blaCMY-2 in P. mirabilis. Two major 3GC-resistant E. coli clonal lineages were detected: O25b:H4-B2-ST131 and ST648. The mecA gene was detected in 9.2% (n = 11/119) of Staphylococcus spp., including MRSA clonal complex (CC) 5 (n = 2) and methicillin-resistant Staphylococcus epidermidis CC5 (n = 4). A temporal increase in MDR methicillin-resistant Staphylococcus pseudintermedius was detected (P = 0.0069). Some ampicillin-resistant and/or HLGR Enterococcus spp. were found to belong to hospital-adapted CCs, namely Enterococcus faecalis ST6-CC6 (n = 1) and Enterococcus faecium CC17 (n = 8). Conclusions The temporal increase in antimicrobial resistance and in MDR bacteria causing UTI in dogs and cats creates important therapeutic limitations in veterinary medicine. Furthermore, the detection of MDR high-risk clonal lineages raises public health concerns since companion animals with UTI may contribute to the spread of such bacteria.
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Affiliation(s)
- Cátia Marques
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Adriana Belas
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Andreia Franco
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Catarina Aboim
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Luís Telo Gama
- Animal Genetic Resources, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
| | - Constança Pomba
- Laboratory of Resistance to Antibiotics and Biocides, CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa (FMV-UL), Lisbon, Portugal
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Abstract
Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.
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32
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Sparo M, Delpech G, García Allende N. Impact on Public Health of the Spread of High-Level Resistance to Gentamicin and Vancomycin in Enterococci. Front Microbiol 2018; 9:3073. [PMID: 30619158 PMCID: PMC6305282 DOI: 10.3389/fmicb.2018.03073] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/28/2018] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance has turned into a global public health issue. Enterococci are intrinsically resistant to many antimicrobials groups. These bacteria colonize dairy and meat products and integrate the autochthonous microbiota of mammal's gastrointestinal tract. Over the last decades, detection of vanA genotype in Enterococcus faecium from animals and from food of animal origin has been reported. Vancomycin-resistant E. faecium has become a prevalent nosocomial pathogen. Hospitalized patients are frequently treated with broad-spectrum antimicrobials and this leads to an increase in the presence of VanA or VanB vancomycin-resistant enterococci in patients' gastrointestinal tract and the risk of invasive infections. In humans, E. faecium is the main reservoir of VanA and VanB phenotypes. Acquisition of high-level aminoglycoside resistance is a significant therapeutic problem for patients with severe infections because it negates the synergistic effect between aminoglycosides and a cell-wall-active agent. The aac(6')-Ie-aph (2″)-Ia gene is widely spread in E. faecalis and has been detected in strains of human origin and in the food of animal origin. Enzyme AAC(6')-Ie-APH(2″)-Ia confers resistance to available aminoglycosides, except to streptomycin. Due to the fast dissemination of this genetic determinant, the impact of its horizontal transferability among enterococcal species from different origin has been considered. The extensive use of antibiotics in food-producing animals contributes to an increase in drug-resistant animal bacteria that can be transmitted to humans. Innovation is needed for the development of new antibacterial drugs and for the design of combination therapies with conventional antibiotics. Nowadays, semi-purified bacteriocins and probiotics are becoming an attractive alternative to the antibiotic in animal production. Therefore, a better understanding of a complex and relevant issue for Public Health such as high-level vancomycin and gentamicin resistance in enterococci and their impact is needed. Hence, it is necessary to consider the spread of vanA E. faecium and high-level gentamicin resistant E. faecalis strains of different origin in the environment, and also highlight the potential horizontal transferability of these resistance determinants to other bacteria.
