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Zaidi SEZ, Zaheer R, Zovoilis A, McAllister TA. Enterococci as a One Health indicator of antimicrobial resistance. Can J Microbiol 2024; 70:303-335. [PMID: 38696839 DOI: 10.1139/cjm-2024-0024] [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: 05/04/2024]
Abstract
The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.
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Affiliation(s)
- Sani-E-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Kardos G, Laczkó L, Kaszab E, Timmer B, Szarka K, Prépost E, Bányai K. Phylogenetic Analysis of the Genes in D-Ala-D-Lactate Synthesizing Glycopeptide Resistance Operons: The Different Origins of Functional and Regulatory Genes. Antibiotics (Basel) 2024; 13:573. [PMID: 39061255 PMCID: PMC11273654 DOI: 10.3390/antibiotics13070573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 07/28/2024] Open
Abstract
The phylogenetic relationships of glycopeptide resistance proteins were investigated. The amino acid sequences of vanA, vanB, vanR and vanS were used as queries to search against bacterial genomes in the NCBI RefSeq database. Hits with >60% amino acid identity and >90% query coverage were aligned, and phylogenetic trees were reconstructed. The ligase gene phylogenies were highly similar for both queries, revealing two major clusters. One contained [[vanA:vanM][vanB:vanD]vanF] and related proteins, with proteins from different Bacillaceae, mostly from Paenibacillus spp., in basal positions to all, except vanB. Ligases from streptomycetes formed the other cluster. The relative positions of vanH and vanX differed from those of the associated ligases, but the basal position of the Paenibacillus spp. and the separation of proteins of Streptomyces origin were similar. The accessory genes vanW, vanY and vanZ were associated with vanB, vanA/vanM and vanA, respectively; the basal branches were always proteins from different Bacillaceae but never from streptomycetes. Multiple homologs of the regulatory genes vanR and vanS were found in the genomes; those associated with the different ligases were unique to the ligases. Similarly to the accessory genes, vanRS from Bacillales and Clostridia, but never from streptomycetes, was found in the basal positions. In conclusion, the core genes vanA/B/D/F/M, vanH and vanX originate most probably from glycopeptide-producing streptomycetes, with Paenibacillus spp. (or other Bacillaceae) mediating the transfer, while the accessory genes and the regulatory apparatus probably originate from these Bacillaceae.
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Affiliation(s)
- Gábor Kardos
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- HUN-REN-UD Conservation Biology Research Group, H-4032 Debrecen, Hungary
| | - Eszter Kaszab
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1078 Budapest, Hungary
| | - Bálint Timmer
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- Department of Medical Microbiology and Immunology, University of Pécs, H-7624 Pécs, Hungary
| | - Krisztina Szarka
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Eszter Prépost
- Department of Health Industry, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Krisztián Bányai
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, H-1143 Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, H-1078 Budapest, Hungary
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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 PMCID: PMC11237509 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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4
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BELITSKY BORISR. Histidine kinase-mediated cross-regulation of the vancomycin-resistance operon in Clostridioides difficile. Mol Microbiol 2024; 121:1182-1199. [PMID: 38690761 PMCID: PMC11176017 DOI: 10.1111/mmi.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
The dipeptide D-Ala-D-Ala is an essential component of peptidoglycan and the target of vancomycin. Most Clostridioides difficile strains possess the vanG operon responsible for the synthesis of D-Ala-D-Ser, which can replace D-Ala-D-Ala in peptidoglycan. The C. difficile vanG operon is regulated by a two-component system, VanRS, but is not induced sufficiently by vancomycin to confer resistance to this antibiotic. Surprisingly, in the absence of the VanS histidine kinase (HK), the vanG operon is still induced by vancomycin and also by another antibiotic, ramoplanin, in a VanR-dependent manner. This suggested the cross-regulation of VanR by another HK or kinases that are activated in the presence of certain lipid II-targeting antibiotics. We identified these HKs as CD35990 and CD22880. However, mutations in either or both HKs did not affect the regulation of the vanG operon in wild-type cells suggesting that intact VanS prevents the cross-activation of VanR by non-cognate HKs. Overproduction of VanR in the absence of VanS, CD35990, and CD22880 led to high expression of the vanG operon indicating that VanR can potentially utilize at least one more phosphate donor for its activation. Candidate targets of CD35990- and CD22880-mediated regulation in the presence of vancomycin or ramoplanin were identified by RNA-Seq.
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Affiliation(s)
- BORIS R. BELITSKY
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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5
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Baines SL, Guérillot R, Ballard S, Johnson PDR, Stinear TP, Roberts S, Howden BP. Genomic investigation of the emergence of vanD vancomycin-resistant Enterococcus faecium. Access Microbiol 2023; 5:000712.v3. [PMID: 38188239 PMCID: PMC10765050 DOI: 10.1099/acmi.0.000712.v3] [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: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Vancomycin-resistant Enterococcus (VRE) is an increasingly identified cause of human disease, with most infections resulting from the vanA and vanB genotypes; less is known about other clinically relevant genotypes. Here we report a genomic exploration of a vanD VRE faecium (VREfm), which arose de novo during a single infectious episode. The genomes of the vancomycin-susceptible E. faecium (VSEfm) recipient and resulting VREfm were subjected to long-read sequencing and closed, with whole-genome alignments, cross-mapping and orthologue clustering used to identify genomic variation. Three key differences were identified. (i) The VREfm chromosome gained a 142.6 kb integrative conjugative element (ICE) harbouring the vanD locus. (ii) The native ligase (ddl) was disrupted by an ISEfm1 insertion. (iii) A large 1.74 Mb chromosomal inversion of unknown consequence occurred. Alignment and phylogenetic-based comparisons of the VREfm with a global collection of vanD-harbouring genomes identified strong similarities in the 120-160 kb genomic region surrounding vanD, suggestive of a common mobile element and integration site, irrespective of the diverse taxonomic, geographical and host origins of the isolates. This isolate diversity revealed that this putative ICE (and its source) is globally disseminated and is capable of being acquired by different genera. Although the incidence of vanD VREfm is low, understanding its emergence and potential for spread is crucial for the ongoing efforts to reduce antimicrobial resistance.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Paul D. R. Johnson
- Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sally Roberts
- Department of Microbiology, LabPlus, Auckland City Hospital, Auckland, New Zealand
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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6
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BELITSKY BORISR. VanG- and D-Ala-D-Ser-dependent peptidoglycan synthesis and vancomycin resistance in Clostridioides difficile. Mol Microbiol 2022; 118:526-540. [PMID: 36065735 PMCID: PMC9671823 DOI: 10.1111/mmi.14980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022]
Abstract
A Clostridioides difficile strain deficient in the ddl gene is unable to synthesize the dipeptide D-Ala-D-Ala, an essential component of peptidoglycan and the target of vancomycin. We isolated spontaneous suppressors of a ∆ddl mutation that allowed cell growth in the absence of D-Ala-D-Ala. The mutations caused constitutive or partly constitutive expression of the vancomycin-inducible vanG operon responsible for the synthesis of D-Ala-D-Ser, which can replace D-Ala-D-Ala in peptidoglycan. The mutations mapped to the vanS or vanR genes, which regulate expression of the vanG operon. The constitutive level of vanG expression was about 10-fold above that obtained by vancomycin induction. The incorporation of D-Ala-D-Ser into peptidoglycan due to high expression of the vanG operon conferred only low-level resistance to vancomycin, but VanG was found to synthesize D-Ala-D-Ala in addition to D-Ala-D-Ser. However, the same, low resistance to vancomycin was also observed in cells completely unable to synthesize D-Ala-D-Ala and grown in the presence of D-Ala-D-Ser. D-Ala-D-Ala presence was required for efficient vancomycin induction of the vanG operon showing that vancomycin is not by itself able to activate VanS. D-Ala-D-Ser, similar to D-Ala-D-Ala, served as an anti-activator of DdlR, the positive regulator of the ddl gene, thereby coupling vanG and ddl expression.
