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Molecular and Kinetic Characterization of MOX-9, a Plasmid-Mediated Enzyme Representative of a Novel Sublineage of MOX-Type Class C β-Lactamases. Antimicrob Agents Chemother 2022; 66:e0059522. [PMID: 36040170 PMCID: PMC9487596 DOI: 10.1128/aac.00595-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MOX lineage of β-lactamases includes a group of molecular class C enzymes (AmpCs) encoded by genes mobilized from the chromosomes of Aeromonas spp. to plasmids. MOX-9, previously identified as a plasmid-encoded enzyme from a Citrobacter freundii isolate, belongs to a novel sublineage of MOX enzymes, derived from the resident Aeromonas media AmpC. The blaMOX-9 gene was found to be carried on a transposon, named Tn7469, likely responsible for its mobilization to plasmidic context. MOX-9 was overexpressed in Escherichia coli, purified, and subjected to biochemical characterization. Kinetic analysis showed a relatively narrow-spectrum profile with strong preference for cephalosporin substrates, with some differences compared with MOX-1 and MOX-2. MOX-9 was not inhibited by clavulanate and sulbactam, while both tazobactam and avibactam acted as inhibitors in the micromolar range.
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2
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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3
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Abstract
Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (64SXSK, 150YXN, 315KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet 150YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.
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Martin C, Stebbins B, Ajmani A, Comendul A, Hamner S, Hasan NA, Colwell R, Ford T. Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1572-1585. [PMID: 33459951 DOI: 10.1007/s10646-020-02342-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.
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Affiliation(s)
| | | | - Asha Ajmani
- University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | | | | | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Timothy Ford
- University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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5
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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6
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Cherak Z, Loucif L, Moussi A, Rolain JM. Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review. J Glob Antimicrob Resist 2021; 25:287-309. [PMID: 33895415 DOI: 10.1016/j.jgar.2021.03.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/20/2021] [Indexed: 01/05/2023] Open
Abstract
Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.
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Affiliation(s)
- Zineb Cherak
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna, Algeria.
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; and Assistance Publique des Hôpitaux de Marseille, Marseille, France
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7
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Bonnin RA, Jousset AB, Emeraud C, Oueslati S, Dortet L, Naas T. Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales. Front Med (Lausanne) 2021; 7:616490. [PMID: 33553210 PMCID: PMC7855592 DOI: 10.3389/fmed.2020.616490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Gram-negative bacteria, especially Enterobacterales, have emerged as major players in antimicrobial resistance worldwide. Resistance may affect all major classes of anti-gram-negative agents, becoming multidrug resistant or even pan-drug resistant. Currently, β-lactamase-mediated resistance does not spare even the most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The dissemination of carbapenemases-encoding genes among Enterobacterales is a matter of concern, given the importance of carbapenems to treat nosocomial infections. Based on their amino acid sequences, carbapenemases are grouped into three major classes. Classes A and D use an active-site serine to catalyze hydrolysis, while class B (MBLs) require one or two zinc ions for their activity. The most important and clinically relevant carbapenemases are KPC, IMP/VIM/NDM, and OXA-48. However, several carbapenemases belonging to the different classes are less frequently detected. They correspond to class A (SME-, Nmc-A/IMI-, SFC-, GES-, BIC-like…), to class B (GIM, TMB, LMB…), class C (CMY-10 and ACT-28), and to class D (OXA-372). This review will address the genetic diversity, biochemical properties, and detection methods of minor acquired carbapenemases in Enterobacterales.
