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Luo X, Hounmanou YMG, Ndayisenga F, Yu Z. Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172712. [PMID: 38677439 DOI: 10.1016/j.scitotenv.2024.172712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.
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Affiliation(s)
- Xiao Luo
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbojlen 4, 1870 Frederiksberg, Denmark
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China
| | - Zhisheng Yu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China.
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Oelschlaeger P, Kaadan H, Dhungana R. Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues. Antibiotics (Basel) 2023; 12:1746. [PMID: 38136780 PMCID: PMC10740994 DOI: 10.3390/antibiotics12121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Heba Kaadan
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Rinku Dhungana
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts & Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Qu L, Dai K, Wang J, Cao L, Rao Z, Han R. Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita. Front Microbiol 2023; 14:1168179. [PMID: 37303801 PMCID: PMC10247985 DOI: 10.3389/fmicb.2023.1168179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops. Methods To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods. Results Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents. Discussion These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.
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Li P, Lei T, Zhou Y, Dai Y, Yang Z, Luo H. EBR-5, a Novel Variant of Metallo-β-Lactamase EBR from Multidrug-Resistant Empedobacter stercoris. Microbiol Spectr 2023; 11:e0003923. [PMID: 36719228 PMCID: PMC10101081 DOI: 10.1128/spectrum.00039-23] [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: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
A novel chromosome-encoded metallo-β-lactamase (MBL) EBR variant, namely, EBR-5, was identified in a multidrug-resistant Empedobacter stercoris strain SCVM0123 that was isolated from chicken anal swab samples. EBR-5 shared 82.13% amino acid identity with the previously known EBR-1. The expression of EBR-5 in Escherichia coli reduced susceptibility to expanded-spectrum cephalosporins and carbapenems. Compared with blaEBR-1, the recombinant strain harboring blaEBR-5 exhibited higher minimum inhibitory concentrations of piperacillin, cefotaxime, and meropenem. Despite the genetic diversity, EBR-5 and EBR-1 possessed similar kinetic parameters, except for cefepime, cefotaxime, cefoxitin, cephalothin, and meropenem, which were hydrolyzed more by EBR-5. In addition to blaEBR-1, a whole-genome sequencing analysis of SCVM0123 also revealed a plasmid-mediated blaRAA-1 gene. This study underlines the importance of E. stercoris monitoring, as it could be a potential reservoir of these β-lactamase genes. IMPORTANCE Carbapenemases are one of the greatest threats to clinical therapy, as they could confer resistance by hydrolyzing carbapenems and other β-lactam antimicrobials. In this study, we identified a novel metallo-β-lactamase EBR variant, namely, EBR-5, in Empedobacter stercoris. The biochemical properties, substrate hydrolysis abilities, and inhibition profiles of EBR-5 were reported. Through whole-genome sequencing and bioinformatic analyses, we revealed for the first time that the ESBL gene blaRAA-1 was located on a plasmid. This study extends the database of class B metallo-β-lactamases. Meanwhile, E. stercoris could be a major reservoir of blaEBR-5 and blaRAA-1, which have potential to spread to pathogens.
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Affiliation(s)
- Pei Li
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Ting Lei
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Yang Zhou
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Yujie Dai
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hongyan Luo
- College of Veterinary Medicine, Southwest University, Beibei, Chongqing, China
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Olowo-Okere A, Ibrahim YKE, Olayinka BO, Mohammed Y, Nabti LZ, Lupande-Mwenebitu D, Rolain JM, Diene SM. Genomic features of an isolate of Empedobacter falsenii harbouring a novel variant of metallo-β-lactamase, bla EBR-4 gene. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105234. [PMID: 35121093 DOI: 10.1016/j.meegid.2022.105234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Empedobacter falsenii is an emerging opportunistic pathogen that has been occasionally implicated in various human infections. In this study, we described the genomic features of a multidrug resistant E. falsenii Q1655 obtained from a patient attending a public hospital in Sokoto, northwest Nigeria. The isolate, E. falsenii Q1655, was isolated from the stool sample of a patient in Sokoto, Nigeria. The identity of the isolate was confirmed by MALDITOF-MS. The disc diffusion test and modified Carba-NP test were used for phenotypic antibiotic susceptibility test and carbapenemase enzyme production test, respectively. The whole genome of the strain was sequenced using the Illumina MiSeq technique. Resistome analysis was done by annotation of the WGS against the ARG-ANNOT database. The isolate was resistant to all β-lactam antibiotics with the exception of cefepime. The MICs of imipenem and ertapenem as determined by E-test were 12 μg/ml and 2 μg/ml, respectively. Modified Carba NP test showed that the strain was carbapenemase producing. Resistome analysis revealed the presence of a novel metallo-β-lactamase, a chromosomal blaEBR-4, which exhibited 94.92% and 97.02% nucleotide and protein sequence identities respectively with blaEBR-3 gene of E. falsenii 174,820. Seven and eight amino-acid substitutions were observed with the blaEBR-1 and blaEBR-2, respectively. We reported the first isolation and genomic description of an extensively drug resistant isolate of Empedobacter falsenii in Nigeria. This report broadens our knowledge of carbapenem resistance in E. falsenii and it will serve as a useful guide in the development of antibiotic use policy.