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Affiliation(s)
- BORIS R. BELITSKY
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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7
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Hashimoto Y, Hisatsune J, Suzuki M, Kurushima J, Nomura T, Hirakawa H, Kojima N, Ono Y, Hasegawa Y, Tanimoto K, Sugai M, Tomita H. Elucidation of host diversity of the VanD-carrying genomic islands in enterococci and anaerobes. JAC Antimicrob Resist 2022; 4:dlab189. [PMID: 34993479 PMCID: PMC8725431 DOI: 10.1093/jacamr/dlab189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022] Open
Abstract
Background VanD is a rare type of vancomycin resistance worldwide. However, the host diversity of the vanD gene cluster and the structural similarity of their genomic islands are not well understood. Methods Three VanD-type Enterococcus faecium strains (AA620, AA622 and AA624) isolated from a Japanese patient who underwent vancomycin treatment in 2017 were analysed. This study utilized WGS analysis to characterize the three VanD-type E. faecium strains and describes the diversity of hosts possessing VanD-carrying genomic islands. Results The three isolates exhibited variable MICs of vancomycin. In the relatively vancomycin-resistant AA620, mutations were identified in vanSD and ddl. The strains AA622 and AA624 had intact ddl and harboured two vanD gene clusters. qRT-PCR results revealed the ddl mutation to be a factor affecting the high vancomycin resistance range of AA620. WGS data showed the 155 kb and 185 kb genomic islands harbouring the vanD gene cluster inserted in the coding region of the lysS gene, located in the chromosome in AA620 and AA622/624, respectively. Comparing the VanD-carrying genomic islands to available sequences of other enterococci and enteric anaerobes revealed how the genomic islands of these organisms isolated worldwide shared similar core genes and backbones. These anaerobes belonged to various genera within the order Eubacteriales. The phylogenetic cluster of the genomic island core genome alignment did not correlate with the host-species lineage, indicating horizontal gene transfer in the gut microbiota. Conclusions By horizontal gene transfer, various bacteria forming the gut microbiota maintain VanD-carrying genomic islands.
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Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Junzo Hisatsune
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan
| | - Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Naoko Kojima
- Infection Control Team, Gunma Prefectural Cardiovascular Center, 3-12 Ko Kameizumi-machi, Maebashi, Gunma 371-0004, Japan
| | - Yuichi Ono
- Infection Control Team, Gunma Prefectural Cardiovascular Center, 3-12 Ko Kameizumi-machi, Maebashi, Gunma 371-0004, Japan
| | - Yutaka Hasegawa
- Infection Control Team, Gunma Prefectural Cardiovascular Center, 3-12 Ko Kameizumi-machi, Maebashi, Gunma 371-0004, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Motoyuki Sugai
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8551, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
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Novel genomic islands and a new vanD-subtype in the first sporadic VanD-type vancomycin resistant enterococci in Norway. PLoS One 2021; 16:e0255187. [PMID: 34297779 PMCID: PMC8301612 DOI: 10.1371/journal.pone.0255187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/11/2021] [Indexed: 02/02/2023] Open
Abstract
Background Vancomycin-resistant enterococci (VRE) represent several types of transferable vancomycin resistance gene clusters. The vanD type, associated with moderate to high level vancomycin resistance, has only sporadically been described in clinical isolates. The aim of this study was to perform a genetic characterization of the first VanD-type VRE strains detected in Norway. Methods The VanD-type VRE-strains (n = 6) from two patient cases were examined by antimicrobial susceptibility testing and whole genome sequencing (WGS) to uncover Van-phenotype, strain phylogeny, the vanD gene clusters, and their genetic surroundings. The putative transferability of vanD was examined by circularization PCR and filter mating. Results The VanD-type Enterococcus faecium (n = 4) and Enterococcus casseliflavus (n = 2) strains recovered from two cases (A and B), expressed moderate to high level vancomycin resistance (MIC 64—>256 mg/L) and various levels of teicoplanin susceptibility (MIC 2—>256 mg/L). WGS analyses revealed phylogenetically different E. faecium strains (A1, A2, and A3 of case A and B1 from case B) as well as vanD gene clusters located on different novel genomic islands (GIs). The E. casseliflavus strains (B2 and B3 of case B) were not clonally related, but harbored nearly identical novel GIs. The vanD cluster of case B strains represents a novel vanD-subtype. All the vanD-GIs were integrated at the same chromosomal site and contained genes consistent with a Clostridiales origin. Circular forms of the vanD-GIs were detected in all strains except B1. Transfer of vanD to an E. faecium recipient was unsuccessful. Conclusions We describe the first VanD-type E. casseliflavus strains, a novel vanD-subtype, and three novel vanD-GIs with a genetic content consistent with a Clostridiales order origin. Despite temporal occurrence, case A and B E. faecium strains were phylogenetically diverse and harbored different vanD subtypes and vanD-GIs.
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Marom R, Mandel D, Haham A, Berger I, Ovental A, Raskind C, Grisaru-Soen G, Adler A, Lellouche J, Schwartz D, Carmeli Y, Schechner V. A silent outbreak of vancomycin-resistant Enterococcus faecium in a neonatal intensive care unit. Antimicrob Resist Infect Control 2020; 9:87. [PMID: 32546210 PMCID: PMC7298964 DOI: 10.1186/s13756-020-00755-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
Objective To describe the containment of a widespread silent outbreak of vancomycin-resistant Enterococcus faecium (VRE-fm) in the Tel-Aviv Medical Center (TASMC) neonatal intensive care unit (NICU). Methods Setting - an NICU, participants - 49 cases of VRE-fm-colonized neonatal inpatients. Results A newborn was transferred from the TASMC NICU to another hospital and screened positive for VRE-fm upon arrival. All TASMC NICU patients were then immediately screened for VRE and 21/38 newborns were identified as VRE carriers. Interventional measures were strictly enforced. By the end of the outbreak, 49 cases of VRE carriage had been identified. There were no VRE clinical infections. The source of the outbreak was not identified. Conclusion Our study highlights the importance of screening implementation in a NICU setting since this outbreak could have been prevented by active screening of all out-born transfer patients and by having adopted mandatory screening into the NICU’s routine procedures. Screening for multi-drug resistant organisms upon admission of all transferred patients to the NICU has been implemented.