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Affiliation(s)
- Rémy A Bonnin
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Agnès B Jousset
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Cécile Emeraud
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Laurent Dortet
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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8
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Kim Y, Ko S, Yeon YE, Kim H, Oh CS, Ahn JK, Kim D. Genomic and Phenotypic Characterization of a Lytic Bacteriophage CF1 Infecting the Multi-drug Resistant Bacterium Citrobacter freundii. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0505-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Rodríguez EA, Garzón LM, Gómez ID, Jiménez JN. Multidrug resistance and diversity of resistance profiles in carbapenem-resistant Gram-negative bacilli throughout a wastewater treatment plant in Colombia. J Glob Antimicrob Resist 2020; 22:358-366. [PMID: 32200126 DOI: 10.1016/j.jgar.2020.02.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/13/2020] [Accepted: 02/29/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Carbapenem-resistant Gram-negative bacilli (CRGNB) have been reported in different wastewater treatment plants (WWTPs) throughout the world; however, few studies have described the antimicrobial resistance profile in different CRGNB throughout WWTPs, information that would identify points of selection of resistant bacteria. The objective of this work was to characterize the resistance profile of CRGNB harbouring blaKPC-2 from a Colombian WWTP. METHODS Six samples were taken from four points of a WWTP. CRGNB were selected in chromID® CARBA and identified by 16S rRNA. Carbapenemases were determined by polymerase chain reaction (PCR), and susceptibility was assessed using VITEK2. RESULTS One hundred and forty-two CRGNB harbouring blaKPC-2 were detected: 41% corresponded to Aeromonas spp. (n = 58) and 59% to Enterobacteriaceae. To establish the resistance profile, 50% of the isolates were selected proportionally by family and sampling point (26 Aeromonadaceae and 45 Enterobacteriaceae). All Enterobacteriaceae showed resistance to carbapenems and penicillins + inhibitors, high percentages of resistance to ceftriaxone (88.9%), and ciprofloxacin (44.4%), and low resistance to other antibiotics (>30%). In Aeromonadaceae, 76.9% were resistant to ceftriaxone, 58% to carbapenems, and 65.4% to ciprofloxacin. Twenty-one resistance profiles were observed, the most common of which were resistant to penicillins + inhibitor, cephalosporins (third to fourth generation), and carbapenems (19%). The percentage of multidrug resistance was 91% and was similar at all points of the WWTP. CONCLUSIONS The high frequency of multidrug resistance and great diversity of resistance profiles observed throughout the WWTP is of concern, and shows the role of WWTP as a reservoir and dissemination source of antimicrobial resistance to water sources.
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Affiliation(s)
- E A Rodríguez
- Bacterial Molecular Epidemiology Line, Research Group in Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia, Medellín, Colombia.
| | - L M Garzón
- Bacterial Molecular Epidemiology Line, Research Group in Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia, Medellín, Colombia
| | - I D Gómez
- Bacterial Molecular Epidemiology Line, Research Group in Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia, Medellín, Colombia
| | - J Natalia Jiménez
- Bacterial Molecular Epidemiology Line, Research Group in Basic and Applied Microbiology (MICROBA), School of Microbiology, University of Antioquia, Medellín, Colombia.
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10
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Chen Q, Zhou W, Qian C, Shen K, Zhu X, Zhou D, Sun Z, Lu W, Liu H, Li K, Xu T, Bao Q, Lu J. OXA-830, a Novel Chromosomally Encoded Extended-Spectrum Class D β-Lactamase in Aeromonas simiae. Front Microbiol 2019; 10:2732. [PMID: 31849884 PMCID: PMC6902050 DOI: 10.3389/fmicb.2019.02732] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/11/2019] [Indexed: 12/04/2022] Open
Abstract
The diversity of class D β-lactamases mediating resistance to β-lactams has been increasingly reported recently. In this study, a novel class D oxacillinase named OXA-830 was identified in a fully sequenced Aeromonas simiae strain, which was isolated from sewage discharged from a farm in southern China. OXA-830 shares the highest amino acid identity of 79.3% with an OXA-12-like variant named OXA-725. When expressed in E. coli DH5α, OXA-830 conferred resistance to penicillins and selected β-lactamase inhibitors but not to cephalosporins and carbapenems. Kinetic analysis of OXA-830 revealed a broad substrate profile including penicillins, cefazolin, cefoxitin, and ceftazidime but not carbapenems. The hydrolytic activity was significantly inhibited by sulbactam, followed by tazobactam, but was less effectively inhibited by clavulanic acid. The blaOXA–830 gene was located on the A. simiae A6 chromosome and the blaOXA–830-related region was bracketed by a pair of perfect inverted repeats.