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Affiliation(s)
- Ahmed Olowo-Okere
- Department of Pharmaceutics and Pharmaceutical Microbiology, Usmanu Danfodiyo University Sokoto, Nigeria; MEPHI, IRD, APHM, IHU-Mediterranee Infection, Faculté de Pharmacie, Aix-Marseille University, Marseille, France.
| | | | - Busayo Olalekan Olayinka
- Department of Pharmaceutics and Pharmaceutical Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | - Yahaya Mohammed
- Department of Medical Microbiology, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Larbi Zakaria Nabti
- Université de Sétif 1, Laboratoire de Microbiologie (CHU de Sétif), Sétif, Algeria
| | - David Lupande-Mwenebitu
- MEPHI, IRD, APHM, IHU-Mediterranee Infection, Faculté de Pharmacie, Aix-Marseille University, Marseille, France
| | - Jean-Marc Rolain
- MEPHI, IRD, APHM, IHU-Mediterranee Infection, Faculté de Pharmacie, Aix-Marseille University, Marseille, France
| | - Seydina M Diene
- MEPHI, IRD, APHM, IHU-Mediterranee Infection, Faculté de Pharmacie, Aix-Marseille University, Marseille, France.
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Maaroufi R, Dziri O, Hadjadj L, Diene SM, Rolain JM, Chouchani C. Detection by Whole-Genome Sequencing of a Novel Metallo-β-Lactamase Produced by Wautersiella falsenii Causing Urinary Tract Infection in Tunisia. Pol J Microbiol 2022; 71:73-81. [PMID: 35635163 PMCID: PMC9152918 DOI: 10.33073/pjm-2022-010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Wautersiella falsenii is a rarely non-fermenting Gram-negative bacterium and belongs to the Flavobacteriaceae family. This nosocomial pathogen can cause several human infections, especially among immunocompromised patients. Here, we describe the whole genome sequence of a clinical W. falsenii strain isolated from a urine sample of a 35-year-old woman with a urinary tract infection in Tunisia. We investigated its phenotype and genotype. After bacterial identification by the MALDI-TOF method, the whole-genome sequencing of this strain was performed. This isolate was not susceptible to various antibiotics, including β-lactams, aminoglycosides, and quinolones. However, it remains susceptible to imipenem (MIC = 0.25 mg/l), ertapenem (MIC = 0.75 mg/l), and meropenem (MIC = 0.19 mg/l). Interestingly, the E-TEST® (MP/MPI) showed a reduced MIC of meropenem +/− EDTA (0.064 μg/ml). Besides, the color change from yellow to red in the β CARBA test only after 24 hours of incubation can be interpreted in two ways. On the one hand, as a likely low expression of the gene encoding metallo-β-lactamase. On the other hand, and more likely, it may be a false-positive result because, according to the test manufacturer's recommendations, the test should be read after 30 minutes. Perhaps, therefore, this gene is not expressed in the tested strain. Moreover, the whole-genome sequence analysis demonstrated the presence of a novel chromosomally located subclass B1 metallo-β-lactamase EBR-like enzyme, sharing 94.92% amino acid identity with a previously described carbapenemase produced by Empedobacter brevis, EBR-1. The results also showed the detection of other antibiotic resistance genes and the absence of plasmids. So far, this study is the first report on the detection of W. falsenii in Tunisia. These findings prove that W. falsenii could be a potential reservoir of antibiotic resistance genes, e.g., β-lactamases. Collaborative efforts and effective hygiene measures should be established to prevent the emergence of this species in our health care settings.