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Affiliation(s)
- Ronella Marom
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Dror Mandel
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alon Haham
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Irit Berger
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amit Ovental
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Craig Raskind
- Department of Neonatology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Weizmann Street, 6423906, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Galia Grisaru-Soen
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatric Infectious Disease Unit, Dana Dwek Children;s Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Amos Adler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jonathan Lellouche
- National Laboratory for Antibiotic Resistance and Investigation of Outbreaks in Medical Institutions, National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - David Schwartz
- National Laboratory for Antibiotic Resistance and Investigation of Outbreaks in Medical Institutions, National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel
| | - Yehuda Carmeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,National Laboratory for Antibiotic Resistance and Investigation of Outbreaks in Medical Institutions, National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Department of Epidemiology and Preventive Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Vered Schechner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Epidemiology and Preventive Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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10
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Akpınar Kankaya D, Tuncer Y. Antibiotic resistance in vancomycin‐resistant lactic acid bacteria (VRLAB) isolated from foods of animal origin. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Didem Akpınar Kankaya
- Department of Food Engineering Faculty of Engineering Süleyman Demirel University Isparta Turkey
- Department of Food Technology Gelendost Vocational School Isparta Uygulamalı Bilimler University Isparta Turkey
| | - Yasin Tuncer
- Department of Food Engineering Faculty of Engineering Süleyman Demirel University Isparta Turkey
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11
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Shen WJ, Deshpande A, Hevener KE, Endres BT, Garey KW, Palmer KL, Hurdle JG. Constitutive expression of the cryptic vanGCd operon promotes vancomycin resistance in Clostridioides difficile clinical isolates. J Antimicrob Chemother 2020; 75:859-867. [PMID: 31873741 PMCID: PMC7069472 DOI: 10.1093/jac/dkz513] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/01/2019] [Accepted: 11/09/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To describe, for the first time (to the best of our knowledge), the genetic mechanisms of vancomycin resistance in clinical isolates of Clostridioides difficile ribotype 027. METHODS Clinical isolates and laboratory mutants were analysed: genomically to identify resistance mutations; by transcriptional analysis of vanGCd, the vancomycin resistance operon encoding lipid II d-alanine-d-serine that is less bound by vancomycin than native lipid II d-alanine-d-alanine; by imaging of vancomycin binding to cell walls; and for changes in vancomycin bactericidal activity and autolysis. RESULTS Vancomycin-resistant laboratory mutants and clinical isolates acquired mutations to the vanSR two-component system that regulates vanGCd. The substitutions impaired VanSR's function, resulting in constitutive transcription of vanGCd. Resistance was reversed by silencing vanG, encoding d-alanine-d-serine ligase in the vanGCd operon. In resistant cells, vancomycin was less bound to the cell wall septum, the site where vancomycin interacts with lipid II. Vancomycin's bactericidal activity was reduced against clinical isolates and laboratory mutants (64 and ≥1024 mg/L, respectively) compared with WT strains (4 mg/L). Truncation of the potassium transporter TrkA occurred in laboratory mutants, which were refractory to autolysis, accounting for their survival in high drug concentrations. CONCLUSIONS Ribotype 027 evolved first-step resistance to vancomycin by constitutively expressing vanGCd, which is otherwise silent. Experimental evolutions and bactericidal assays show that ribotype 027 can acquire mutations to drastically enhance its tolerance to vancomycin. Thus, further epidemiological studies are warranted to examine the extent to which vancomycin resistance impacts clinical outcomes and the potential for these strains to evolve higher-level resistance, which would be devastating.
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Affiliation(s)
- Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
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12
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Manson AL, Van Tyne D, Straub TJ, Clock S, Crupain M, Rangan U, Gilmore MS, Earl AM. Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. Appl Environ Microbiol 2019; 85:e01559-19. [PMID: 31471308 PMCID: PMC6821970 DOI: 10.1128/aem.01559-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.
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Affiliation(s)
- Abigail L Manson
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daria Van Tyne
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Timothy J Straub
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah Clock
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael Crupain
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Urvashi Rangan
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael S Gilmore
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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13
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Sheikh AF, Hamidi H, Shahin M, Shahmohammadi S. The prevalence of phenotypic and genotypic glycopeptides resistance among clinical isolates of enterococci in Ahvaz, southwestern Iran. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant public health threat and was listed on the World Health Organization's 2017 list of high-priority pathogens for which new treatments are urgently needed. Treatment options for invasive VREfm infections are very limited, and outcomes are often poor. Whole-genome sequencing is providing important new insights into VREfm evolution, drug resistance and hospital adaptation, and is increasingly being used to track VREfm transmission within hospitals to detect outbreaks and inform infection control practices. This mini-review provides an overview of recent data on the use of genomics to understand and respond to the global problem of VREfm.
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Affiliation(s)
- Claire Gorrie
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen Carter
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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15
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Lee T, Pang S, Abraham S, Coombs GW. Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future. J Glob Antimicrob Resist 2018; 16:36-47. [PMID: 30149193 DOI: 10.1016/j.jgar.2018.08.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 01/23/2023] Open
Abstract
Enterococcus faecium is a robust opportunistic pathogen that is most commonly found as a commensal of the human and animal gut but can also survive in the environment. Since the introduction and use of antimicrobials, E. faecium has been found to rapidly acquire resistance genes that, when expressed, can effectively circumvent the effects of most antimicrobials. The rapid acquisition of multiple antimicrobial resistances has led to the adaptation of specific E. faecium clones in the hospital environment, collectively known as clonal complex 17 (CC17). CC17 E. faecium are responsible for a significant proportion of hospital-associated infections, which can cause severe morbidity and mortality. Here we review the history of E. faecium from commensal to a significant hospital-associated pathogen, its robust phenotypic characteristics, commonly used laboratory typing schemes, and antimicrobial resistances with a focus on vancomycin and its associated mechanism of resistance. Finally, we review the global epidemiology of vancomycin-resistant E. faecium and potential solutions to problems faced in public health.
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Affiliation(s)
- Terence Lee
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Perth, WA, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Perth, WA, Australia; PathWest Laboratory Medicine, Nedlands, WA, Australia
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Perth, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Perth, WA, Australia; PathWest Laboratory Medicine, Nedlands, WA, Australia.
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16
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Nosocomial outbreak of vanD-carrying vancomycin-resistant Enterococcus faecium. Infect Control Hosp Epidemiol 2018; 39:1266-1268. [PMID: 30111383 DOI: 10.1017/ice.2018.174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Identification of a Novel Genomic Island Associated with vanD-Type Vancomycin Resistance in Six Dutch Vancomycin-Resistant Enterococcus faecium Isolates. Antimicrob Agents Chemother 2018; 62:AAC.01793-17. [PMID: 29311068 DOI: 10.1128/aac.01793-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/19/2017] [Indexed: 01/06/2023] Open
Abstract
Genomic comparison of the first six Dutch vanD-type vancomycin-resistant Enterococcus faecium (VRE) isolates with four vanD gene clusters from other enterococcal species and anaerobic gut commensals revealed that the vanD gene cluster was located on a genomic island of variable size. Phylogenetic inferences revealed that the Dutch VRE isolates were genetically not closely related and that genetic variation of the vanD-containing genomic island was not species specific, suggesting that this island is transferred horizontally between enterococci and anaerobic gut commensals.
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18
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Zhang G, Lin X, Cai J, Zhang R, Xiu H, Tian B, Cui W. Characteristics of clinical and environmental vanM-carrying vancomycin-resistant enterococci isolates from an infected patient. Int J Antimicrob Agents 2018; 51:932-935. [PMID: 29339295 DOI: 10.1016/j.ijantimicag.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/03/2018] [Accepted: 01/06/2018] [Indexed: 11/17/2022]
Abstract
vanM, an uncommon glycopeptide resistance gene, was first identified in an Enterococcus faecium isolate (Efm-HS0661) from Shanghai, China, in 2006 and has been predominant in this city since 2011. A vanM-carrying E. faecium was isolated from the bloodstream of a patient in an intensive care unit (ICU) in Hangzhou, China, in 2014. Further surveillance screening of a rectal swab and environmental surfaces of the patient yielded a large number of vanM-positive E. faecium. These isolates (including 1 from the bloodstream, 1 from the rectal swab and 43 representative isolates from environmental samples) were classified into four pulsed-field gel electrophoresis (PFGE) patterns and two sequence types (ST78 and ST564). PCR amplification and sequence analysis indicated that the genetic structure surrounding the vanM gene of these isolates was similar to that of the original vanM-carrying isolate Efm-HS0661. This study highlights the emergence of infections and environmental contamination caused by vanM-carrying E. faecium in an ICU of another Chinese city outside of Shanghai.