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Affiliation(s)
- Qianqian Chen
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Wangxiao Zhou
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Changrui Qian
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kai Shen
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xinyi Zhu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Zhewei Sun
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Tongji University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Qiyu Bao
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China.,School of Medical and Health, Lishui University, Lishui, China
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11
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Cheng G, Ning J, Ahmed S, Huang J, Ullah R, An B, Hao H, Dai M, Huang L, Wang X, Yuan Z. Selection and dissemination of antimicrobial resistance in Agri-food production. Antimicrob Resist Infect Control 2019; 8:158. [PMID: 31649815 PMCID: PMC6805589 DOI: 10.1186/s13756-019-0623-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
Public unrest about the use of antimicrobial agents in farming practice is the leading cause of increasing and the emergences of Multi-drug Resistant Bacteria that have placed pressure on the agri-food industry to act. The usage of antimicrobials in food and agriculture have direct or indirect effects on the development of Antimicrobial resistance (AMR) by bacteria associated with animals and plants which may enter the food chain through consumption of meat, fish, vegetables or some other food sources. In addition to antimicrobials, recent reports have shown that AMR is associated with tolerance to heavy metals existing naturally or used in agri-food production. Besides, biocides including disinfectants, antiseptics and preservatives which are widely used in farms and slaughter houses may also contribute in the development of AMR. Though the direct transmission of AMR from food-animals and related environment to human is still vague and debatable, the risk should not be neglected. Therefore, combined global efforts are necessary for the proper use of antimicrobials, heavy metals and biocides in agri-food production to control the development of AMR. These collective measures will preserve the effectiveness of existing antimicrobials for future generations.
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Affiliation(s)
- Guyue Cheng
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jianan Ning
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Saeed Ahmed
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Junhong Huang
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Rizwan Ullah
- 3State key laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 China
| | - Boyu An
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haihong Hao
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Menghong Dai
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingli Huang
- 2National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xu Wang
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zonghui Yuan
- 1MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China.,2National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
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12
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Wang S, Dai E, Jiang X, Zeng L, Cheng Q, Jing Y, Hu L, Yin Z, Gao B, Wang J, Duan G, Cai X, Zhou D. Characterization of the plasmid of incompatibility groups IncFII pKF727591 and Inc pKPHS1 from Enterobacteriaceae species. Infect Drug Resist 2019; 12:2789-2797. [PMID: 31564929 PMCID: PMC6735626 DOI: 10.2147/idr.s212321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/08/2019] [Indexed: 11/23/2022] Open
Abstract
Background Multiple incompatibility (Inc) groups of plasmids have been identified in Enterobacteriaceae species, but there are still quite a few sequenced plasmids that could not be assigned to any known Inc groups. Methods One IncFIIpKF727591β plasmid p205880-qnrS and two IncpKPHS1 plasmids p11219-CTXM and p205880-NR1 were fully sequenced in this work. Detailed genomic comparison was applied to all available sequenced plasmids of IncFIIpKF727591 or IncpKPHS1 group. Results p205880-qnrS carried a novel transposon Tn6396, which was an ISKpn19-compsite transposon and represented a prototype transposable element carrying a minimum core qnrS1 module. p11219-CTXM harbored a novel transposon Tn6559, which was generated from integration of a truncated IS903D–blaCTX-M-14–ISEcp1 unit into the Tn3-family cryptic unit transposon Tn1722. Two Inc groups, IncFIIpKF727591 and IncpKPHS1, of plasmids from Enterobacteriaceae species were proposed, and IncFIIpKF727591 was further grouped into two subgroups IncFIIpKF727591α and IncFIIpKF727591β. Each of the 11 IncFIIpKF727591 plasmids carried multiple accessory modules including at least one resistance module, and the relatively small IncFIIpKF727591 backbones could acquire a wealth of foreign genetic contents. The modular structures of plasmid backbones were conserved within each of IncFIIpKF727591α and IncFIIpKF727591β subgroups but dramatically different, although with similar gene organizations, between these two subgroups. The IncpKPHS1 backbones were conserved with respect to modular structures, and only four of the 14 IncpKPHS1 plasmids carried accessory modules, two of which contained resistance genes. Conclusion A genomic comparison of sequenced IncpKPHS1 or IncFIIpKF727591 plasmids provides insights into modular differences and genetic diversification of these plasmids, some of which carries antimicrobial resistance genes.