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Affiliation(s)
- Raouaa Maaroufi
- Aix-Marseille Université MEPHI, AP-HM, IRD, IHU Méditerranée Infection , Marseille , France
- Laboratoire des Microorganismes et Biomolécules Actives , Faculté des Sciences de Tunis , Université Tunis El-Manar , Tunis , Tunisie
- Laboratoire de Recherche Sciences et Technologies de l’Environnement , Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria , Hammam-Lif Université de Carthage , Tunisie
| | - Olfa Dziri
- Laboratoire des Microorganismes et Biomolécules Actives , Faculté des Sciences de Tunis , Université Tunis El-Manar , Tunis , Tunisie
- Laboratoire de Recherche Sciences et Technologies de l’Environnement , Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria , Hammam-Lif Université de Carthage , Tunisie
- Unité de Service en Commun pour la Recherche « Plateforme Génomique », Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, Hammam-Lif , Université de Carthage , Tunisie
| | - Linda Hadjadj
- Aix-Marseille Université MEPHI, AP-HM, IRD, IHU Méditerranée Infection , Marseille , France
| | - Seydina M. Diene
- Aix-Marseille Université MEPHI, AP-HM, IRD, IHU Méditerranée Infection , Marseille , France
| | - Jean-Marc Rolain
- Aix-Marseille Université MEPHI, AP-HM, IRD, IHU Méditerranée Infection , Marseille , France
| | - Chedly Chouchani
- Laboratoire des Microorganismes et Biomolécules Actives , Faculté des Sciences de Tunis , Université Tunis El-Manar , Tunis , Tunisie
- Laboratoire de Recherche Sciences et Technologies de l’Environnement , Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria , Hammam-Lif Université de Carthage , Tunisie
- Unité de Service en Commun pour la Recherche « Plateforme Génomique », Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, Hammam-Lif , Université de Carthage , Tunisie
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Zeng Y, Dong N, Zhang R, Liu C, Sun Q, Lu J, Shu L, Cheng Q, Chan EWC, Chen S. Emergence of an Empedobacter falsenii strain harbouring a tet(X)-variant-bearing novel plasmid conferring resistance to tigecycline. J Antimicrob Chemother 2021; 75:531-536. [PMID: 31778164 DOI: 10.1093/jac/dkz489] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate the genomic and phenotypic characteristics of an MDR Empedobacter falsenii strain isolated from a Chinese patient, which was phenotypically resistant to all last-line antibiotics (carbapenems, colistin and tigecycline). METHODS Species identity was determined by MALDI-TOF MS analysis. The complete genome sequence of the isolate was determined by WGS and the genetic elements conferring antimicrobial resistance were determined. The origin of this strain was tracked by phylogenetic analysis. RESULTS The E. falsenii strain was genetically most closely related to an Empedobacter sp. strain isolated from the USA. Members of E. falsenii are speculated to be intrinsically resistant to colistin. The carbapenem resistance of this strain was conferred by a chromosomal blaEBR-2 variant gene. Phylogenetic analysis indicated that the gene encoding the EBR β-lactamase was widely distributed in Empedobacter spp. Tigecycline resistance was mediated by a tet(X) variant gene encoded by a non-conjugative and non-typeable plasmid. CONCLUSIONS The MDR phenotype of the E. falsenii isolate was conferred by different mechanisms. Findings from us and others indicate that E. falsenii may serve as a reservoir for carbapenem and tigecycline resistance determinants.