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Affiliation(s)
- Gensheng Zhang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Xiuhui Lin
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China; Department of Respiratory Medicine, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jiachang Cai
- Clinical Microbiology Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Rong Zhang
- Clinical Microbiology Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huiqing Xiu
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Baoping Tian
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Wei Cui
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
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19
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Ahmed MO, Baptiste KE. Vancomycin-Resistant Enterococci: A Review of Antimicrobial Resistance Mechanisms and Perspectives of Human and Animal Health. Microb Drug Resist 2017; 24:590-606. [PMID: 29058560 DOI: 10.1089/mdr.2017.0147] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistant infections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including "last resort antibiotics" ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.
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Affiliation(s)
- Mohamed O Ahmed
- 1 Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli , Tripoli, Libya
| | - Keith E Baptiste
- 2 Department of Veterinary Medicine, Danish Medicines Agency , Copenhagen South, Denmark
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20
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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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21
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Zeng D, Debabov D, Hartsell TL, Cano RJ, Adams S, Schuyler JA, McMillan R, Pace JL. Approved Glycopeptide Antibacterial Drugs: Mechanism of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026989. [PMID: 27663982 DOI: 10.1101/cshperspect.a026989] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The glycopeptide antimicrobials are a group of natural product and semisynthetic glycosylated peptides that show antibacterial activity against Gram-positive organisms through inhibition of cell-wall synthesis. This is achieved primarily through binding to the d-alanyl-d-alanine terminus of the lipid II bacterial cell-wall precursor, preventing cross-linking of the peptidoglycan layer. Vancomycin is the foundational member of the class, showing both clinical longevity and a still preferential role in the therapy of methicillin-resistant Staphylococcus aureus and of susceptible Enterococcus spp. Newer lipoglycopeptide derivatives (telavancin, dalbavancin, and oritavancin) were designed in a targeted fashion to increase antibacterial activity, in some cases through secondary mechanisms of action. Resistance to the glycopeptides emerged in delayed fashion and occurs via a spectrum of chromosome- and plasmid-associated elements that lead to structural alteration of the bacterial cell-wall precursor substrates.
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Affiliation(s)
- Daina Zeng
- Agile Sciences, Raleigh, North Carolina 27606
| | | | - Theresa L Hartsell
- Department of Anesthesiology/Critical Care Medicine, The Johns Hopkins School of Medicine and Nursing, Baltimore, Maryland 21287
| | - Raul J Cano
- ATCC Center for Translational Microbiology, Union, New Jersey 07083.,Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407
| | - Stacy Adams
- Center for Skin Biology, GlaxoSmithKline, Durham, North Carolina 27703
| | | | - Ronald McMillan
- ATCC Center for Translational Microbiology, Union, New Jersey 07083
| | - John L Pace
- ATCC Center for Translational Microbiology, Union, New Jersey 07083.,STEM Program, Kean University, Union, New Jersey 07083.,Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, North Carolina 27707
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22
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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: 370] [Impact Index Per Article: 41.1] [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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23
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Affiliation(s)
- Hee-Kyoung Kang
- Department of Biomedical Sciences, Chosun University, Gwangju, Korea
| | - Yoonkyung Park
- Department of Biomedical Sciences, Chosun University, Gwangju, Korea
- Research Center for Proteinaceous Materials, Chosun University, Gwangju, Korea
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24
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Binda E, Marinelli F, Marcone GL. Old and New Glycopeptide Antibiotics: Action and Resistance. Antibiotics (Basel) 2014; 3:572-94. [PMID: 27025757 PMCID: PMC4790382 DOI: 10.3390/antibiotics3040572] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/05/2022] Open
Abstract
Glycopeptides are considered antibiotics of last resort for the treatment of life-threatening infections caused by relevant Gram-positive human pathogens, such as Staphylococcus aureus, Enterococcus spp. and Clostridium difficile. The emergence of glycopeptide-resistant clinical isolates, first among enterococci and then in staphylococci, has prompted research for second generation glycopeptides and a flurry of activity aimed at understanding resistance mechanisms and their evolution. Glycopeptides are glycosylated non-ribosomal peptides produced by a diverse group of soil actinomycetes. They target Gram-positive bacteria by binding to the acyl-d-alanyl-d-alanine (d-Ala-d-Ala) terminus of the growing peptidoglycan on the outer surface of the cytoplasmatic membrane. Glycopeptide-resistant organisms avoid such a fate by replacing the d-Ala-d-Ala terminus with d-alanyl-d-lactate (d-Ala-d-Lac) or d-alanyl-d-serine (d-Ala-d-Ser), thus markedly reducing antibiotic affinity for the cellular target. Resistance has manifested itself in enterococci and staphylococci largely through the expression of genes (named van) encoding proteins that reprogram cell wall biosynthesis and, thus, evade the action of the antibiotic. These resistance mechanisms were most likely co-opted from the glycopeptide producing actinomycetes, which use them to avoid suicide during antibiotic production, rather than being orchestrated by pathogen bacteria upon continued treatment. van-like gene clusters, similar to those described in enterococci, were in fact identified in many glycopeptide-producing actinomycetes, such as Actinoplanes teichomyceticus, which produces teicoplanin, and Streptomyces toyocaensis, which produces the A47934 glycopeptide. In this paper, we describe the natural and semi-synthetic glycopeptide antibiotics currently used as last resort drugs for Gram-positive infections and compare the van gene-based strategies of glycopeptide resistance among the pathogens and the producing actinomycetes. Particular attention is given to the strategy of immunity recently described in Nonomuraea sp. ATCC 39727. Nonomuraea sp. ATCC 39727 is the producer of A40926, which is the natural precursor of the second generation semi-synthetic glycopeptide dalbavancin, very recently approved for acute bacterial skin and skin structure infections. A thorough understanding of glycopeptide immunity in this producing microorganism may be particularly relevant to predict and eventually control the evolution of resistance that might arise following introduction of dalbavancin and other second generation glycopeptides into clinics.
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Affiliation(s)
- Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
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25
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Bhatt P, Sahni AK, Praharaj AK, Grover N, Kumar M, Chaudhari CN, Khajuria A. Detection of glycopeptide resistance genes in enterococci by multiplex PCR. Med J Armed Forces India 2014; 71:43-7. [PMID: 25609863 DOI: 10.1016/j.mjafi.2014.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND Vancomycin Resistant Enterococci (VRE) are a major cause of nosocomial infections. There are various phenotypic and genotypic methods of detection of glycopeptide resistance in enterococci. This study utilizes multiplex PCR for reliable detection of various glycopeptides resistance genes in VRE. METHOD This study was conducted to detect and to assess the prevalence of vancomycin resistance among enterococci isolates. From October 2011 to June 2013, a total of 96 non-repetitive isolates of enterococci from various clinical samples were analyzed. VRE were identified by Kirby Bauer disc diffusion method with Clinical and Laboratory Standards Institute (CLSI) guidelines. Minimum inhibitory concentration (MIC) of all isolates for vancomycin and teicoplanin was determined by E-test. Multiplex PCR was carried out for all enterococci isolates using six sets of primers. RESULTS Out of 96 isolates, 14 (14.6%) were found to be resistant to vancomycin by vancomycin E-test method (MIC ≥32 μg/ml). Out of these 14 isolates, 13 were also resistant to teicoplanin (MIC ≥16 μg/ml). VanA gene was detected in all the 14 isolates by Multiplex PCR. One of the PCR amplicons was sent for sequencing and the sequence received was submitted in the GenBank (GenBank accession no. KF181100). CONCLUSION Prevalence of VRE in this study was 14.6%. Multiplex PCR is a robust, sensitive and specific technique, which can be used for rapid detection of various glycopeptide resistance genes. Rapid identification of patients infected or colonized with VRE is essential for implementation of appropriate control measures to prevent their spread.