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Affiliation(s)
- Shujie Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, People's Republic of China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Qiaoxiang Cheng
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, People's Republic of China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Guixin Duan
- Animal Science and Technology College, Heilongjiang Bayi Agricultural University, Daqing 163000, People's Republic of China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, People's Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
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13
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Boutal H, Vogel A, Bernabeu S, Devilliers K, Creton E, Cotellon G, Plaisance M, Oueslati S, Dortet L, Jousset A, Simon S, Naas T, Volland H. A multiplex lateral flow immunoassay for the rapid identification of NDM-, KPC-, IMP- and VIM-type and OXA-48-like carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 2019; 73:909-915. [PMID: 29365094 PMCID: PMC5890661 DOI: 10.1093/jac/dkx521] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022] Open
Abstract
Objectives The global spread of carbapenemase-producing Enterobacteriaceae represents a substantial challenge in clinical practice and rapid and reliable detection of these organisms is essential. The aim of this study was to develop and validate a lateral flow immunoassay (Carba5) for the detection of the five main carbapenemases (KPC-, NDM-, VIM- and IMP-type and OXA-48-like). Methods Carba5 was retrospectively and prospectively evaluated using 296 enterobacterial isolates from agar culture. An isolated colony was suspended in extraction buffer and then loaded on the manufactured Carba5. Results All 185 isolates expressing a carbapenemase related to one of the Carba5 targets were correctly and unambiguously detected in <15 min. All other isolates gave negative results except those producing OXA-163 and OXA-405, which are considered low-activity carbapenemases. No cross-reaction was observed with non-targeted carbapenemases, ESBLs, AmpCs or oxacillinases (OXA-1, -2, -9 and -10). Overall, this assay reached 100% sensitivity and 95.3% (retrospectively) to 100% (prospectively) specificity. Conclusions Carba5 is efficient, rapid and easy to implement in the routine workflow of a clinical microbiology laboratory for confirmation of the five main carbapenemases encountered in Enterobacteriaceae.
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Affiliation(s)
- Hervé Boutal
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Anaïs Vogel
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Sandrine Bernabeu
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Karine Devilliers
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Elodie Creton
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Garence Cotellon
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Marc Plaisance
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Saoussen Oueslati
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Agnès Jousset
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Stéphanie Simon
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, AP-HP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Hervé Volland
- Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Laboratoire d'Etudes et de Recherches en Immunonalyse, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
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14
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Glupczynski Y, Jousset A, Evrard S, Bonnin RA, Huang TD, Dortet L, Bogaerts P, Naas T. Prospective evaluation of the OKN K-SeT assay, a new multiplex immunochromatographic test for the rapid detection of OXA-48-like, KPC and NDM carbapenemases. J Antimicrob Chemother 2018; 72:1955-1960. [PMID: 28369469 PMCID: PMC5890672 DOI: 10.1093/jac/dkx089] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 02/27/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives: There is an urgent need for accurate and fast diagnostic tests capable of identifying carbapenemase producers. Here, we assessed the performance of a new multiplex lateral flow assay (OKN K-SeT) for the rapid detection of OXA-48-like, KPC and NDM carbapenemase-producing Enterobacteriaceae from culture colonies. Methods: Two hundred collection isolates with characterized β-lactamase content and 183 non-duplicate consecutive isolates referred to two National Reference Centres over a 2 month period in 2016 were used to evaluate the OKN K-SeT assay. Results: The assay correctly detected all 42 OXA-48-like-, 27 KPC- and 30 NDM-producing isolates from the collection panel, including 7 isolates that co-produced NDM and OXA-181 carbapenemases. No cross-reactivity was observed with non-targeted carbapenemases (n = 41) or with non-carbapenemase producers (n = 60). Prospectively, all OXA-48-like (n = 69), KPC (n = 9) and NDM (n = 19) carbapenemase-producing Enterobacteriaceae isolates were correctly detected, while 11 carbapenemase producers not targeted by the assay went undetected [VIM (n = 8) and OXA-23/OXA-58-like (n = 3)]. Overall, the sensitivity and specificity of the assay were 100%. Conclusions: The OKN assay is efficient, rapid and easy to implement in the workflow of a clinical microbiology laboratory for the confirmation of OXA-48, NDM and KPC carbapenemases. This test represents a powerful diagnostic tool as it enables the rapid detection of the most clinically important carbapenemases without the need for more costly and less frequently available molecular assays.