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Affiliation(s)
- Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Ning Dong
- State Key Lab of Chemical Science and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Lingbin Shu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Qipeng Cheng
- State Key Lab of Chemical Science and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Science and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- State Key Lab of Chemical Science and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
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9
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Diversity and Genetic Basis for Carbapenem Resistance in a Coastal Marine Environment. Appl Environ Microbiol 2020; 86:AEM.02939-19. [PMID: 32198174 DOI: 10.1128/aem.02939-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/07/2020] [Indexed: 11/20/2022] Open
Abstract
Resistance to the "last-resort" antibiotics, such as carbapenems, has led to very few antibiotics being left to treat infections by multidrug-resistant bacteria. Spread of carbapenem resistance (CR) has been well characterized for the clinical environment. However, there is a lack of information about its environmental distribution. Our study reveals that CR is present in a wide range of Gram-negative bacteria in the coastal seawater environment, including four phyla, eight classes, and 30 genera. These bacteria were likely introduced into seawater via stormwater flows. Some CR isolates found here, such as Acinetobacter junii, Acinetobacter johnsonii, Brevundimonas vesicularis, Enterococcus durans, Pseudomonas monteilii, Pseudomonas fulva, and Stenotrophomonas maltophilia, are further relevant to human health. We also describe a novel metallo-β-lactamase (MBL) for marine Rheinheimera isolates with CR, which has likely been horizontally transferred to Citrobacter freundii or Enterobacter cloacae In contrast, another MBL of the New Delhi type was likely acquired by environmental Variovorax isolates from Escherichia coli, Klebsiella pneumoniae, or Acinetobacter baumannii utilizing a plasmid. Our findings add to the growing body of evidence that the aquatic environment is both a reservoir and a vector for novel CR genes.IMPORTANCE Resistance against the "last-resort" antibiotics of the carbapenem family is often based on the production of carbapenemases, and this has been frequently observed in clinical samples. However, the dissemination of carbapenem resistance (CR) in the environment has been less well explored. Our study shows that CR is commonly found in a range of bacterial taxa in the coastal aquatic environment and can involve the exchange of novel metallo-β-lactamases from typical environmental bacteria to potential human pathogens or vice versa. The outcomes of this study contribute to a better understanding of how aquatic and marine bacteria can act as reservoirs and vectors for CR outside the clinical setting.
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Co-occurrence of two tet(X) variants in an Empedobacter brevis of shrimp origin. Antimicrob Agents Chemother 2019:AAC.01636-19. [PMID: 31570401 DOI: 10.1128/aac.01636-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emerging novel resistance mechanisms pose a great public health concern.….
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Socha RD, Chen J, Tokuriki N. The Molecular Mechanisms Underlying Hidden Phenotypic Variation among Metallo-β-Lactamases. J Mol Biol 2019; 431:1172-1185. [PMID: 30769117 DOI: 10.1016/j.jmb.2019.01.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Genetic variation among orthologous genes has been largely formed through neutral genetic drift while maintaining the functional role of these genes. However, because the evolution of gene occurs in the context of each host organism, their sequence changes are also associated with adaptation to a specific environment. Thus, genetic variation can create critical phenotypic variation, particularly when genes are transferred to a new host by horizontal gene transfer. Unveiling "hidden phenotypic variation" is particularly important for genes that confer resistance to antibiotics. However, our understanding of the molecular mechanisms that underlie phenotypic variation remains limited. Here we sought to determine the extent of phenotypic variation in the B1 metallo-β-lactamase (MBL) family and its molecular basis by systematically characterizing eight MBL orthologs, including NDM-1 and VIM-2 and IMP-1. We found that these MBLs confer diverse levels of resistance. The phenotypic variation cannot be explained by variation in catalytic efficiency alone; rather, it is the combination of the catalytic efficiency and abundance of functional periplasmic enzyme that best predicts the observed variation in resistance. The level of functional periplasmic expression varied dramatically between MBL orthologs. This was the result of changes at multiple levels of each ortholog's: (1) quantity of mRNA, (2) amount of MBL expressed, and (3) efficacy of functional enzyme translocation to the periplasm. Overall, it is the interaction between each gene and the host's underlying cellular processes (transcription, translation, and translocation) that determines MBL genetic incompatibility through horizontal gene transfer. These host-specific processes may constrain the effective spread and deployment of MBLs to certain host species and could explain the current observed distribution bias.
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Affiliation(s)
- Raymond D Socha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - John Chen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Gatica J, Jurkevitch E, Cytryn E. Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment. Front Microbiol 2019; 10:146. [PMID: 30804916 PMCID: PMC6378392 DOI: 10.3389/fmicb.2019.00146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
The β-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with β-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of β-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed β-lactamase database, and subsequently analyzed β-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated β-lactamase clusters encompassed all of the human and bovine feces metagenomes, while β-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate "environmental" cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the "feces" and "environmental" clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The β-lactamase diversity in the "environmental" cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D β-lactamase homologs (bla CTX-M, bla KPC, bla GES) were ubiquitous in the "environmental" cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) β-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of β-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of β-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities.
