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Mullally CA, Fahriani M, Mowlaboccus S, Coombs GW. Non- faecium non- faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance. Clin Microbiol Rev 2024; 37:e0012123. [PMID: 38466110 DOI: 10.1128/cmr.00121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.
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Affiliation(s)
- Christopher A Mullally
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marhami Fahriani
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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Kim YH, Lee DH, Seo HS, Eun SH, Lee DS, Choi YK, Lee SH, Kim TY. Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product. Int Microbiol 2024:10.1007/s10123-024-00496-9. [PMID: 38466360 DOI: 10.1007/s10123-024-00496-9] [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: 12/31/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.
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Affiliation(s)
- Young-Hoo Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | | | - Han Sol Seo
- Yunovia Co., Ltd, Hwaseong, 18449, South Korea
| | | | - Do Sup Lee
- Yunovia Co., Ltd, Hwaseong, 18449, South Korea
| | | | - Sang Hyun Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Tae-Yoon Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea.
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Chen W, Wang Q, Wu H, Xia P, Tian R, Li R, Xia L. Molecular epidemiology, phenotypic and genomic characterization of antibiotic-resistant enterococcal isolates from diverse farm animals in Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168683. [PMID: 37996027 DOI: 10.1016/j.scitotenv.2023.168683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Multidrug-resistant (MDR) bacteria in farm environments can be transferred to humans through the food chain and occupational exposure. Enterococcus infections caused by linezolid resistant enterococci (LRE) are becoming more challenging to treat as their resistance to antibiotics intensifies. Therefore, this study investigated the molecular epidemiology, phenotypic and genomic characterization of enterococci in seven species of farm animals (sheep, chicken, swine, camel, cattle, equine, pigeon) anal swab from Xinjiang, China by agar dilution method, polymerase chain reaction (PCR), whole-genome sequencing (WGS) and bioinformatics analysis. A total of 771 samples were collected, 599 (78 %) were contaminated with Enterococcus spp., among which Enterococcus faecalis (350/599) was dominant. Antimicrobial susceptibility testing showed that high resistance was observed in rifampicin (80 %), tetracycline (71 %), doxycycline (71 %), and erythromycin (69 %). The results of PCR showed the highest prevalent antibiotic resistance genes (ARGs) were aac(6')-aph(2″) (85 %), followed by tet(M) (73 %), erm(B) (62 %), and aph(3')-IIIa (61 %). Besides, 29 optrA-carrying E. faecalis isolates belonging to 13 STs (including 3 new alleles) were detected, with ST714 (31 %, 9/29) being the dominant ST type. The phylogenetic tree showed that optrA-carrying E. faecalis prevalent in the intensive swine farm is mainly caused by clonal transmission. Notably, optrA gene in Enterococcus spp. isolate from camel was first characterized here. WGS of E. faecalis F109 isolate from camel confirmed the colocalization of optrA with other five ARGs in the same plasmid (pAFL-109F). The optrA-harboring genetic context is IS1216E-fexA-optrA-erm(A)-IS1216E. This study highlights the prevalence of MDR Enterococcus (≥88 %) and four ARGs (≥75 %) in swine (intensive farming), cattle (commercial farming), and chickens (backyard farming) are high and also highlights that optrA-carrying E. faecalis of farm animals incur a transmission risk to humans through environment, food consumption and others. Therefore, antibiotic-resistant bacteria (ARB) monitoring and effective control measures should be strengthened and implemented in diverse animals.
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Affiliation(s)
- Wanzhao Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Huimin Wu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Panpan Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Rui Tian
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China.
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Messele YE, Trott DJ, Hasoon MF, Veltman T, McMeniman JP, Kidd SP, Petrovski KR, Low WY. Phylogeny, Virulence, and Antimicrobial Resistance Gene Profiles of Enterococcus faecium Isolated from Australian Feedlot Cattle and Their Significance to Public and Environmental Health. Antibiotics (Basel) 2023; 12:1122. [PMID: 37508218 PMCID: PMC10376260 DOI: 10.3390/antibiotics12071122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
The extent of similarity between E. faecium strains found in healthy feedlot beef cattle and those causing extraintestinal infections in humans is not yet fully understood. This study used whole-genome sequencing to analyse the antimicrobial resistance profile of E. faecium isolated from beef cattle (n = 59) at a single feedlot and compared them to previously reported Australian isolates obtained from pig (n = 60) and meat chicken caecal samples (n = 8), as well as human sepsis cases (n = 302). The E. faecium isolated from beef cattle and other food animal sources neither carried vanA/vanB responsible for vancomycin nor possessed gyrA/parC and liaR/liaS gene mutations associated with high-level fluoroquinolone and daptomycin resistance, respectively. A small proportion (7.6%) of human isolates clustered with beef cattle and pig isolates, including a few isolates belonging to the same sequence types ST22 (one beef cattle, one pig, and two human isolates), ST32 (eight beef cattle and one human isolate), and ST327 (two beef cattle and one human isolate), suggesting common origins. This provides further evidence that these clonal lineages may have broader host range but are unrelated to the typical hospital-adapted human strains belonging to clonal complex 17, significant proportions of which contain vanA/vanB and liaR/liaS. Additionally, none of the human isolates belonging to these STs contained resistance genes to WHO critically important antimicrobials. The results confirm that most E. faecium isolated from beef cattle in this study do not pose a significant risk for resistance to critically important antimicrobials and are not associated with current human septic infections.