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Affiliation(s)
- Mónica Sparo
- Clinical Department, Medicine School, National University of Central Buenos Aires, Tandil, Argentina
| | - Gaston Delpech
- Clinical Department, Medicine School, National University of Central Buenos Aires, Tandil, Argentina
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Ben Yahia H, Chairat S, Hamdi N, Gharsa H, Ben Sallem R, Ceballos S, Torres C, Ben Slama K. Antimicrobial resistance and genetic lineages of faecal enterococci of wild birds: Emergence of vanA and vanB2 harbouring Enterococcus faecalis. Int J Antimicrob Agents 2018; 52:936-941. [DOI: 10.1016/j.ijantimicag.2018.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 10/16/2022]
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Yin M, Jiang Y, Qian C, Wu F, Ying Y, Wu C, Li P, Ying J, Li K, Xu T, Bao Q, Sun C. Molecular characteristics and comparative genomics analysis of a clinical Enterococcus casseliflavus with a resistance plasmid. Infect Drug Resist 2018; 11:2159-2167. [PMID: 30464559 PMCID: PMC6223339 DOI: 10.2147/idr.s180254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose The aim of this work was to investigate the molecular characterization of a clinical Enterococcus casseliflavus strain with a resistance plasmid. Materials and methods En. casseliflavus EC369 was isolated from a patient in a hospital in southern China. The minimum inhibitory concentration was found by means of the agar dilution method to determine the antimicrobial susceptibilities of the strains. Whole-genome sequencing and comparative genomics analysis were performed to analyze the mechanism of antibiotic resistance and the horizontal gene transfer of the resistance gene-related mobile genetic elements. Results En. casseliflavus EC369 showed resistance to erythromycin, kanamycin, and streptomycin, but was susceptible to vancomycin, ampicillin, and streptothricin and other antimicrobials. There were six resistance genes (aph3′, ant6, bla, sat4, and two ermBs) carried by a transposon identified on the plasmid pEC369 and a complete resistance gene cluster of vancomycin and a tet (M) gene encoded on the chromosome. This is the first complete plasmid sequence reported in clinically isolated En. casseliflavus. The plasmid with the greatest sequence identity with pEC369 was the plasmid of Enterococcus sp. FDAARGOS_375, followed by the plasmids of Enterococcus faecium strains F12085 and pRE25, whereas the sequence with the greatest identity to the resistance genes carrying a transposon of pEC369 was on the chromosome of Staphylococcus aureus strain GD1677. Conclusion The resistance profiles of En. casseliflavus EC369 might contribute to the resistance genes encoded on the plasmid. The fact that the most similar sequence to the transposon carrying resistance genes of pEC369 was encoded in the chromosome of a S. aureus strain provides insights into the mechanism of dissemination of multidrug resistance between bacteria of different species or genera through horizontal gene transfer.
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Affiliation(s)
- Min Yin
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Yi Jiang
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Changrui Qian
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Fei Wu
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Yuanyuan Ying
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Chongyang Wu
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Peizhen Li
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Jun Ying
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Kewei Li
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Teng Xu
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Qiyu Bao
- Department of Microbiology and Immunology, School of Laboratory Medicine and Life Sciences/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China,
| | - Caixia Sun
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China,
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Kuroda M, Sekizuka T, Matsui H, Suzuki K, Seki H, Saito M, Hanaki H. Complete Genome Sequence and Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolate KUB3006 Carrying a cfr(B)-Transposon on Its Chromosome and optrA-Plasmid. Front Microbiol 2018; 9:2576. [PMID: 30410481 PMCID: PMC6209644 DOI: 10.3389/fmicb.2018.02576] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by Enterococcus species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene cfr, and ribosomal protection genes (optrA and poxtA). Recently, a cfr gene variant, cfr(B), was identified in a Tn6218-like transposon (Tn) in a Clostridioides difficile isolate. Here, we isolated an LR Enterococcus faecalis clinical isolate, KUB3006, from a urine specimen of a patient with urinary tract infection during hospitalization in 2017. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in E. faecalis isolate KUB3006. Complete genome sequencing of KUB3006 revealed that it carried cfr(B) on a chromosomal Tn6218-like element. Surprisingly, this Tn6218-like element was almost (99%) identical to that of C. difficile Ox3196, which was isolated from a human in the UK in 2012, and to that of Enterococcus faecium 5_Efcm_HA-NL, which was isolated from a human in the Netherlands in 2012. An additional oxazolidinone and phenicol resistance gene, optrA, was also identified on a plasmid. KUB3006 is sequence type (ST) 729, suggesting that it is a minor ST that has not been reported previously and is unlikely to be a high-risk E. faecalis lineage. In summary, LR E. faecalis KUB3006 possesses a notable Tn6218-like-borne cfr(B) and a plasmid-borne optrA. This finding raises further concerns regarding the potential declining effectiveness of LZD treatment in the future.