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Affiliation(s)
- Joao Gatica
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel.,The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
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Ku YH, Lee MF, Chuang YC, Yu WL. Detection of Plasmid-Mediated β-Lactamase Genes and Emergence of a Novel AmpC (CMH-1) in Enterobacter cloacae at a Medical Center in Southern Taiwan. J Clin Med 2018; 8:jcm8010008. [PMID: 30577544 PMCID: PMC6352282 DOI: 10.3390/jcm8010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/03/2022] Open
Abstract
The plasmid-mediated extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in Enterobacter spp. have increasingly been reported. In this study, we investigated the prevalence of the plasmid-mediated β-lactamases in Enterobacter cloacae from bloodstream isolates at a medical center in southern Taiwan. ESBL and ampC genes were detected by PCRs and DNA sequencing. Conjugation experiments were conducted to confirm the transferability of the genetic resistance trait. Among 41 non-repetitive blood isolates of cefuroxime-resistant E. cloacae, eight isolates exhibited ESBL phenotype confirmed by double-disk synergistic tests. Nearly all the strains were susceptible to carbapenems. The prevalence rate of the plasmid-mediated blaampC genes was 73% (30/41), including one blaDHA-1, one blaMIR-6, two novel blaCMH-1 genes and other blaACT-like genes. Coexistence of plasmid-mediated blaACT and ESBL genes (10 with blaSHV-12 and one with blaCTX-M-3) was observed. Successful transmissions of the blaACT and blaCMH-1 were demonstrated in some transconjugants. The inducible or derepressed CMH-1 had expanded activity of isolates versus ceftazidime. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis and pulsotype showed distinct patterns suggesting non-clonal relationship. In conclusion, plasmid-mediated blaACT-likeampC genes in E. cloacae isolates have been highly prevalent in southern Taiwan and may continue genetic evolution, contributing to the complexities in antibiotic-resistant mechanisms.
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Affiliation(s)
- Yee-Huang Ku
- Division of Infectious Disease, Department of Internal Medicine, Chi Mei Medical Center-Liouying, Tainan 710, Taiwan.
| | - Mei-Feng Lee
- Laboratory of Environmental Health, Research Center of Humanities and Technology, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Yin-Ching Chuang
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan.
| | - Wen-Liang Yu
- Department of Intensive Care Medicine, Chi Mei Medical Center, Tainan 710, Taiwan.
- Department of Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
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Somboro AM, Osei Sekyere J, Amoako DG, Essack SY, Bester LA. Diversity and Proliferation of Metallo-β-Lactamases: a Clarion Call for Clinically Effective Metallo-β-Lactamase Inhibitors. Appl Environ Microbiol 2018; 84:e00698-18. [PMID: 30006399 PMCID: PMC6121990 DOI: 10.1128/aem.00698-18] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The worldwide proliferation of life-threatening metallo-β-lactamase (MBL)-producing Gram-negative bacteria is a serious concern to public health. MBLs are compromising the therapeutic efficacies of β-lactams, particularly carbapenems, which are last-resort antibiotics indicated for various multidrug-resistant bacterial infections. Inhibition of enzymes mediating antibiotic resistance in bacteria is one of the major promising means for overcoming bacterial resistance. Compounds having potential MBL-inhibitory activity have been reported, but none are currently under clinical trials. The need for developing safe and efficient MBL inhibitors (MBLIs) is obvious, particularly with the continuous spread of MBLs worldwide. In this review, the emergence and escalation of MBLs in Gram-negative bacteria are discussed. The relationships between different class B β-lactamases identified up to 2017 are represented by a phylogenetic tree and summarized. In addition, approved and/or clinical-phase serine β-lactamase inhibitors are recapitulated to reflect the successful advances made in developing class A β-lactamase inhibitors. Reported MBLIs, their inhibitory properties, and their purported modes of inhibition are delineated. Insights into structural variations of MBLs and the challenges involved in developing potent MBLIs are also elucidated and discussed. Currently, natural products and MBL-resistant β-lactam analogues are the most promising agents that can become clinically efficient MBLIs. A deeper comprehension of the mechanisms of action and activity spectra of the various MBLs and their inhibitors will serve as a bedrock for further investigations that can result in clinically useful MBLIs to curb this global menace.