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Affiliation(s)
- Yohannes E Messele
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
| | - Darren J Trott
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mauida F Hasoon
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tania Veltman
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joe P McMeniman
- Meat & Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
| | - Stephen P Kidd
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
- Research Centre for Infectious Disease, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kiro R Petrovski
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Wai Y Low
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
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Demay F, Hallier M, Georgeault S, Com E, Cattoir V, Goude R, Gillet R. Simple purification and characterization of soluble and homogenous ABC-F translation factors from Enterococcus faecium. Protein Expr Purif 2023:106325. [PMID: 37354924 DOI: 10.1016/j.pep.2023.106325] [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: 12/05/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023]
Abstract
The family of ATP-binding cassette F proteins (ABC-F) is mainly made up of cytosolic proteins involved in regulating protein synthesis, and they are often part of a mechanism that confers resistance to ribosome-targeting antibiotics. The existing literature has emphasized the difficulty of purifying these recombinant proteins because of their very low solubility and stability. Here, we describe a rapid and efficient three-step purification procedure that allows for the production of untagged ABC-F proteins from Enterococcus faecium in the heterologous host Escherichia coli. After four purified ABC-F proteins were produced using this protocol, their biological activities were validated by in vitro experiment. In conclusion, our study provides an invaluable tool for obtaining large amounts of untagged and soluble ABC-F proteins that can then be used for in vitro experiments.
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Affiliation(s)
- Fanny Demay
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Marc Hallier
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Sylvie Georgeault
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France; Univ Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, F-35000, Rennes, France
| | - Vincent Cattoir
- Department of Clinical Microbiology, Rennes University Hospital, Rennes, France; Univ. Rennes, Inserm, UMR 1230 BRM, Rennes, France
| | - Renan Goude
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Reynald Gillet
- Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France.
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Rozman V, Mohar Lorbeg P, Treven P, Accetto T, Janežič S, Rupnik M, Bogovič Matijašić B. Genomic insights into antibiotic resistance and mobilome of lactic acid bacteria and bifidobacteria. Life Sci Alliance 2023; 6:e202201637. [PMID: 36781180 PMCID: PMC9930590 DOI: 10.26508/lsa.202201637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Lactic acid bacteria (LAB) and Bifidobacterium sp. (bifidobacteria) can carry antimicrobial resistance genes (ARGs), yet data on resistance mechanisms in these bacteria are limited. The aim of our study was to identify the underlying genetic mechanisms of phenotypic resistance in 103 LAB and bifidobacteria using whole-genome sequencing. Sequencing data not only confirmed the presence of 36 acquired ARGs in genomes of 18 strains, but also revealed wide dissemination of intrinsic ARGs. The presence of acquired ARGs on known and novel mobile genetic elements raises the possibility of their horizontal spread. In addition, our data suggest that mutations may be a common mechanism of resistance. Several novel candidate resistance mechanisms were uncovered, providing a basis for further in vitro studies. Overall, 1,314 minimum inhibitory concentrations matched with genotypes in 92.4% of the cases; however, prediction of phenotype based on genotypic data was only partially efficient, especially with respect to aminoglycosides and chloramphenicol. Our study sheds light on resistance mechanisms and their transferability potential in LAB and bifidobacteria, which will be useful for risk assessment analysis.
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Affiliation(s)
- Vita Rozman
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Domžale, Slovenia
| | - Petra Mohar Lorbeg
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Domžale, Slovenia
| | - Primož Treven
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Domžale, Slovenia
| | - Tomaž Accetto
- University of Ljubljana, Biotechnical Faculty, Department of Microbiology, Chair of Microbial Diversity, Microbiomics and Biotechnology, Ljubljana, Slovenia
| | - Sandra Janežič
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory of Health, Environment and Food, Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Maribor, Slovenia
| | - Bojana Bogovič Matijašić
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, Domžale, Slovenia
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Web-based prediction of antimicrobial resistance in enterococcal clinical isolates by whole-genome sequencing. Eur J Clin Microbiol Infect Dis 2023; 42:67-76. [PMID: 36378364 DOI: 10.1007/s10096-022-04527-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Besides phenotypic antimicrobial susceptibility testing (AST), whole genome sequencing (WGS) is a promising alternative approach for detection of resistance phenotypes. The aim of this study was to investigate the concordance between WGS-based resistance prediction and phenotypic AST results for enterococcal clinical isolates using a user-friendly online tools and databases. A total of 172 clinical isolates (34 E. faecalis, 138 E. faecium) received at the French National Reference Center for enterococci from 2017 to 2020 were included. AST was performed by disc diffusion or MIC determination for 14 antibiotics according to CA-SFM/EUCAST guidelines. The genome of all strains was sequenced using the Illumina technology (MiSeq) with bioinformatic analysis from raw reads using online tools ResFinder 4.1 and LRE-finder 1.0. For both E. faecalis and E. faecium, performances of WGS-based genotype to predict resistant phenotypes were excellent (concordance > 90%), particularly for antibiotics commonly used for treatment of enterococcal infections such as ampicillin, gentamicin, vancomycin, teicoplanin, and linezolid. Note that 100% very major errors were found for quinupristin-dalfopristin, tigecycline, and rifampicin for which resistance mutations are not included in databases. Also, it was not possible to predict phenotype from genotype for daptomycin for the same reason. WGS combined with online tools could be easily used by non-expert clinical microbiologists as a rapid and reliable tool for prediction of phenotypic resistance to first-line antibiotics among enterococci. Nonetheless, some improvements should be made such as the implementation of resistance mutations in the database for some antibiotics.