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Affiliation(s)
- Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hidehito Matsui
- Infection Control Research Center, Kitasato University, Tokyo, Japan
| | - Katsunori Suzuki
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Hiroyuki Seki
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Mitsumasa Saito
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan.,Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Hideaki Hanaki
- Infection Control Research Center, Kitasato University, Tokyo, Japan
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Dabul ANG, Avaca-Crusca JS, Navais RB, Merlo TP, Van Tyne D, Gilmore MS, Camargo ILBDC. Molecular basis for the emergence of a new hospital endemic tigecycline-resistant Enterococcus faecalis ST103 lineage. INFECTION GENETICS AND EVOLUTION 2018; 67:23-32. [PMID: 30393188 DOI: 10.1016/j.meegid.2018.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 11/25/2022]
Abstract
Enterococcus faecalis are a major cause of nosocomial infection worldwide, and the spread of vancomycin resistant strains (VRE) limits treatment options. Tigecycline-resistant VRE began to be isolated from inpatients at a Brazilian hospital within months following the addition of tigecycline to the hospital formulary. This was found to be the result of a spread of an ST103 E. faecalis clone. Our objective was to identify the basis for tigecycline resistance in this lineage. The genomes of two closely related tigecycline-susceptible (MIC = 0.06 mg/L), and three representative tigecycline-resistant (MIC = 1 mg/L) ST103 isolates were sequenced and compared. Further, efforts were undertaken to recapitulate the emergence of resistant strains in vitro. The specific mutations identified in clinical isolates in several cases were within the same genes identified in laboratory-evolved strains. The contribution of various polymorphisms to the resistance phenotype was assessed by trans-complementation of the wild type or mutant alleles, by testing for differences in mRNA abundance, and/or by examining the phenotype of transposon insertion mutants. Among tigecycline-resistant clinical isolates, five genes contained non-synonymous mutations, including two genes known to be related to enterococcal tigecycline resistance (tetM and rpsJ). Finally, within the in vitro-selected resistant variants, mutation in the gene for a MarR-family response regulator was associated with tigecycline resistance. This study shows that E. faecalis mutates to attain tigecycline resistance through the complex interplay of multiple mechanisms, along multiple evolutionary trajectories.
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Affiliation(s)
| | | | - Roberto Barranco Navais
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 135560-970 São Carlos, SP, Brazil
| | - Thaís Panhan Merlo
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 135560-970 São Carlos, SP, Brazil
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, USA; Department of Microbiology and Immunobiology, Harvard Medical School, 25 Shattuck Street, Boston, USA
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, USA; Department of Microbiology and Immunobiology, Harvard Medical School, 25 Shattuck Street, Boston, USA
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Linezolid resistance genes and genetic elements enhancing their dissemination in enterococci and streptococci. Plasmid 2018; 99:89-98. [PMID: 30253132 DOI: 10.1016/j.plasmid.2018.09.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
Linezolid is considered a last resort drug in treatment of severe infections caused by Gram-positive pathogens, resistant to other antibiotics, such as vancomycin-resistant enterococci (VRE), methicillin-resistant staphylococci and multidrug resistant pneumococci. Although the vast majority of Gram-positive pathogenic bacteria remain susceptible to linezolid, resistant isolates of enterococci, staphylococci and streptococci have been reported worldwide. In these bacteria, apart from mutations, affecting mostly the 23S rRNA genes, acquisition of such genes as cfr, cfr(B), optrA and poxtA, often associated with mobile genetic elements (MGE), plays an important role for resistance. The purpose of this paper is to provide an overview on diversity and epidemiology of MGE carrying linezolid-resistance genes among clinically-relevant Gram-positive pathogens such as enterococci and streptococci.