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Affiliation(s)
- Puneet Bhatt
- Resident, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - A K Sahni
- Professor & Head, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - A K Praharaj
- Professor and Head, Dept of Microbiology, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Naveen Grover
- Associate Professor, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - Mahadevan Kumar
- Associate Professor, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - C N Chaudhari
- Professor (Microbiology), INHS Asvini, Mumbai, India
| | - Atul Khajuria
- Resident (Microbiology), All India Institute of Medical Sciences, Bhubaneswar, India
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26
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Chancey ST, Zähner D, Stephens DS. Acquired inducible antimicrobial resistance in Gram-positive bacteria. Future Microbiol 2013; 7:959-78. [PMID: 22913355 DOI: 10.2217/fmb.12.63] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A major contributor to the emergence of antibiotic resistance in Gram-positive bacterial pathogens is the expansion of acquired, inducible genetic elements. Although acquired, inducible antibiotic resistance is not new, the interest in its molecular basis has been accelerated by the widening distribution and often 'silent' spread of the elements responsible, the diagnostic challenges of such resistance and the mounting limitations of available agents to treat Gram-positive infections. Acquired, inducible antibiotic resistance elements belong to the accessory genome of a species and are horizontally acquired by transformation/recombination or through the transfer of mobile DNA elements. The two key, but mechanistically very different, induction mechanisms are: ribosome-sensed induction, characteristic of the macrolide-lincosamide-streptogramin B antibiotics and tetracycline resistance, leading to ribosomal modifications or efflux pump activation; and resistance by cell surface-associated sensing of β-lactams (e.g., oxacillin), glycopeptides (e.g., vancomycin) and the polypeptide bacitracin, leading to drug inactivation or resistance due to cell wall alterations.
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Affiliation(s)
- Scott T Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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Glycopeptide resistance in gram-positive cocci: a review. Interdiscip Perspect Infect Dis 2012; 2012:781679. [PMID: 22778729 PMCID: PMC3388329 DOI: 10.1155/2012/781679] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/16/2012] [Accepted: 04/30/2012] [Indexed: 02/01/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) have emerged as important nosocomial pathogens in the past two decades all over the world and have seriously limited the choices available to clinicians for treating infections caused by these agents. Methicillin-resistant Staphylococcus aureus, perhaps the most notorious among the nosocomial pathogens, was till recently susceptible to vancomycin and the other glycopeptides. Emergence of vancomycin nonsusceptible strains of S. aureus has led to a worrisome scenario where the options available for treating serious infections due to these organisms are very limited and not well evaluated. Vancomycin resistance in clinically significant isolates of coagulase-negative staphylococci is also on the rise in many setups. This paper aims to highlight the genetic basis of vancomycin resistance in Enterococcus species and S. aureus. It also focuses on important considerations in detection of vancomycin resistance in these gram-positive bacteria. The problem of glycopeptide resistance in clinical isolates of coagulase-negative staphylococci and the phenomenon of vancomycin tolerance seen in some strains of Streptococcus pneumoniae has also been discussed. Finally, therapeutic options available and being developed against these pathogens have also found a mention.
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Staphylococcus aureus VRSA-11B is a constitutive vancomycin-resistant mutant of vancomycin-dependent VRSA-11A. Antimicrob Agents Chemother 2012; 56:4693-6. [PMID: 22710116 DOI: 10.1128/aac.00454-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Vancomycin-resistant Staphylococcus aureus VRSA-10 was isolated in 2009, whereas VRSA-11A and VRSA-11B were isolated from the same patient in 2010. Growth curves and determination of the nature of the peptidoglycan precursors and of the VanX d,d-dipeptidase activity in the absence and in the presence of vancomycin indicated that vancomycin resistance was inducible in VRSA-10, that VRSA-11A was partially dependent on glycopeptide for growth, and that VRSA-11B was constitutively resistant. Both VRSA-11A and -11B harbored an insertion sequence, ISEf1, at the same locus in the vanX-vanY intergenic region of Tn1546 and an S(183)A mutation in the chromosomal d-alanyl:d-alanine ligase (Ddl). This substitution has been shown to be responsible for a drastic diminution of the affinity of the enzyme for d-Ala at subsite 1 in Escherichia coli DdlB. VRSA-11B exhibited an additional mutation, P(216)T, in the transcriptional regulator VanR, most probably associated with constitutive expression of vancomycin resistance. It is thus likely that VRSA-11B is a constitutive derivative of VRSA-11A selected during prolonged vancomycin therapy. Synthesis of peptidoglycan precursors ending in d-Ala-d-lactate was responsible for oxacillin susceptibility of VRSA-11A and VRSA-11B despite the presence of a wild-type mecA gene in both strains.
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vanM, a new glycopeptide resistance gene cluster found in Enterococcus faecium. Antimicrob Agents Chemother 2010; 54:4643-7. [PMID: 20733041 DOI: 10.1128/aac.01710-09] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since glycopeptide-resistant enterococci (GRE) were reported in 1988, they have appeared in hospitals worldwide. Seven van gene cluster types (vanA, vanB, vanC, vanD, vanE, vanG, and vanL) are currently known. We investigated a clinical strain of Enterococcus faecium Efm-HS0661 that was isolated in 2006 from an inpatient with intra-abdominal infection in Shanghai. It was resistant to most antimicrobials, including vancomycin (MIC, >256 μg/ml) and teicoplanin (MIC, 96 μg/ml). Glycopeptide resistance could be transferred to E. faecium BM4105RF by conjugation. The donor and its transconjugant were negative by PCR for the known van genes. By cloning and primer walk sequencing, we discovered a novel van gene cluster, designated vanM. The vanM ligase gene was 1,032-bp in length and encoded a 343-amino-acid protein that shared 79.9, 70.8, 66.3, and 78.8% amino acid identity with VanA, VanB, VanD, and VanF, respectively. Although the vanM DNA sequence was closest to vanA, the organization of the vanM gene cluster was most similar to that of vanD. Upstream from the vanM cluster was an IS1216-like element, which may play a role in the dissemination of this resistance determinant. Liquid chromatography-mass spectrometry analysis of peptidoglycan precursors extracted from the VanM-type strain Efm-HS0661 treated with vancomycin or teicoplanin revealed a modified precursor (UDP-N-acetylmuramic acid [MurNAc]-tetrapeptide-D-Lac), indicating that VanM, like VanA, confers glycopeptide resistance by the inducible synthesis of precursor ending in D-Ala-D-Lac.