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Kowalewicz C, Timmermans M, Fretin D, Wattiau P, Boland C. An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria. Microbiologyopen 2022; 12:e1341. [PMID: 36825880 PMCID: PMC9791161 DOI: 10.1002/mbo3.1341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022] Open
Abstract
Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018-2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.
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Affiliation(s)
| | | | - David Fretin
- Veterinary Bacteriology, SciensanoIxellesBelgium
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Yi L, Chen S, Li G, Ren J, Zhou R, Zeng K. Prevalence of antibiotic resistance pathogens in online fresh-cut fruit from Chongqing, China and controlling Enterococcus faecalis by bacteriocin GF-15. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Boodaghi Malidareh E, Ahanjan M, Asgharzadeh Marghmalek S, Goli HR. Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium. Mol Biol Rep 2022; 49:7929-7937. [PMID: 35716285 DOI: 10.1007/s11033-022-07627-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Streptogramins and linezolid are important in the treatment of infections caused by vancomycin-resistant enterococci. PURPOSE Then, we aimed to evaluate the resistance rates against these drugs and the prevalence of genes involved in hospital environmental and fecal normal-flora isolates of Enterococcus faecalis and Enterococcus faecium. METHODS AND RESULTS The strains were isolated from the stool samples and hospital environments by culturing on M-Enterococcus (ME) agar, and identified by phenotypic and genotypic microbiological tests. The disk agar diffusion method was used to identify the antimicrobial susceptibility pattern of the isolates. The genomic DNA extraction was done by the alkaline lysis method, and the PCR test was used to detect the resistance genes. A total of 145 enterococci isolates were taken, from which 84 (57.9%) isolates were detected as E. faecalis and 61 (42.06%) isolates were E. faecium. Moreover, 70 (83.33), 4 (4.76%), 1 (1.19%), and 40 (47.61%) isolates of E. faecalis and 20 (32.78%), 1 (1.63%), 4 (6.55%), and 26 (42.62%) E. faecium isolates were resistant against quinupristin-dalfopristin, linezolid, vancomycin, and erythromycin, respectively. Also, 112 (77.24%), 50 (34.48%), 39 (26.89%), 27 (18.62%), 19 (13.1%), 4 (2.75%), and 1 (0.68%) isolates were contained LsaA, vatD, vgbB, vatE, cfr, lsaE and optrA genes, respectively. None of the isolates carried the vgbA gene. CONCLUSIONS High-level streptogramin resistance rate and high prevalence of resistance genes in enterococci isolated from the stool of healthy persons and the hospital environment indicates the importance of possible transmission of resistance genes from these isolates to clinical ones.
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Affiliation(s)
- Elham Boodaghi Malidareh
- Antimicrobial Resistance Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Ahanjan
- Antimicrobial Resistance Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Medical Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Saba Asgharzadeh Marghmalek
- Department of Medical Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hamid Reza Goli
- Antimicrobial Resistance Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
- Department of Medical Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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Azimonti G, Bampidis V, Bastos MDL, Christensen H, Dusemund B, Fašmon Durjava M, Kouba M, López-Alonso M, López Puente S, Marcon F, Mayo B, Pechová A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Brantom P, Maradona MP, Tosti L, Anguita M, Brozzi R, Galobart J, Pizzo F, Revez J, Ortuño J, Tarrés-Call J, Pettenati E. Safety and efficacy of a feed additive consisting of Bacillus subtilis FERM BP-07462, Enterococcus lactis FERM BP-10867 and Clostridium butyricum FERM BP-10866 (BIO-THREE ®) for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, all avian species for rearing/fattening to slaughter and all avian species reared for laying or breeding to point of lay (TOA BIOPHARMA Co., Ltd.). EFSA J 2022; 20:e07342. [PMID: 35757152 PMCID: PMC9201748 DOI: 10.2903/j.efsa.2022.7342] [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] [Indexed: 12/02/2022] Open
Abstract
Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of BIO‐THREE® when used as a feed additive for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, all avian species for rearing/fattening to slaughter and all avian species reared for laying or breeding to point of lay. The product under assessment is based on viable cells/spores of Bacillus subtilis FERM BP‐07462, Enterococcus lactis FERM BP‐10867 and Clostridium butyricum FERM BP‐10866. Based on the tolerance study provided, the Panel concluded that the additive is safe for the target species under the conditions of use. The additive is safe for the consumers of products derived from animals receiving the additive. The additive is not irritant to skin and eyes. The additive is a respiratory sensitiser. No conclusions could be drawn on its potential to be a skin sensitiser. The use of the product as a feed additive is of no concern for the environment. The FEEDAP Panel was not in the position to conclude on the efficacy of BIO‐THREE® for the target species. BIO‐THREE® is compatible with diclazuril, decoquinate and halofuginone. No conclusions could be drawn on the compatibility of BIO‐THREE® with monensin sodium, salinomycin sodium, narasin, robenidine hydrochloride and maduramicin ammonium.
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Fu X, Lyu L, Wang Y, Zhang Y, Guo X, Chen Q, Liu C. Safety assessment and probiotic characteristics of Enterococcus lactis JDM1. Microb Pathog 2022; 163:105380. [PMID: 34979271 DOI: 10.1016/j.micpath.2021.105380] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1. METHODS Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability. RESULTS E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect. CONCLUSION E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.