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Hygienemaßnahmen zur Prävention der Infektion durch Enterokokken mit speziellen Antibiotikaresistenzen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:1310-1361. [DOI: 10.1007/s00103-018-2811-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature. Drug Resist Updat 2018; 40:25-39. [DOI: 10.1016/j.drup.2018.10.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 08/10/2018] [Accepted: 10/30/2018] [Indexed: 01/04/2023]
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40
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Dai D, Wang H, Xu X, Chen C, Song C, Jiang D, Du P, Zhang Y, Zeng H. The emergence of multi-resistant Enterococcus faecalis clonal complex, CC4, causing nosocomial infections. J Med Microbiol 2018; 67:1069-1077. [PMID: 29923823 DOI: 10.1099/jmm.0.000761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
PURPOSE Enterococcus faecalis is commonly found as a commensal gut bacteria, but some linages have caused increasing extra-gastrointestinal infections. In particular, strains with high-level virulence or antimicrobial resistance are prevalent in healthcare settings as nosocomial pathogens. This study was performed to elucidate the epidemiological characteristics and antimicrobial susceptibility profiles of E. faecalis causing nosocomial infections in a Chinese general hospital over a 4-year period. METHODOLOGY We collected 77 isolates causing extra-gastrointestinal infections from patients at 14 different wards in a tertiary hospital from 2011 to 2014. The population relationship was assessed by multilocus sequence typing and multilocus variable-number tandem repeat analysis. The Kirby-Bauer disk diffusion method was used to evaluate susceptibility against 11 antimicrobial agents. RESULTS The isolates showed high-level resistance to tetracycline (86.5 %), erythromycin (78.4 %), rifampin (62.2 %), etc. The major clonal complexes (CCs) included CC4, CC16 and CC21. As the most dominant subtype, CC16 was identified in almost all of the wards and all types of samples, but the isolation rate decreased continually. In contrast, the isolation rates of CC4 and CC21 increased and the proportion of these two CCs in 2014 was more than three times that in 2011. In addition, CC4 showed higher resistance than CC16. CONCLUSIONS This study demonstrated the prevalent subtypes and resistance profiles of E. faecalis causing nosocomial infection, and indicated that CC4 may be a newly emerging high-risk, multi-resistant cluster. More surveillance is urgently needed, which will increase our understanding of the prevention and treatment of such infections.
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Affiliation(s)
- Dongfa Dai
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Huizhu Wang
- 2Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Xinmin Xu
- 2Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Chen Chen
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Chuan Song
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Dong Jiang
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Pengcheng Du
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Yuanyuan Zhang
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
| | - Hui Zeng
- 1Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, PR China
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Crouzet L, Derrien M, Cherbuy C, Plancade S, Foulon M, Chalin B, van Hylckama Vlieg JET, Grompone G, Rigottier-Gois L, Serror P. Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge. Sci Rep 2018; 8:5098. [PMID: 29572473 PMCID: PMC5865147 DOI: 10.1038/s41598-018-23437-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/13/2018] [Indexed: 12/30/2022] Open
Abstract
Enterococci, in particular vancomycin-resistant enterococci (VRE), are a leading cause of hospital-acquired infections. Promoting intestinal resistance against enterococci could reduce the risk of VRE infections. We investigated the effects of two Lactobacillus strains to prevent intestinal VRE. We used an intestinal colonisation mouse model based on an antibiotic-induced microbiota dysbiosis to mimic enterococci overgrowth and VRE persistence. Each Lactobacillus spp. was administered daily to mice starting one week before antibiotic treatment until two weeks after antibiotic and VRE inoculation. Of the two strains, Lactobacillus paracasei CNCM I-3689 decreased significantly VRE numbers in the feces demonstrating an improvement of the reduction of VRE. Longitudinal microbiota analysis showed that supplementation with L. paracasei CNCM I-3689 was associated with a better recovery of members of the phylum Bacteroidetes. Bile salt analysis and expression analysis of selected host genes revealed increased level of lithocholate and of ileal expression of camp (human LL-37) upon L. paracasei CNCM I-3689 supplementation. Although a direct effect of L. paracasei CNCM I-3689 on the VRE reduction was not ruled out, our data provide clues to possible anti-VRE mechanisms supporting an indirect anti-VRE effect through the gut microbiota. This work sustains non-antibiotic strategies against opportunistic enterococci after antibiotic-induced dysbiosis.