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Kato Y, Suzuki T, Ida T, Maebashi K. Genetic changes associated with glycopeptide resistance in Staphylococcus aureus: predominance of amino acid substitutions in YvqF/VraSR. J Antimicrob Chemother 2010; 65:37-45. [PMID: 19889788 DOI: 10.1093/jac/dkp394] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To further understand the mechanism of intermediate-level glycopeptide resistance, resulting from multiple endogenous mutations, in both laboratory-derived and clinically isolated Staphylococcus aureus. METHODS Laboratory-derived S. aureus strains were generated under selection using a variety of cell-wall-active antibiotics. Complete sequences of 27 genes, including 17 two-component histidine kinase sensors, were then compared with those of their susceptible parent strain. Further genetic analysis was performed on 125 clinical S. aureus isolates and 42 geographically diverse isolates of vancomycin-intermediate S. aureus (VISA). RESULTS Selective pressure using imipenem resulted in single point mutations leading to amino acid substitutions in two genes: vraS, encoding a two-component histidine kinase sensor; and SA1702 (also called yvqF, located immediately upstream of vraS), encoding a conserved hypothetical protein. The accumulation of the mutation in two distinct proteins-MsrR, a peptide methionine sulphoxide reductase regulator, and TcaA, a teicoplanin-resistance-associated protein-correlated with further increases in the glycopeptide MIC. The prevalence of YvqF/VraSR mutants among 125 clinical isolates along with the corresponding teicoplanin MICs was as follows: 0% (0/39), < or =1 mg/L; 48.6% (17/35), 2 mg/L; 72.7% (24/33), 4 mg/L; 93.8% (15/16), 8 mg/L; and 100% (2/2), 16 mg/L. Genetic analysis of 42 VISA isolates also identified the predominant amino acid substitutions in YvqF/VraS: 9 isolates (21.4%) revealed mutations in YvqF, followed by 7 isolates with mutations in VraS (16.7%). CONCLUSIONS Our findings provide novel insights into the high prevalence and genetic diversity of YvqF/VraSR mutants among clinical S. aureus isolates with reduced susceptibility to teicoplanin.
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Affiliation(s)
- Yoshihisa Kato
- Pharmaceutical Research Center, Meiji Seika Kaisha, Ltd, Kohoku-ku, Yokohama, Japan.
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VanB-type Enterococcus faecium clinical isolate successively inducibly resistant to, dependent on, and constitutively resistant to vancomycin. Antimicrob Agents Chemother 2009; 53:1974-82. [PMID: 19273676 DOI: 10.1128/aac.00034-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three Enterococcus faecium strains isolated successively from the same patient, vancomycin-resistant strain BM4659, vancomycin-dependent strain BM4660, and vancomycin-revertant strain BM4661, were indistinguishable by pulsed-field gel electrophoresis and harbored plasmid pIP846, which confers VanB-type resistance. The vancomycin dependence of strain BM4660 was due to mutation P(175)L, which suppressed the activity of the host Ddl D-Ala:D-Ala ligase. Reversion to resistance in strain BM4661 was due to a G-to-C transversion in the transcription terminator of the vanRS(B) operon that lowered the free energy of pairing from -13.08 to -6.65 kcal/mol, leading to low-level constitutive expression of the resistance genes from the P(RB) promoter, as indicated by analysis of peptidoglycan precursors and of VanX(B) D,D-dipeptidase activity. Transcription of the resistance genes, studied by Northern hybridization and reverse transcription, initiated from the P(YB) resistance promoter, was inducible in strains BM4659 and BM4660, whereas it started from the P(RB) regulatory promoter in strain BM4661, where it was superinducible. Strain BM4661 provides the first example of reversion to vancomycin resistance of a VanB-type dependent strain not due to a compensatory mutation in the ddl or vanS(B) gene. Instead, a mutation in the transcription terminator of the regulatory genes resulted in transcriptional readthrough of the resistance genes from the P(RB) promoter in the absence of vancomycin.
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New combinations of mutations in VanD-Type vancomycin-resistant Enterococcus faecium, Enterococcus faecalis, and Enterococcus avium strains. Antimicrob Agents Chemother 2009; 53:1952-63. [PMID: 19258279 DOI: 10.1128/aac.01348-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the clinical isolates Enterococcus faecium NEF1, resistant to high levels of vancomycin (MIC, 512 microg/ml) and teicoplanin (MIC, 64 microg/ml); Enterococcus faecium BM4653 and BM4656 and Enterococcus avium BM4655, resistant to moderate levels of vancomycin (MIC, 32 microg/ml) and to low levels of teicoplanin (MIC, 4 microg/ml); and Enterococcus faecalis BM4654, moderately resistant to vancomycin (MIC, 16 microg/ml) but susceptible to teicoplanin (MIC, 0.5 microg/ml). The strains were distinct, were constitutively resistant via the synthesis of peptidoglycan precursors ending in D-alanyl-D-lactate, and harbored a chromosomal vanD gene cluster that was not transferable. New mutations were found in conserved domains of VanS(D): at T(170)I near the phosphorylation site in NEF1, at V(67)A at the membrane surface in BM4653, at G(340)S in the G2 ATP-binding domain in BM4655, in the F domain in BM4656 (a 6-bp insertion), and in the G1 and G2 domains of BM4654 (three mutations). The mutations resulted in constitutivity, presumably through the loss of the phosphatase activity of the sensor. The chromosomal Ddl D-Ala:D-Ala ligase had an IS19 copy in NEF1, a mutation in the serine (S(185)F) or near the arginine (T(289)P) involved in D-Ala1 binding in BM4653 or BM4655, respectively, and a mutation next to the lysine (P(180)S) involved in D-Ala2 binding in BM4654, leading to the production of an impaired enzyme. In BM4653 vanY(D), a new insertion sequence, ISEfa9, belonging to the IS3 family, resulted in the absence of D,D-carboxypeptidase activity. Strain BM4656 had a functional D-Ala:D-Ala ligase, associated with high levels of both VanX(D) and VanY(D) activities, and is the first example of a VanD-type strain with a functional Ddl enzyme. Study of these five clinical isolates, displaying various assortments of mutations, confirms that all VanD-type strains isolated so far have undergone mutations in the vanS(D) or vanR(D) gene, leading to constitutive resistance, but that the Ddl host ligase is not always impaired. Based on sequence differences, the vanD gene clusters could be assigned to two subtypes: vanD-1 and vanD-4.
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Werner G, Strommenger B, Witte W. Acquired vancomycin resistance in clinically relevant pathogens. Future Microbiol 2008; 3:547-62. [DOI: 10.2217/17460913.3.5.547] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Acquired resistance to vancomycin is an increasing problem in pathogenic bacteria. It is best studied and most prevalent among Enterococcus and still remains rare in other pathogenic bacteria. Different genotypes of vancomycin resistance, vanA–G, have been described. The different van gene clusters consist of up to nine genes encoding proteins of different functions; their interplay leads to an alternative cell wall precursor less susceptible to glycopeptide binding. Variants of vanA and vanB types are found worldwide, with vanA predominating; their reservoir is Enterococcus faecium. Within this species a subpopulation of hospital-adapted types exists that acquired van gene clusters and which is responsible for outbreaks of vancomycin-resistant enterococci all over the world. Acquisition of vanA by methicillin-resistant Staphylococcus aureus (MRSA) is worrisome and seven cases have been described. Nonsusceptibility to glycopeptides also occurs independently from van genes and is a growing therapeutic challenge, especially in MRSA.