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Affiliation(s)
- Xiaomei Fu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Lyu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Wang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Chen
- Institute of Intestinal Diseases, Shanghai Tenth People's Hospital Affiliated to Tongji University, Shanghai, 200072, China.
| | - Chang Liu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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13
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Tóth AG, Csabai I, Judge MF, Maróti G, Becsei Á, Spisák S, Solymosi N. Mobile Antimicrobial Resistance Genes in Probiotics. Antibiotics (Basel) 2021; 10:antibiotics10111287. [PMID: 34827225 PMCID: PMC8614787 DOI: 10.3390/antibiotics10111287] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.
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Affiliation(s)
- Adrienn Gréta Tóth
- Health Services Management Training Centre, Semmelweis University, 1125 Budapest, Hungary;
| | - István Csabai
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Maura Fiona Judge
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, 6726 Szeged, Hungary;
- Faculty of Water Sciences, University of Public Service, 6500 Baja, Hungary
| | - Ágnes Becsei
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA;
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
- Correspondence: ; Tel.: +36-30-9347-069
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14
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From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant Enterococcus spp. in Intensive Pig Farming in South Africa. Microorganisms 2021; 9:microorganisms9050882. [PMID: 33918989 PMCID: PMC8142977 DOI: 10.3390/microorganisms9050882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/18/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022] Open
Abstract
Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of Enterococcus spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. Enterococcus spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert®/Quanti-Tray® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% E. faecalis, 6.7% E. faecium, 2.5% E. casseliflavus, 0.4% E. gallinarum, and 11.2% other Enterococcus spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. E. faecium displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the tetM, aph(3′)-IIIa, and ermB genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was gelE. Clonality revealed that E. faecalis isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). E. faecium isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including Enterococcus spp. as an indicator in antibiotic resistance surveillance systems in food animals.
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15
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Shi YZ, Yoshida T, Fujiwara A, Nishiki I. Characterization of lsa(D), a Novel Gene Responsible for Resistance to Lincosamides, Streptogramins A, and Pleuromutilins in Fish Pathogenic Lactococcus garvieae Serotype II. Microb Drug Resist 2021; 27:301-310. [PMID: 32706619 DOI: 10.1089/mdr.2020.0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: Fish pathogenic Lactococcus garvieae serotype II has been isolated from cultured fish species in Japan. This study aimed to investigate the molecular mechanisms of lincomycin (LCM)-resistant L. garvieae serotype II and assess the molecular basis for lincosamides-streptogramins A-pleuromutilins (LSAP)-resistant phenotype. Results: We identified a novel lsa(D)-encoded 497-aa ATP-binding cassette F (ABC-F) protein in the LSAP-resistant strains. Amino acid identities of 41.25-54.73% were obtained between the deduced amino acids from Lsa(D) and other Lsa-type ABC-F proteins. Furthermore, comparative analysis revealed that the allele of lsa(D) with single point mutation at 233 aa position (TGG → TAG; tryptophan→premature termination codon [PTC]) in LSAP-sensitive strains. The minimum inhibitory concentrations of antimicrobials against the lsa(D) complementary strain and lsa(D)-disrupted mutant confirmed that lsa(D) conferred the LSAP-resistant phenotype. The reverse transcription-polymerase chain reaction could not detect the noncoding region of lsa(D) allelic variant in the LSAP-sensitive strains. Additionally, the PTC (TAG) in LCM-sensitive strains was replaced by TGG, CAG, or TAT in the laboratory-induced revertant mutants. Conclusions: The novel lsa(D) conferred the LSAP-resistant phenotype in clinically LCM-resistant L. garvieae serotype II strains. However, the allele of lsa(D) gene containing the PTC was found in L. garvieae serotype II, resulting in the LSAP-susceptible phenotype.
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Affiliation(s)
- Yin-Ze Shi
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | | | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Japan
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16
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Reissier S, Cattoir V. Streptogramins for the treatment of infections caused by Gram-positive pathogens. Expert Rev Anti Infect Ther 2020; 19:587-599. [PMID: 33030387 DOI: 10.1080/14787210.2021.1834851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Streptogramins (pristinamycin and quinupristin-dalfopristin) can be interesting options for the treatment of infections due to Gram-positive cocci, especially multidrug-resistant isolates. AREAS COVERED This review provides an updated overview of structural and activity characteristics, mechanisms of action and resistance, pharmacokinetic/pharmacodynamic, and clinical use of streptogramins. EXPERT OPINION The streptogramin antibiotics act by inhibition of the bacterial protein synthesis. They are composed of two chemically distinct compounds, namely type A and type B streptogramins, which exert a rapid bactericidal activity against a wide range of Gram-positive bacteria (including methicillin-resistant staphylococci and vancomycin-resistant enterococci). Several mechanisms of resistance have been identified in staphylococci and enterococci but the prevalence of streptogramin resistance among clinical isolates remains very low. Even if only a few randomized clinical trials have been conducted, the efficacy of pristinamycin has been largely demonstrated with an extensive use for 50 years in France and some African countries. Despite its effectiveness in the treatment of severe Gram-positive bacterial infections demonstrated in several studies and the low rate of reported resistance, the clinical use of quinupristin-dalfopristin has remained limited, mainly due to its poor tolerance. Altogether, streptogramins (especially pristinamycin) can be considered as potential alternatives for the treatment of Gram-positive infections.