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Affiliation(s)
- Laureen Crouzet
- Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Medis, INRA Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | | | - Claire Cherbuy
- Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandra Plancade
- Maiage, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mélanie Foulon
- Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Benjamin Chalin
- Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Gianfranco Grompone
- Danone Nutricia Research, F-91120, Palaiseau, France.,Instituto Nacional de Investigación Agropecuaria, Montevideo, Uruguay
| | | | - Pascale Serror
- Micalis, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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Giebułtowicz J, Tyski S, Wolinowska R, Grzybowska W, Zaręba T, Drobniewska A, Wroczyński P, Nałęcz-Jawecki G. Occurrence of antimicrobial agents, drug-resistant bacteria, and genes in the sewage-impacted Vistula River (Poland). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5788-5807. [PMID: 29235021 DOI: 10.1007/s11356-017-0861-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Antimicrobial agents (antimicrobials) are a group of therapeutic and hygienic agents that either kill microorganisms or inhibit their growth. Their occurrence in surface water may reveal harmful effects on aquatic biota and challenge microbial populations. Recently, there is a growing concern over the contamination of surface water with both antimicrobial agents and multidrug-resistant bacteria. The aim of the study was the determination of the presence of selected antimicrobials at specific locations of the Vistula River (Poland), as well as in tap water samples originating from the Warsaw region. Analysis was performed using the liquid chromatography-electrospray ionization-tandem mass spectrometry method. In addition, the occurrence of drug-resistant bacteria and resistance genes was determined using standard procedures. This 2-year study is the first investigation of the simultaneous presence of antimicrobial agents, drug-resistant bacteria, and genes in Polish surface water. In Poland, relatively high concentrations of macrolides are observed in both surface and tap water. Simultaneous to the high macrolide levels in the environment, the presence of the erm B gene, coding the resistance to macrolides, lincosamides, and streptogramin, was detected in almost all sampling sites. Another ubiquitous gene was int1, an element of the 5'-conserved segment of class 1 integrons that encode site-specific integrase. Also, resistant isolates of Enterococcus faecium and Enterococcus faecalis and Gram-negative bacteria were recovered. Multidrug-resistant bacteria isolates of Gram-negative and Enterococcus were also detected. The results show that wastewater treatment plants (WWTP) are the main source of most antimicrobials, resistant bacteria, and genes in the aquatic environment, probably due to partial purification during wastewater treatment processes.
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Affiliation(s)
- Joanna Giebułtowicz
- Department of Bioanalysis and Drugs Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland.
| | - Stefan Tyski
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Renata Wolinowska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Wanda Grzybowska
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Tomasz Zaręba
- Department of Antibiotics and Microbiology, National Medicines Institute, 30/34 Chelmska Street, 00725, Warsaw, Poland
| | - Agata Drobniewska
- Department of Environmental Health Sciences, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Piotr Wroczyński
- Department of Bioanalysis and Drugs Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
| | - Grzegorz Nałęcz-Jawecki
- Department of Environmental Health Sciences, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Street, 02097, Warsaw, Poland
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Genetic characteristics of VanA-type vancomycin-resistant Enterococcus faecalis and Enterococcus faecium in Cuba. New Microbes New Infect 2017; 21:125-127. [PMID: 29348921 PMCID: PMC5766742 DOI: 10.1016/j.nmni.2017.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/05/2022] Open
Abstract
VanA-type vancomycin-resistant enterococci isolates from bloodstream infections in Cuba were genetically characterized. Enterococcus faecalis isolates were assigned to sequence type (ST) 28, closely related to Eastern Europe, while Enterococcus faecium belonged to ST262, ST656 and ST1349, and showed different genetic profiles.