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Affiliation(s)
- Anou M Somboro
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Whole-Genome Analysis of an Extensively Drug-Resistance Empedobacter falsenii Strain Reveals Distinct Features and the Presence of a Novel Metallo-ß-Lactamase (EBR-2). Curr Microbiol 2018; 75:1084-1089. [DOI: 10.1007/s00284-018-1498-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/19/2018] [Indexed: 11/26/2022]
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16
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Juan C, Torrens G, González-Nicolau M, Oliver A. Diversity and regulation of intrinsic β-lactamases from non-fermenting and other Gram-negative opportunistic pathogens. FEMS Microbiol Rev 2018; 41:781-815. [PMID: 29029112 DOI: 10.1093/femsre/fux043] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/18/2017] [Indexed: 01/22/2023] Open
Abstract
This review deeply addresses for the first time the diversity, regulation and mechanisms leading to mutational overexpression of intrinsic β-lactamases from non-fermenting and other non-Enterobacteriaceae Gram-negative opportunistic pathogens. After a general overview of the intrinsic β-lactamases described so far in these microorganisms, including circa. 60 species and 100 different enzymes, we review the wide array of regulatory pathways of these β-lactamases. They include diverse LysR-type regulators, which control the expression of β-lactamases from relevant nosocomial pathogens such as Pseudomonas aeruginosa or Stenothrophomonas maltophilia or two-component regulators, with special relevance in Aeromonas spp., along with other pathways. Likewise, the multiple mutational mechanisms leading to β-lactamase overexpression and β-lactam resistance development, including AmpD (N-acetyl-muramyl-L-alanine amidase), DacB (PBP4), MrcA (PPBP1A) and other PBPs, BlrAB (two-component regulator) or several lytic transglycosylases among others, are also described. Moreover, we address the growing evidence of a major interplay between β-lactamase regulation, peptidoglycan metabolism and virulence. Finally, we analyse recent works showing that blocking of peptidoglycan recycling (such as inhibition of NagZ or AmpG) might be useful to prevent and revert β-lactam resistance. Altogether, the provided information and the identified gaps should be valuable for guiding future strategies for combating multidrug-resistant Gram-negative pathogens.
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Affiliation(s)
- Carlos Juan
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases-Instituto de Investigación Sanitaria de Baleares (IdISBa), 07120 Palma, Illes Balears, Spain
| | - Gabriel Torrens
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases-Instituto de Investigación Sanitaria de Baleares (IdISBa), 07120 Palma, Illes Balears, Spain
| | - Mar González-Nicolau
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases-Instituto de Investigación Sanitaria de Baleares (IdISBa), 07120 Palma, Illes Balears, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases-Instituto de Investigación Sanitaria de Baleares (IdISBa), 07120 Palma, Illes Balears, Spain
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Abstract
Introduction. In December 2014, the Food and Drug Administration issued a recall of all Wallcur simulation products due to reports of their use in clinical practice. We present a case of septic shock and multiorgan failure after the accidental intravenous infusion of a nonsterile Wallcur simulation product. Case. The patient presented with symptoms of rigors and dyspnea occurring immediately after infusion of Wallcur Practi-0.9% saline. Initial laboratory evidence was consistent with severe septic shock and multiorgan dysfunction. His initial lactic acid level was 9 mmol/L (reference range = 0.5-2.2), and he had evidence of acute kidney injury and markers of disseminated intravascular coagulation. All 4 blood culture bottles isolated multidrug-resistant Empedobacter brevis. The patient recovered from his illness and was discharged with ciprofloxacin therapy per susceptibilities. Discussion. This patient represents the first described case of severe septic shock associated with the infusion of a Wallcur simulation product. Intravenous inoculation of a nonsterile fluid is rare and exposes the patient to unusual environmental organisms, toxins, or unsafe fluid characteristics such as tonicity. During course of treatment, we identified the possible culprit to be a multidrug-resistant isolate of Empedobacter brevis. We also discuss the systemic failures that led to this outbreak.
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Affiliation(s)
| | - Catherine O'Neal
- Louisiana State University Health Sciences Center, Baton Rouge, LA, USA
| | - Tonya Jagneaux
- Louisiana State University Health Sciences Center, Baton Rouge, LA, USA
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18
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Empedobacter brevis Bacteremia in a Patient Infected with HIV: Case Report and Review of Literature. Case Rep Infect Dis 2015; 2015:813528. [PMID: 26550499 PMCID: PMC4624922 DOI: 10.1155/2015/813528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/01/2015] [Indexed: 11/22/2022] Open
Abstract
Clinical disease caused by Empedobacter brevis (E. brevis) is very rare. We report the first case of E. brevis bacteremia in a patient with HIV and review the current literature. A 69-year-old man with human immunodeficiency virus (HIV) and CD4 count of 319 presented with chief complaints of black tarry stools, nausea and vomiting for 2 days. Physical exam was significant for abdominal pain on palpation with no rebound or guarding. His total leukocyte count was 32,000 cells/μL with 82% neutrophils and 9% bands. Emergent colonoscopy and endoscopic esophagogastroduodenoscopy showed esophageal candidiasis, a nonbleeding gastric ulcer, and diverticulosis. Blood cultures drawn on days 1, 2, and 3 of hospitalization grew E. brevis. Patient improved with intravenous antibiotics. This case is unusual, raising the possibility of gastrointestinal colonization as a source of the patient's bacteremia. In conclusion, E. brevis is an emerging pathogen that can cause serious health care associated infections.