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Affiliation(s)
| | - Vincent Cattoir
- Université De Rennes 1, Unité Inserm U1230, Rennes, France.,Service De Bactériologie-Hygiène Hospitalière, CHU De Rennes, Rennes, France.,Centre National De Référence De La Résistance Aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU De Rennes, Rennes, France
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17
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Gholizadeh P, Köse Ş, Dao S, Ganbarov K, Tanomand A, Dal T, Aghazadeh M, Ghotaslou R, Ahangarzadeh Rezaee M, Yousefi B, Samadi Kafil H. How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance. Infect Drug Resist 2020; 13:1111-1121. [PMID: 32368102 PMCID: PMC7182461 DOI: 10.2147/idr.s247271] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibiotic-resistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.
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Affiliation(s)
- Pourya Gholizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d’Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Khudaverdi Ganbarov
- Department of Microbiology, Baku State University, Baku, Republic of Azerbaijan
| | - Asghar Tanomand
- Department of Basic Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Tuba Dal
- Department of Clinical Microbiology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum. Sci Rep 2020; 10:3937. [PMID: 32127598 PMCID: PMC7054549 DOI: 10.1038/s41598-020-61002-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/13/2020] [Indexed: 11/24/2022] Open
Abstract
For a One-Health investigation of antimicrobial resistance (AMR) in Enterococcus spp., isolates from humans and beef cattle along with abattoirs, manured fields, natural streams, and wastewater from both urban and cattle feedlot sources were collected over two years. Species identification of Enterococcus revealed distinct associations across the continuum. Of the 8430 isolates collected, Enterococcus faecium and Enterococcus faecalis were the main species in urban wastewater (90%) and clinical human isolates (99%); Enterococcus hirae predominated in cattle (92%) and feedlot catch-basins (60%), whereas natural streams harbored environmental Enterococcus spp. Whole-genome sequencing of E. faecalis (n = 366 isolates) and E. faecium (n = 342 isolates), revealed source clustering of isolates, indicative of distinct adaptation to their respective environments. Phenotypic resistance to tetracyclines and macrolides encoded by tet(M) and erm(B) respectively, was prevalent among Enterococcus spp. regardless of source. For E. faecium from cattle, resistance to β-lactams and quinolones was observed among 3% and 8% of isolates respectively, compared to 76% and 70% of human clinical isolates. Clinical vancomycin-resistant E. faecium exhibited high rates of multi-drug resistance, with resistance to all β-lactam, macrolides, and quinolones tested. Differences in the AMR profiles among isolates reflected antimicrobial use practices in each sector of the One-Health continuum.
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19
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Phenotypic and Genotypic Traits of Vancomycin-Resistant Enterococci from Healthy Food-Producing Animals. Microorganisms 2020; 8:microorganisms8020261. [PMID: 32075283 PMCID: PMC7074742 DOI: 10.3390/microorganisms8020261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Food-producing animals may be a reservoir of vancomycin-resistant enterococci (VRE), potentially posing a threat to animal and public health. The aims of this study were to estimate the faecal carriage of VRE among healthy cattle (n = 362), pigs (n = 350), sheep (n = 218), and poultry (n = 102 flocks) in Switzerland, and to characterise phenotypic and genotypic traits of the isolates. VRE were isolated from caecum content of six bovine, and 12 porcine samples respectively, and from pooled faecal matter collected from 16 poultry flock samples. All isolates harboured vanA. Three different types of Tn1546-like elements carrying the vanA operon were identified. Conjugal transfer of vanA to human Enterococcus faecalis strain JH2-2 was observed for porcine isolates only. Resistance to tetracycline and erythromycin was frequent among the isolates. Our data show that VRE harbouring vanA are present in healthy food-producing animals. The vanA gene from porcine isolates was transferable to other enterococci and these isolates might play a role in the dissemination of VRE in the food production chain.
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20
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Molechan C, Amoako DG, Abia ALK, Somboro AM, Bester LA, Essack SY. Molecular epidemiology of antibiotic-resistant Enterococcus spp. from the farm-to-fork continuum in intensive poultry production in KwaZulu-Natal, South Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:868-878. [PMID: 31539992 DOI: 10.1016/j.scitotenv.2019.07.324] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The poultry industry is among the main protein suppliers worldwide. Thus, this study determined the antibiotic resistance and virulence profiles of Enterococcus spp. along the farm-to-fork production chain of an intensive poultry system in the uMgungundlovu District, Kwazulu-Natal, South Africa. Overall, 162 samples along the continuum (growth phase, transport and post-slaughter) were evaluated for the presence of Enterococcus spp. using selective media, biochemical tests and polymerase chain reaction (PCR). Resistance profiles were assessed by Kirby-Bauer disk diffusion method following the WHO-AGISAR recommended antibiotics panel for Enterococcus spp. Antibiotic resistance and virulence genes were detected using real-time PCR. Clonal relatedness was evaluated by REP-PCR. Overall, 131 isolates were recovered across the continuum, (34% E. faecalis, 32% E. faecium, 2% E. gallinarum and 32% other Enterococcus spp.). Resistance to tetracycline (79%), erythromycin (70%), nitrofurantoin (18%), ampicillin (15%), streptomycin (15%), chloramphenicol (10%), ciprofloxacin (4%), tigecycline (4%), gentamicin (4%), teicoplanin (3%) was observed among all Enterococcus spp.; no vancomycin resistance (0%) was recorded. Also, 24% of E. faecium were resistant to quinupristin-dalfopristin. Twenty-four multidrug resistance (MDR) antibiograms were observed across all species; E. faecium (43%) showed the highest frequency of MDR. The most frequently observed antibiotic resistomes were tetM (76%) and ermB (66%) while smaller percentages were noted for aph(3')-IIIa (12%) and vanC1 (1%). Virulence genes efaAFs (100%), cpd (96%) and gelE (80%) were more prevalent in E. faecalis. Clonality revealed that isolates along the continuum were highly diverse with major REP-types consisting of isolates from the same sampling point. This study highlights the diversity of MDR Enterococcus in the food chain with isolates harbouring resistance and virulence genes. These could be reservoirs for the potential transfer of pathogenic enterococci carrying these genes from poultry to humans through the food chain continuum, thus, underscoring the need for routine antibiotic resistance surveillance in food animals.