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Affiliation(s)
- Guido Werner
- FG 13 Nosocomial Infections, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, Wernigerode, 38855, Germany
| | - Birgit Strommenger
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, Wernigerode, 38855, Germany
| | - Wolfgang Witte
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, Wernigerode, 38855, Germany
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Rea MC, Clayton E, O'Connor PM, Shanahan F, Kiely B, Ross RP, Hill C. Antimicrobial activity of lacticin 3,147 against clinical Clostridium difficile strains. J Med Microbiol 2007; 56:940-946. [PMID: 17577060 DOI: 10.1099/jmm.0.47085-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile-associated diarrhoea (CDAD) is the most common hospital-acquired diarrhoea, and is a major type of gastroenteritis infection in nursing homes and facilities for the elderly. In this study the antimicrobial activity of the two-component lantibiotic, lacticin 3,147, against a range of genetically distinct C. difficile isolates was studied. The bacteriocin exhibited an MIC(50) of 3.6 microg ml(-1) for 10 genetically distinct C. difficile strains isolated from healthy subjects, inflammatory bowel disease patients and culture collection strains. In time-kill studies, 10(6) c.f.u. ml(-1) C. difficile ATCC 42,593 and CDAD isolate DPC 6,220 were killed within 120 or 20 min incubation, respectively, at a concentration of 6 microg lacticin ml(-1). Interestingly, addition of lacticin 3,147 to exponentially growing cells of C. difficile ATCC 43,593 caused rapid lysis of the cells after an initial lag phase, as measured by the concomitant release of the intracellular enzyme, acetate kinase. The addition of a food-grade, milk-based lacticin containing powder to faecal fermentation demonstrated that lacticin is effective in completely eliminating 10(6) c.f.u. C. difficile ml(-1) from a model faecal environment within 30 min when present at concentrations as low as 18 microg ml(-1). While other culturable microflora such as total anaerobes, bacteroides, total non-spore-forming anaerobes and total Gram-negative anaerobes were unaffected, populations of lactobacilli and bifidobacteria were reduced by 3 log cycles at bacteriocin levels sufficient to eliminate over 10(6) C. difficile. In light of these findings, the potential of lacticin 3,147 for treatment of CDAD is discussed.
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Affiliation(s)
- Mary C Rea
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
- Teagasc, Biotechnology Centre, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Evelyn Clayton
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
- Teagasc, Biotechnology Centre, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Paula M O'Connor
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
- Teagasc, Biotechnology Centre, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Fergus Shanahan
- Department of Medicine, University College, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
| | | | - R Paul Ross
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
- Teagasc, Biotechnology Centre, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Colin Hill
- Department of Microbiology, University College, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland
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Domingo MC, Huletsky A, Giroux R, Picard FJ, Bergeron MG. vanD and vanG-like gene clusters in a Ruminococcus species isolated from human bowel flora. Antimicrob Agents Chemother 2007; 51:4111-7. [PMID: 17724150 PMCID: PMC2151448 DOI: 10.1128/aac.00584-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A vancomycin-resistant, anaerobic, gram-positive coccus containing the vanD and vanG-like genes (strain CCRI-16110) was isolated from a human fecal specimen during a hospital surveillance program to detect carriers of vancomycin-resistant enterococci. Comparison of the 16S rRNA gene sequence of strain CCRI-16110 with databases revealed a potentially novel Ruminococcus species that was most similar (<94% identity) to Clostridium and Ruminococcus species. Strain CCRI-16110 was highly resistant to vancomycin and teicoplanin (MICs of >256 microg/ml). The complete DNA sequence of the vanD cluster was most similar (98.2% identity) to that of Enterococcus faecium BM4339, containing the vanD1 allele. An intD gene with 99% identity with that of this E. faecium strain was found to be associated with the vanD gene cluster of this novel anaerobic bacterium. Strain CCRI-16110 also harbors genes encoding putative VanS(G), VanG, and VanT(G) proteins displaying 56, 73.6, and 55% amino acid sequence identity, respectively, compared to the corresponding proteins encoded by the vanG1 and vanG2 operons of Enterococcus faecalis BM4518 and N03-0233. This study reports for the first time an anaerobic bacterium containing the vanD gene cluster. This strain also harbors a partial vanG-like gene cluster. The presence of vanD- and vanG-containing anaerobic bacteria in the human bowel flora suggests that these bacteria may serve as a reservoir for the vanD and vanG vancomycin resistance genes.
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Affiliation(s)
- M-C Domingo
- Centre de Recherche en Infectiologie de l'Université Laval, CHUQ, 2705 boul. Laurier, Québec, Québec G1V 4G2, Canada
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Depardieu F, Podglajen I, Leclercq R, Collatz E, Courvalin P. Modes and modulations of antibiotic resistance gene expression. Clin Microbiol Rev 2007; 20:79-114. [PMID: 17223624 PMCID: PMC1797629 DOI: 10.1128/cmr.00015-06] [Citation(s) in RCA: 246] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Since antibiotic resistance usually affords a gain of function, there is an associated biological cost resulting in a loss of fitness of the bacterial host. Considering that antibiotic resistance is most often only transiently advantageous to bacteria, an efficient and elegant way for them to escape the lethal action of drugs is the alteration of resistance gene expression. It appears that expression of bacterial resistance to antibiotics is frequently regulated, which indicates that modulation of gene expression probably reflects a good compromise between energy saving and adjustment to a rapidly evolving environment. Modulation of gene expression can occur at the transcriptional or translational level following mutations or the movement of mobile genetic elements and may involve induction by the antibiotic. In the latter case, the antibiotic can have a triple activity: as an antibacterial agent, as an inducer of resistance to itself, and as an inducer of the dissemination of resistance determinants. We will review certain mechanisms, all reversible, that bacteria have elaborated to achieve antibiotic resistance by the fine-tuning of the expression of genetic information.
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Affiliation(s)
- Florence Depardieu
- Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15, France
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Fang H, Hedin G, Telander B, Li G, Nord CE. Emergence of VanD-type vancomycin-resistant Enterococcus faecium in Stockholm, Sweden. Clin Microbiol Infect 2007; 13:106-8. [PMID: 17184299 DOI: 10.1111/j.1469-0691.2006.01569.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A vancomycin-resistant Enterococcus faecium isolate from the urine of a liver transplant patient in Stockholm was found to contain a vanD gene. The sequence of the vanD PCR product shared 100% identity with the vanD5 allele. The isolate was resistant to a relatively high level of vancomycin (128 mg/L) and a low level of teicoplanin (4 mg/L). This is the first VanD-type vancomycin-resistant E. faecium isolate reported in Sweden. The emergence of this strain reinforces the necessity of infection control efforts to interrupt the spread of these organisms.