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WILD BIRDS AS A POTENTIAL SOURCE OF KNOWN AND NOVEL MULTILOCUS SEQUENCE TYPES OF ANTIBIOTIC-RESISTANT ENTEROCOCCUS FAECALIS. J Wildl Dis 2017; 54:219-228. [PMID: 29148887 DOI: 10.7589/2017-05-118] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We assessed the antibiotic resistance and genetic diversity of 27 Enterococcus faecalis isolates from 25 wild bird species in Poland. Resistance to lincomycin (100%) was most common followed by tetracycline (48%), erythromycin (44%), and ciprofloxacin (22%). High-level resistance to streptomycin and kanamycin was observed in 19% and 15% of isolates, respectively. One isolate (4%) exhibited low-level resistance to penicillin and vancomycin, and all isolates were susceptible to gentamicin and chloramphenicol. Antibiotic resistance was linked to the tet(M), tet(L), erm(A), erm(B), msr(A/B), ant(6)-Ia, and aph(3')-IIIa genes. None of the tested van ( vanA, vanB, vanC1, vanC2/C3, vanD, vanE, vanG) genes were found in the vancomycin-resistant isolate. Based on pulsed-field gel electrophoresis and multilocus sequence typing analysis, the E. faecalis population from wild birds revealed high genetic diversity. All isolates were divided into 22 pulsotypes and 18 sequence types (STs), among which seven STs were newly assigned (ST748-ST753 and ST764). The most-prevalent STs were ST290 and ST374 followed by ST287 and ST34. The coexistence of strains assigned to the same STs in wild birds and in nonwildlife populations strongly indicated that many wild bird species could constitute a source of E. faecalis for infections in humans, pets, and farm animals.
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Santos BA, Oliveira JS, Cardoso NT, Barbosa AV, Superti SV, Teixeira LM, Neves FP. Major globally disseminated clonal complexes of antimicrobial resistant enterococci associated with infections in cancer patients in Brazil. INFECTION GENETICS AND EVOLUTION 2017; 55:56-62. [DOI: 10.1016/j.meegid.2017.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 08/15/2017] [Accepted: 08/27/2017] [Indexed: 11/30/2022]
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Shettigar K, Bhat DV, Satyamoorthy K, Murali TS. Severity of drug resistance and co-existence of Enterococcus faecalis in diabetic foot ulcer infections. Folia Microbiol (Praha) 2017; 63:115-122. [PMID: 28889401 DOI: 10.1007/s12223-017-0547-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/01/2017] [Indexed: 01/04/2023]
Abstract
The genes encoding aminoglycoside resistance in Enterococcus faecalis may promote collateral aminoglycoside resistance in polymicrobial wounds. We studied a total of 100 diabetic foot ulcer samples for infection and found 60 samples to be polymicrobial, 5 to be monomicrobial, and 35 samples to be culture negative. A total of 65 E. faecalis isolates were screened for six genes coding for aminoglycoside resistance, antibiotic resistance patterns, and biofilm production. Infectious Diseases Society of America/International Working Group on the Diabetic Foot system was used to classify the wound ulcers. Majority of the subjects with culture-positive wound were recommended conservative management, while 14 subjects underwent amputation. Enterococcal isolates showed higher resistance for erythromycin, tetracycline, and ciprofloxacin. Isolates from grade 3 ulcer showed higher frequency of aac(6')-Ie-aph(2″)-Ia, while all the isolates were negative for aph(2″)-Ib, aph(2″)-Ic, and aph(2″)-Id. The isolates from grade 3 ulcers showed higher resistance to aminoglycosides as well as teicoplanin and chloramphenicol. All the 39 biofilm producers were obtained from polymicrobial wound and showed higher resistance when compared to biofilm non-producers. Higher frequency of isolates carrying aac(6')-Ie-aph(2″)-Ia in polymicrobial community showing resistance to key antibiotics suggests widespread distribution of aminoglycoside-resistant E. faecalis and their role in worsening diabetic foot ulcers.
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Affiliation(s)
- Kavitha Shettigar
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Deepika V Bhat
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cellular and Molecular Biology, School of Life Sciences, Manipal University, Manipal, 576104, India
| | - Thokur Sreepathy Murali
- Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, 576104, India.