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Affiliation(s)
- Chantal Molechan
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou M Somboro
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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21
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Ousalem F, Singh S, Chesneau O, Hunt JF, Boël G. ABC-F proteins in mRNA translation and antibiotic resistance. Res Microbiol 2019; 170:435-447. [PMID: 31563533 DOI: 10.1016/j.resmic.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/01/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022]
Abstract
The ATP binding cassette protein superfamily comprises ATPase enzymes which are, for the most part, involved in transmembrane transport. Within this superfamily however, some protein families have other functions unrelated to transport. One example is the ABC-F family, which comprises an extremely diverse set of cytoplasmic proteins. All of the proteins in the ABC-F family characterized to date act on the ribosome and are translation factors. Their common function is ATP-dependent modulation of the stereochemistry of the peptidyl transferase center (PTC) in the ribosome coupled to changes in its global conformation and P-site tRNA binding geometry. In this review, we give an overview of the function, structure, and theories for the mechanisms-of-action of microbial proteins in the ABC-F family, including those involved in mediating resistance to ribosome-binding antibiotics.
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Affiliation(s)
- Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Shikha Singh
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 75724, Paris Cedex 15, France.
| | - John F Hunt
- Department of Biological, 702A Sherman Fairchild Center, Columbia University, New York, NY, 10027, United States.
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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22
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Murina V, Kasari M, Hauryliuk V, Atkinson GC. Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest. Nucleic Acids Res 2019; 46:3753-3763. [PMID: 29415157 PMCID: PMC5909423 DOI: 10.1093/nar/gky050] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022] Open
Abstract
Several ATPases in the ATP-binding cassette F (ABCF) family confer resistance to macrolides, lincosamides and streptogramins (MLS) antibiotics. MLS are structurally distinct classes, but inhibit a common target: the peptidyl transferase (PTC) active site of the ribosome. Antibiotic resistance (ARE) ABCFs have recently been shown to operate through direct ribosomal protection, but the mechanistic details of this resistance mechanism are lacking. Using a reconstituted translational system, we dissect the molecular mechanism of Staphylococcus haemolyticus VgaALC and Enterococcus faecalis LsaA on the ribosome. We demonstrate that VgaALC is an NTPase that operates as a molecular machine strictly requiring NTP hydrolysis (not just NTP binding) for antibiotic protection. Moreover, when bound to the ribosome in the NTP-bound form, hydrolytically inactive EQ2 ABCF ARE mutants inhibit peptidyl transferase activity, suggesting a direct interaction between the ABCF ARE and the PTC. The likely structural candidate responsible for antibiotic displacement by wild type ABCF AREs, and PTC inhibition by the EQ2 mutant, is the extended inter-ABC domain linker region. Deletion of the linker region renders wild type VgaALC inactive in antibiotic protection and the EQ2 mutant inactive in PTC inhibition.
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Affiliation(s)
- Victoriia Murina
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Marje Kasari
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Gemma C Atkinson
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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23
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Lemonidis K, Salih TS, Dancer SJ, Hunter IS, Tucker NP. Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland. PLoS One 2019; 14:e0218185. [PMID: 31194809 PMCID: PMC6563996 DOI: 10.1371/journal.pone.0218185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022] Open
Abstract
Multi-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two neighbouring hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains in both hospitals, while the fifth was multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested vanA-type pstS-null VREfm strains (5 English and 68 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.
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Affiliation(s)
- Kimon Lemonidis
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
| | - Talal S. Salih
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Stephanie J. Dancer
- Department of Microbiology, Hairmyres Hospital, NHS Lanarkshire, United Kingdom
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Nicholas P. Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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Abstract
During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.
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Shaw TD, Fairley DJ, Schneiders T, Pathiraja M, Hill RLR, Werner G, Elborn JS, McMullan R. The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism. Eur J Clin Microbiol Infect Dis 2018; 37:959-967. [PMID: 29478197 PMCID: PMC5916979 DOI: 10.1007/s10096-018-3214-x] [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] [Received: 01/10/2018] [Accepted: 02/13/2018] [Indexed: 12/01/2022]
Abstract
High-throughput sequencing (HTS) has successfully identified novel resistance genes in enterococci and determined clonal relatedness in outbreak analysis. We report the use of HTS to investigate two concurrent outbreaks of glycopeptide-resistant Enterococcus faecium (GRE) with an uncharacterised resistance mechanism to quinupristin-dalfopristin (QD). Seven QD-resistant and five QD-susceptible GRE isolates from a two-centre outbreak were studied. HTS was performed to identify genes or predicted proteins that were associated with the QD-resistant phenotype. MLST and SNP typing on HTS data was used to determine clonal relatedness. Comparative genomic analysis confirmed this GRE outbreak involved two distinct clones (ST80 and ST192). HTS confirmed the absence of known QD resistance genes, suggesting a novel mechanism was conferring resistance. Genomic analysis identified two significant genetic determinants with explanatory power for the high level of QD resistance in the ST80 QD-resistant clone: an additional 56aa leader sequence at the N-terminus of the lsaE gene and a transposon containing seven genes encoding proteins with possible drug or drug-target modification activities. However, HTS was unable to conclusively determine the QD resistance mechanism and did not reveal any genetic basis for QD resistance in the ST192 clone. This study highlights the usefulness of HTS in deciphering the degree of relatedness in two concurrent GRE outbreaks. Although HTS was able to reveal some genetic candidates for uncharacterised QD resistance, this study demonstrates the limitations of HTS as a tool for identifying putative determinants of resistance to QD.