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Zhao WH, Hu ZQ. Acquired metallo-β-lactamases and their genetic association with class 1 integrons and ISCR elements in Gram-negative bacteria. Future Microbiol 2015; 10:873-87. [DOI: 10.2217/fmb.15.18] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT Metallo-β-lactamases (MBLs) can hydrolyze almost all β-lactam antibiotics and are resistant to clinically available β-lactamase inhibitors. Numerous types of acquired MBLs have been identified, including IMP, VIM, NDM, SPM, GIM, SIM, DIM, KHM, TMB, FIM and AIM. IMPs and VIMs are the most frequent MBLs and disseminate in members of the family Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp. Acquired MBL genes are often embedded in integrons, and some are associated with insertion sequence (IS) elements. The class 1 integrons and IS common region (ISCR) elements are usually harbored in transposons and/or plasmids, forming so-called mobile vesicles for horizontal transfer of captured genes between bacteria. Here, we review the MBL superfamily identified in Gram-negative bacteria, with an emphasis on the phylogeny of acquired MBLs and their genetic association with class 1 integrons and IS common region elements.
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Affiliation(s)
- Wei-Hua Zhao
- Department of Microbiology & Immunology, Showa University School of Medicine, 1–5–8 Hatanodai, Shinagawa-ku, Tokyo 142–8555, Japan
| | - Zhi-Qing Hu
- Department of Microbiology & Immunology, Showa University School of Medicine, 1–5–8 Hatanodai, Shinagawa-ku, Tokyo 142–8555, Japan
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20
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Miraula M, Whitaker JJ, Schenk G, Mitić N. β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health. J Biol Inorg Chem 2015; 20:639-51. [PMID: 25773168 DOI: 10.1007/s00775-015-1250-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Metallo-β-lactamases (MBLs) are a family of Zn(II)-dependent enzymes that inactivate most of the commonly used β-lactam antibiotics. They have emerged as a major threat to global healthcare. Recently, we identified two novel MBL-like proteins, Maynooth IMipenemase-1 (MIM-1) and Maynooth IMipenemase-2 (MIM-2), in the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans, respectively. Here, we demonstrate that MIM-1 and MIM-2 have catalytic activities comparable to those of known MBLs, but from the pH dependence of their catalytic parameters it is evident that both enzymes differ with respect to their mechanisms, with MIM-1 preferring alkaline and MIM-2 acidic conditions. Both enzymes require Zn(II) but activity can also be reconstituted with other metal ions including Co(II), Mn(II), Cu(II) and Ca(II). Importantly, the substrate preference of MIM-1 and MIM-2 appears to be influenced by their metal ion composition. Since neither N. pentaromativorans nor S. agarivorans are human pathogens, the precise biological role(s) of MIM-1 and MIM-2 remains to be established. However, due to the similarity of at least some of their in vitro functional properties to those of known MBLs, MIM-1 and MIM-2 may provide essential structural insight that may guide the design of as of yet elusive clinically useful MBL inhibitors.