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Affiliation(s)
- H Fang
- Division of Clinical Bacteriology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, Stockholm, Sweden
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Beltrametti F, Consolandi A, Carrano L, Bagatin F, Rossi R, Leoni L, Zennaro E, Selva E, Marinelli F. Resistance to glycopeptide antibiotics in the teicoplanin producer is mediated by van gene homologue expression directing the synthesis of a modified cell wall peptidoglycan. Antimicrob Agents Chemother 2007; 51:1135-41. [PMID: 17220405 PMCID: PMC1855507 DOI: 10.1128/aac.01071-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycopeptide resistance has been studied in detail in enterococci and staphylococci. In these microorganisms, high-level resistance is achieved by replacing the C-terminal D-alanyl-D-alanine of the nascent peptidoglycan with D-alanyl-D-lactate or D-alanyl-D-serine, thus reducing the affinities of glycopeptides for cell wall targets. Reorganization of the cell wall is directed by the expression of the van gene clusters. The identification of van gene homologs in the genomes of several glycopeptide-producing actinomycetes suggests the involvement of a similar self-resistance mechanism to avoid suicide. This report describes a comprehensive study of self-resistance in Actinoplanes teichomyceticus ATCC 31121, the producer of the clinically relevant glycopeptide teicoplanin. A. teichomyceticus ATCC 31121 showed a MIC of teicoplanin of 25 microg/ml and a MIC of vancomycin of 90 microg/ml during vegetative growth. The vanH, vanA, and vanX genes of A. teichomyceticus were found to be organized in an operon whose transcription was constitutive. Analysis of the UDP-linked peptidoglycan precursors revealed the presence of UDP-glycomuramyl pentadepsipeptide terminating in D-alanyl-D-lactate. No trace of precursors ending in d-alanyl-d-alanine was detected. Thus, the van gene complex was transcribed and expressed in the genetic background of A. teichomyceticus and conferred resistance to vancomycin and teicoplanin through the modification of cell wall biosynthesis. During teicoplanin production (maximum productivity, 70 to 80 microg/ml), the MIC of teicoplanin remained in the range of 25 to 35 microg/ml. Teicoplanin-producing cells were found to be tolerant to high concentrations of exogenously added glycopeptides, which were not bactericidal even at 5,000 microg/ml.
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Camargo ILBC, Dalla Costa LM, Woodford N, Gilmore MS, Darini ALC. Sequence analysis of Enterococcus faecium strain 10/96A (VanD4), the original vancomycin-resistant E. faecium strain in Brazil. J Clin Microbiol 2006; 44:2635-7. [PMID: 16825401 PMCID: PMC1489496 DOI: 10.1128/jcm.00509-06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecium strain 10/96A (VanD4) was the first vancomycin-resistant enterococcus (VRE) isolated in Brazil. Subsequent Brazilian VRE strains have all had the VanA phenotype. Multilocus sequence typing showed that strain 10/96A was isolated sporadically, has a unique sequence type (ST 281), and was not the progenitor of the VRE strains isolated from hospital outbreaks in Brazil.
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Affiliation(s)
- Ilana L B C Camargo
- Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de São Paulo, and Hospital de Clinicas, Curitiba, Brazil 14040-903
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Tanimoto K, Nomura T, Maruyama H, Tomita H, Shibata N, Arakawa Y, Ike Y. First VanD-Type vancomycin-resistant Enterococcus raffinosus isolate. Antimicrob Agents Chemother 2006; 50:3966-7. [PMID: 17000737 PMCID: PMC1635183 DOI: 10.1128/aac.00607-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Abstract
The first vancomycin-resistant clinical isolates of Enterococcus species were reported in Europe in 1988. Similar strains were later detected in hospitals on the East Coast of the United States. Since then, vancomycin-resistant enterococci have spread with unexpected rapidity and are now encountered in hospitals in most countries. This article reviews the mode of action and the mechanism of bacterial resistance to glycopeptides, as exemplified by the VanA type, which is mediated by transposon Tn1546 and is widely spread in enterococci. The diversity, regulation, evolution, and recent dissemination of methicillin-resistant Staphylococcus aureus are then discussed.
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Boyd DA, Miller MA, Mulvey MR. Enterococcus gallinarum N04-0414 harbors a VanD-type vancomycin resistance operon and does not contain a D-alanine:D-alanine 2 (ddl2) gene. Antimicrob Agents Chemother 2006; 50:1067-70. [PMID: 16495270 PMCID: PMC1426452 DOI: 10.1128/aac.50.3.1067-1070.2006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococcus gallinarum N04-0414 (MIC for vancomycin, 256 microg/ml) harbored a vanD-type vancomycin resistance operon as well as the intrinsic vanC1 operon. The D-Ala:D-Ala ligase 2 gene (ddl2) was not present in the strain, though it is found downstream of the vanS gene from the vanC operon in E. gallinarum ATCC 49573 and 19 other E. gallinarum strains tested.
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Affiliation(s)
- David A Boyd
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St., Winnipeg, Manitoba, Canada R3E 3R2
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Abstract
PURPOSE OF REVIEW This review updates epidemiologic trends and our understanding of glycopeptide resistance in enterococci. RECENT FINDINGS Colonization and infection rates with vancomycin resistant enterococci continue to increase throughout the world while factors contributing to this rise continue to be defined. While no interventions exist to eradicate colonization, infection control procedures are cost effective and decrease the prevalence of vancomycin resistant enterococcal colonization and infection. New molecular methods show great promise in strengthening our ability to detect colonization with these bacteria. Furthermore, our understanding of the origin of vancomycin resistant enterococci continues to grow. Paenibacillus species found in soil have been found to carry homologues of vanA-associated glycopeptide resistance genes found in enterococci. Also, additional evidence supports previous data that VanB-associated resistance may have been horizontally transferred from gastrointestinal tract bacteria to enterococci. Finally, glycopeptide resistance has been transferred to methicillin-resistant Staphylococcus aureus in clinical practice on several occasions. SUMMARY The prevalence of vancomycin resistant enterococci will likely continue to increase. Implementation of infection control strategies, in conjunction with deployment of advanced technologies for detection of vancomycin resistant enterococci, may curb this rise. The emergence of vancomycin resistant S. aureus is of concern.
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Affiliation(s)
- Ali Zirakzadeh
- Division of General Internal Medicine, Department of Internal Medicine, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
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Lavigne JP, Marchandin H, Bouziges N, Sotto A. First infection with VanD-type glycopeptide-resistant Enterococcus faecium in Europe. J Clin Microbiol 2005; 43:3512-5. [PMID: 16000493 PMCID: PMC1169091 DOI: 10.1128/jcm.43.7.3512-3515.2005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We report the first strain of glycopeptide-resistant Enterococcus faecium from Europe that contains a vanD allele isolated from blood cultures of an immunocompromised patient hospitalized in a French university hospital. Based on phenotypic results, PCR sequencing, pulsed-field gel electrophoresis, and Southern blotting, the isolate was assigned to E. faecium with a chromosomally located VanD allele most closely related to the VanD1 allele.
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Affiliation(s)
- Jean-Philippe Lavigne
- Laboratoire Universitaire d'Antibiologie, Faculté de Médecine, CS83021, Avenue Kennedy, 30908 Nîmes Cedex 02, France
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Depardieu F, Perichon B, Courvalin P. Detection of the van alphabet and identification of enterococci and staphylococci at the species level by multiplex PCR. J Clin Microbiol 2004; 42:5857-60. [PMID: 15583325 PMCID: PMC535300 DOI: 10.1128/jcm.42.12.5857-5860.2004] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 08/23/2004] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR assay was developed for detection of the six types of glycopeptide resistance characterized in enterococci and for identification of Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus epidermidis at the species level. Primers targeting the genes vanA, vanB, vanC, vanD, vanE, vanG, and ddl of E. faecium and E. faecalis and nuc of S. aureus and a chromosomal portion specific to S. epidermidis were designed to allow amplification of fragments with various sizes. This specific and sensitive technique allows detection of glycopeptide-resistant strains, in particular methicillin-resistant S. aureus, that may escape phenotype-based automated rapid methods.
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Affiliation(s)
- Florence Depardieu
- Unité des Agents Antibactériens, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France
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