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Affiliation(s)
- Timothy D Shaw
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK. .,Department of Medical Microbiology, Kelvin Laboratory, Royal Victoria Hospital, Belfast, Northern Ireland, UK.
| | - D J Fairley
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Department of Medical Microbiology, Kelvin Laboratory, Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - T Schneiders
- Division of Infection and Pathway Medicine, University of Edinburgh Medical School, Edinburgh, Scotland, UK
| | - M Pathiraja
- Department of Medical Microbiology, Kelvin Laboratory, Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - R L R Hill
- Antimicrobial Resistance & Healthcare-Associated Infection, Public Health England, London, UK
| | - G Werner
- National Reference Centre for Staphylococci and Enterococci, Robert Koch-Institute, Wernigerode Branch, Berlin, Germany
| | - J S Elborn
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - R McMullan
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK.,Department of Medical Microbiology, Kelvin Laboratory, Royal Victoria Hospital, Belfast, Northern Ireland, UK
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26
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Miller WR, Murray BE, Rice LB, Arias CA. Vancomycin-Resistant Enterococci: Therapeutic Challenges in the 21st Century. Infect Dis Clin North Am 2017; 30:415-439. [PMID: 27208766 DOI: 10.1016/j.idc.2016.02.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vancomycin-resistant enterococci are serious health threats due in part to their ability to persist in rugged environments and their propensity to acquire antibiotic resistance determinants. Enterococci have now established a home in our hospitals and possess mechanisms to defeat most currently available antimicrobials. This article reviews the history of the struggle with this pathogen, what is known about the traits associated with its rise in the modern medical environment, and the current understanding of therapeutic approaches in severe infections caused by these microorganisms. As the 21st century progresses, vancomycin-resistant enterococci continue to pose a daunting clinical challenge.
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Affiliation(s)
- William R Miller
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Barbara E Murray
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA; Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Louis B Rice
- Departments of Medicine, Microbiology and Immunology, Warren Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Cesar A Arias
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA; Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA; Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Avenue Cra 9 No. 131 A - 02, Bogotá, Colombia.
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28
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Schwarz S, Shen J, Kadlec K, Wang Y, Brenner Michael G, Feßler AT, Vester B. Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. Cold Spring Harb Perspect Med 2016; 6:a027037. [PMID: 27549310 PMCID: PMC5088508 DOI: 10.1101/cshperspect.a027037] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.
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Affiliation(s)
- Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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29
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Discovery of Novel MLSB Resistance Methylase Genes and Their Associated Genetic Elements in Staphylococci. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Characterization of a Novel lsa(E)- and lnu(B)-Carrying Structure Located in the Chromosome of a Staphylococcus aureus Sequence Type 398 Strain. Antimicrob Agents Chemother 2015; 60:1164-6. [PMID: 26596938 DOI: 10.1128/aac.01178-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Si H, Zhang WJ, Chu S, Wang XM, Dai L, Hua X, Dong Z, Schwarz S, Liu S. Novel plasmid-borne multidrug resistance gene cluster including lsa(E) from a linezolid-resistant Enterococcus faecium isolate of swine origin. Antimicrob Agents Chemother 2015; 59:7113-6. [PMID: 26324271 PMCID: PMC4604366 DOI: 10.1128/aac.01394-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 08/20/2015] [Indexed: 01/18/2023] Open
Abstract
A novel nonconjugative plasmid of 28,489 bp from a porcine linezolid-resistant Enterococcus faecium isolate was completely sequenced. This plasmid harbored a novel type of multiresistance gene cluster that comprised the resistance genes lnu(B), lsa(E), spw, aadE, aphA3, and two copies of erm(B), which account for resistance to macrolides, lincosamides, streptogramins, pleuromutilins, streptomycin, spectinomycin, and kanamycin/neomycin. Structural comparisons suggested that this plasmid might have developed from other enterococcal plasmids by insertion element (IS)-mediated interplasmid recombination processes.
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Affiliation(s)
- Hongbin Si
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Wan-Jiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shengbo Chu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiu-Mei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Xin Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhimin Dong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Miller WR, Munita JM, Arias CA. Mechanisms of antibiotic resistance in enterococci. Expert Rev Anti Infect Ther 2015; 12:1221-36. [PMID: 25199988 DOI: 10.1586/14787210.2014.956092] [Citation(s) in RCA: 364] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multidrug-resistant (MDR) enterococci are important nosocomial pathogens and a growing clinical challenge. These organisms have developed resistance to virtually all antimicrobials currently used in clinical practice using a diverse number of genetic strategies. Due to this ability to recruit antibiotic resistance determinants, MDR enterococci display a wide repertoire of antibiotic resistance mechanisms including modification of drug targets, inactivation of therapeutic agents, overexpression of efflux pumps and a sophisticated cell envelope adaptive response that promotes survival in the human host and the nosocomial environment. MDR enterococci are well adapted to survive in the gastrointestinal tract and can become the dominant flora under antibiotic pressure, predisposing the severely ill and immunocompromised patient to invasive infections. A thorough understanding of the mechanisms underlying antibiotic resistance in enterococci is the first step for devising strategies to control the spread of these organisms and potentially establish novel therapeutic approaches.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, University of Texas Medical School, 6431 Fannin St. Rm. MSB 2.112, Houston, TX 77030, USA
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Barber KE, King ST, Stover KR, Pogue JM. Therapeutic options for vancomycin-resistant enterococcal bacteremia. Expert Rev Anti Infect Ther 2015; 13:363-77. [DOI: 10.1586/14787210.2015.1001839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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Bikard D, Euler C, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 2014; 32:1146-50. [PMID: 25282355 PMCID: PMC4317352 DOI: 10.1038/nbt.3043] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/09/2014] [Indexed: 01/14/2023]
Abstract
Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas9 (refs.1,2) delivered by a bacteriophage. We show that Cas9, reprogrammed to target virulence genes, kills virulent, but not avirulent, Staphylococcus aureus. Reprogramming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also show that CRISPR-Cas9 antimicrobials function in vivo to kill S. aureus in a mouse skin colonization model. This technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.