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Affiliation(s)
- Manfredi Miraula
- Department of Chemistry, Maynooth University, Maynooth, Co., Kildare, Ireland
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Phelan EK, Miraula M, Selleck C, Ollis DL, Schenk G, Mitić N. Metallo-β-Lactamases: A Major Threat to Human Health. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajmb.2014.43011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Carbapenem resistance in Elizabethkingia meningoseptica is mediated by metallo-β-lactamase BlaB. Antimicrob Agents Chemother 2012; 56:1686-92. [PMID: 22290979 DOI: 10.1128/aac.05835-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Elizabethkingia meningoseptica, a Gram-negative rod widely distributed in the environment, is resistant to most β-lactam antibiotics. Three bla genes have been identified in E. meningoseptica, coding for the extended-spectrum serine-β-lactamase CME (class D) and two unrelated wide-spectrum metallo-β-lactamases, BlaB (subclass B1) and GOB (subclass B3). E. meningoseptica is singular in being the only reported microorganism possessing two chromosomally encoded MBL genes. Real-time PCR and biochemical analysis demonstrate that the three bla genes are actively expressed in vivo as functional β-lactamases. However, while CME elicits cephalosporin resistance, BlaB is the only β-lactamase responsible for E. meningoseptica resistance to imipenem, as GOB activity is masked by higher cellular levels of BlaB. On the other hand, we demonstrate that bla(BlaB) expression is higher in the stationary phase or under conditions that mimic the nutrient-limiting cerebrospinal fluid colonized by E. meningoseptica in human meningitis.
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Characterization of DIM-1, an integron-encoded metallo-beta-lactamase from a Pseudomonas stutzeri clinical isolate in the Netherlands. Antimicrob Agents Chemother 2010; 54:2420-4. [PMID: 20308383 DOI: 10.1128/aac.01456-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A carbapenem-resistant Pseudomonas stutzeri strain isolated from a Dutch patient was analyzed in detail. This isolate produced a metallo-beta-lactamase (MBL) whose gene, with 43.5% GC content, was cloned and expressed in Escherichia coli. beta-Lactamase DIM-1 (for Dutch imipenemase) was weakly related to other Ambler class B beta-lactamases, sharing <52% amino acid identity with the most closely related MBL, GIM-1, and 45% identity with IMP-type MBLs. The beta-Lactamase DIM-1 significantly hydrolyzed broad-spectrum cephalosporins and carbapenems and spared aztreonam. This MBL gene was embedded in a class 1 integron containing two other gene cassettes, encoding resistance to aminoglycosides and disinfectants, that was located on a 70-kb plasmid.
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IND-6, a highly divergent IND-type metallo-beta-lactamase from Chryseobacterium indologenes strain 597 isolated in Burkina Faso. Antimicrob Agents Chemother 2009; 53:4320-6. [PMID: 19651915 DOI: 10.1128/aac.01607-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Chryseobacterium and other genera belonging to the family Flavobacteriaceae include organisms that can behave as human pathogens and are known to cause different kinds of infections. Several species of Flavobacteriaceae, including Chryseobacterium indologenes, are naturally resistant to beta-lactam antibiotics (including carbapenems), due to the production of a resident metallo-beta-lactamase. Although C. indologenes presently constitutes a limited clinical threat, the incidence of infections caused by this organism is increasing in some settings, where isolates that exhibit multidrug resistance phenotypes (including resistance to aminoglycosides and quinolones) have been detected. Here, we report the identification and characterization of a new IND-type variant from a C. indologenes isolate from Burkina Faso that is resistant to beta-lactams and aminoglycosides. The levels of sequence identity of the new variant to other IND-type metallo-beta-lactamases range between 72 and 90% (for IND-4 and IND-5, respectively). The purified enzyme exhibited N-terminal heterogeneity and a posttranslational modification consisting of the presence of a pyroglutamate residue at the N terminus. IND-6 shows a broad substrate profile, with overall higher turnover rates than IND-5 and higher activities than IND-2 and IND-5 against ceftazidime and cefepime.
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Héritier C, Poirel L, Nordmann P. Genetic and biochemical characterization of a chromosome-encoded carbapenem-hydrolyzing ambler class D beta-lactamase from Shewanella algae. Antimicrob Agents Chemother 2004; 48:1670-5. [PMID: 15105119 PMCID: PMC400541 DOI: 10.1128/aac.48.5.1670-1675.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A chromosome-encoded beta-lactamase gene from Shewanella algae clinical isolate KB-1 was cloned and expressed in Escherichia coli. It encoded the Ambler class D enzyme OXA-55, sharing less than 55% identity with any other oxacillinases. Although conferring a narrow-spectrum beta-lactam resistance phenotype, OXA-55 had carbapenem-hydrolyzing activity that mirrored the reduced susceptibility to imipenem observed in S. algae KB-1. Very similar oxacillinases were found in other S. algae isolates.
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Affiliation(s)
- Claire Héritier
- Service de Bactériologie-Virologie, Université Paris XI, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de Médecine Paris-Sud, 94275 Le Kremlin-Bicêtre, France
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27
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