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Holzknecht BJ, Pinholt M, Gumpert H, Hammerum AM, Westh H. Genetic characterisation confirms sporadic occurrence of vancomycin-resistant Enterococcus faecalis in Copenhagen, Denmark. Int J Antimicrob Agents 2017; 50:501-502. [PMID: 28709988 DOI: 10.1016/j.ijantimicag.2017.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/25/2017] [Accepted: 07/05/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Barbara J Holzknecht
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark.
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Kettegård Alle 30, 2650 Hvidovre, Denmark; Institute of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Kettegård Alle 30, 2650 Hvidovre, Denmark
| | - Anette M Hammerum
- Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Kettegård Alle 30, 2650 Hvidovre, Denmark; Institute of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
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48
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Antibiotic Resistance Genes and Antibiotic Susceptibility of Oral Enterococcus faecalis Isolates Compared to Isolates from Hospitalized Patients and Food. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/5584_2017_53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Gawryszewska I, Malinowska K, Kuch A, Chrobak-Chmiel D, Trokenheim LL, Hryniewicz W, Sadowy E. Distribution of antimicrobial resistance determinants, virulence-associated factors and clustered regularly interspaced palindromic repeats loci in isolates of Enterococcus faecalis from various settings and genetic lineages. Pathog Dis 2017; 75:3059201. [PMID: 28334141 DOI: 10.1093/femspd/ftx021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
Enterococcus faecalis represents an important factor of hospital-associated infections (HAIs). The knowledge on its evolution from a commensal to an opportunistic pathogen is still limited; thus, we performed a study to characterise distribution of factors that may contribute to this adaptation. Using a collection obtained from various settings (hospitalised patients, community carriers, animals, fresh food, sewage, water), we investigated differences in antimicrobial susceptibility, distribution of antimicrobial resistance genes, virulence-associated determinants and phenotypes, and CRISPR loci in the context of the clonal relatedness of isolates. Bayesian Analysis of Population Structure revealed the presence of three major groups; two subgroups comprised almost exclusively HAI isolates, belonging to previously proposed enterococcal high-risk clonal complexes (HiRECCs) 6 and 28. Isolates of these two subgroups were significantly enriched in antimicrobial resistance genes, presumably produced a polysaccharide capsule and often carried the aggregation substance asa1; distribution of other virulence-associated genes, such as esp and cyl, formation of a biofilm and gelatinase production were more variable. Moreover, both subgroups showed a low prevalence of CRISPR-Cas 1 and 3 and presence of small CRISPR2 variants. Our study confirms the importance of HiRECCs in the population of E. faecalis and their confinement to the hospital settings.
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Affiliation(s)
- Iwona Gawryszewska
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - Katarzyna Malinowska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - Alicja Kuch
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - Dorota Chrobak-Chmiel
- Department of Preclinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Lucja Laniewska- Trokenheim
- Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, 10-726 Olsztyn, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
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50
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Jørgensen S, Poulsen L, Thorndal L, Ronaghinia A, Bisgaard M, Christensen H. Characterization ofEnterococcus faecalisisolated from the cloaca of ‘fancy breeds’ and confined chickens. J Appl Microbiol 2017; 122:1149-1158. [DOI: 10.1111/jam.13416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/21/2016] [Accepted: 01/26/2017] [Indexed: 01/20/2023]
Affiliation(s)
- S.L. Jørgensen
- Department of Veterinary Disease Biology; University of Copenhagen; Frederiksberg Denmark
| | - L.L. Poulsen
- Department of Veterinary Disease Biology; University of Copenhagen; Frederiksberg Denmark
| | - L. Thorndal
- Department of Veterinary Disease Biology; University of Copenhagen; Frederiksberg Denmark
- Danish Veterinary and Food Administration; Vejle Denmark
| | - A.A. Ronaghinia
- Department of Veterinary Disease Biology; University of Copenhagen; Frederiksberg Denmark
| | | | - H. Christensen
- Department of Veterinary Disease Biology; University of Copenhagen; Frederiksberg Denmark
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