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Affiliation(s)
- David Bikard
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Chad Euler
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
| | - Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | | | | | - Xavier Duportet
- INRIA Paris-Rocquencourt, Rocquencourt, France
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Vincent A. Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
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35
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van Duijkeren E, Greko C, Pringle M, Baptiste KE, Catry B, Jukes H, Moreno MA, Pomba MCMF, Pyörälä S, Rantala M, Ružauskas M, Sanders P, Teale C, Threlfall EJ, Torren-Edo J, Törneke K. Pleuromutilins: use in food-producing animals in the European Union, development of resistance and impact on human and animal health. J Antimicrob Chemother 2014; 69:2022-31. [PMID: 24793902 DOI: 10.1093/jac/dku123] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Pleuromutilins (tiamulin and valnemulin) are antimicrobial agents that are used mainly in veterinary medicine, especially for swine and to a lesser extent for poultry and rabbits. In pigs, tiamulin and valnemulin are used to treat swine dysentery, spirochaete-associated diarrhoea, porcine proliferative enteropathy, enzootic pneumonia and other infections where Mycoplasma is involved. There are concerns about the reported increases in the MICs of tiamulin and valnemulin for porcine Brachyspira hyodysenteriae isolates from different European countries, as only a limited number of antimicrobials are available for the treatment of swine dysentery where resistance to these antimicrobials is already common and widespread. The loss of pleuromutilins as effective tools to treat swine dysentery because of further increases in resistance or as a consequence of restrictions would present a considerable threat to pig health, welfare and productivity. In humans, only one product containing pleuromutilins (retapamulin) is authorized currently for topical use; however, products for oral and intravenous administration to humans with serious multidrug-resistant skin infections and respiratory infections, including those caused by methicillin-resistant Staphylococcus aureus (MRSA), are being developed. The objective of this review is to summarize the current knowledge on the usage of pleuromutilins, resistance development and the potential impact of this resistance on animal and human health.
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Affiliation(s)
| | | | | | | | | | - Helen Jukes
- Veterinary Medicines Directorate, Addlestone, UK
| | - Miguel A Moreno
- Faculty of Veterinary Medicine, Complutense University, Madrid, Spain
| | | | - Satu Pyörälä
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Merja Rantala
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Modestas Ružauskas
- Veterinary Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Pascal Sanders
- Agence Nationale de Sécurité Sanitaire (ANSES), Fougères, France
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Characterization of sal(A), a novel gene responsible for lincosamide and streptogramin A resistance in Staphylococcus sciuri. Antimicrob Agents Chemother 2014; 58:3335-41. [PMID: 24687494 DOI: 10.1128/aac.02797-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Natural resistance to lincosamides and streptogramins A (LSA), which is a species characteristic of Bacillus subtilis and Enterococcus faecalis, has never been documented in the Staphylococcus genus. We investigate here the molecular basis of the LSA phenotype exhibited by seven reference strains of Staphylococcus sciuri, including the type strains of the three described subspecies. By whole-genome sequencing of strain ATCC 29059, we identified a candidate gene that encodes an ATP-binding cassette protein similar to the Lsa and VmlR resistance determinants. Isolation and reverse transcription-quantitative PCR (qRT-PCR) expression studies confirmed that Sal(A) can confer a moderate resistance to lincosamides (8 times the MIC of lincomycin) and a high-level resistance to streptogramins A (64 times the MIC of pristinamycin II). The chromosomal location of sal(A) between two housekeeping genes of the staphylococcal core genome supports the gene's ancient origins and thus innate resistance to these antimicrobials within S. sciuri subspecies.
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Hatoum-Aslan A, Marraffini LA. Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Curr Opin Microbiol 2014; 17:82-90. [PMID: 24581697 PMCID: PMC3942673 DOI: 10.1016/j.mib.2013.12.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 02/08/2023]
Abstract
CRISPR-Cas systems protect prokaryotes from viruses and plasmids and function primarily as an adaptive immune system in these organisms. Recent discoveries, however, revealed unexpected roles for CRISPR loci as barriers to horizontal gene transfer and as modulators of gene expression. We review how both of these functions of CRISPR-Cas systems can affect the emergence and virulence of human bacterial pathogens.
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Affiliation(s)
- Asma Hatoum-Aslan
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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38
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Cattoir V, Giard JC. Antibiotic resistance inEnterococcus faeciumclinical isolates. Expert Rev Anti Infect Ther 2014; 12:239-48. [DOI: 10.1586/14787210.2014.870886] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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