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Affiliation(s)
- Youri Glupczynski
- Laboratory of Clinical Microbiology, National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | | | - Stéphanie Evrard
- Laboratory of Clinical Microbiology, National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | | | - Te-Din Huang
- Laboratory of Clinical Microbiology, National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | | | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, National Reference Centre for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
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15
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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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Dortet L, Bernabeu S, Gonzalez C, Naas T. Evaluation of the Carbapenem Detection Set™ for the detection and characterization of carbapenemase-producing Enterobacteriaceae. Diagn Microbiol Infect Dis 2018; 91:220-225. [PMID: 29548525 DOI: 10.1016/j.diagmicrobio.2018.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/20/2022]
Abstract
The objective of this study was to assess the performance of the Carbapenemase Detection Set™ (CDS; Mast Diagnostics) in association with i) the EUCAST meropenem screening cut-off and ii) the faropenem-temocillin algorithm (FTa) for the screening of carbapenemase-producing Enterobacteriaceae (CPE). A total of 200 well-characterized enterobacterial isolates with reduced susceptibility to at least one carbapenem including 63 non-CPEs and 137 CPEs belonging to different Ambler classes were initially screened for CPEs using i) the EUCAST meropenem cut-off (diameter <25 mm) and ii) the FTa. Highly suspected CPEs underwent further testing using the CDS, which is based on the inhibition zone diameters determination of combined disks (A: meropenem, B: meropenem + dipicolinic acid, C: meropenem + cloxacillin, and D: meropenem + boronic acid). With the FTa, 66.7% of the non-CPE isolates were correctly identified. Most OXA-48-like producers (90.5%) were detected with 98.6% specificity. The FTa discriminates CPE from non-CPE with 100% sensitivity, but complementary tests were still needed for 59 % (118/200) of the strains. The EUCAST cut-off led to 3 false-negative results (2 OXA-181 and 1 NMC-A producer) resulting in a sensitivity of 97.8% for the discrimination between CPE and non-CPE, and 75.5% (151/200) of the strains still required complementary test. The CDS reduced the number of isolates requiring additional tests from 59% to 22%, and from 75.5% to 38% for FTa and EUCAST cut-off, respectively. FTa possesses very good specificities for the detection and classification of Ambler class A and most class B carbapenemase-producers, except for IMP producers, which were almost not detected (10/11). In conclusion, the association of the CDS with the FTa presented only 22% of inconclusive results, while this number was 38% with the EUCAST meropenem CPE screening cut-off.
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Affiliation(s)
- Laurent Dortet
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France; EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France; EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Camille Gonzalez
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France; EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France; EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Paris-Sud University, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
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17
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González-Plaza JJ, Šimatović A, Milaković M, Bielen A, Wichmann F, Udiković-Kolić N. Functional Repertoire of Antibiotic Resistance Genes in Antibiotic Manufacturing Effluents and Receiving Freshwater Sediments. Front Microbiol 2018; 8:2675. [PMID: 29387045 PMCID: PMC5776109 DOI: 10.3389/fmicb.2017.02675] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/21/2017] [Indexed: 11/21/2022] Open
Abstract
Environments polluted by direct discharges of effluents from antibiotic manufacturing are important reservoirs for antibiotic resistance genes (ARGs), which could potentially be transferred to human pathogens. However, our knowledge about the identity and diversity of ARGs in such polluted environments remains limited. We applied functional metagenomics to explore the resistome of two Croatian antibiotic manufacturing effluents and sediments collected upstream of and at the effluent discharge sites. Metagenomic libraries built from an azithromycin-production site were screened for resistance to macrolide antibiotics, whereas the libraries from a site producing veterinary antibiotics were screened for resistance to sulfonamides, tetracyclines, trimethoprim, and beta-lactams. Functional analysis of eight libraries identified a total of 82 unique, often clinically relevant ARGs, which were frequently found in clusters and flanked by mobile genetic elements. The majority of macrolide resistance genes identified from matrices exposed to high levels of macrolides were similar to known genes encoding ribosomal protection proteins, macrolide phosphotransferases, and transporters. Potentially novel macrolide resistance genes included one most similar to a 23S rRNA methyltransferase from Clostridium and another, derived from upstream unpolluted sediment, to a GTPase HflX from Emergencia. In libraries deriving from sediments exposed to lower levels of veterinary antibiotics, we found 8 potentially novel ARGs, including dihydrofolate reductases and beta-lactamases from classes A, B, and D. In addition, we detected 7 potentially novel ARGs in upstream sediment, including thymidylate synthases, dihydrofolate reductases, and class D beta-lactamase. Taken together, in addition to finding known gene types, we report the discovery of novel and diverse ARGs in antibiotic-polluted industrial effluents and sediments, providing a qualitative basis for monitoring the dispersal of ARGs from environmental hotspots such as discharge sites of pharmaceutical effluents.
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Affiliation(s)
- Juan J González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Šimatović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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18
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Dissemination and Characteristics of a Novel Plasmid-Encoded Carbapenem-Hydrolyzing Class D β-Lactamase, OXA-436, Found in Isolates from Four Patients at Six Different Hospitals in Denmark. Antimicrob Agents Chemother 2017; 62:AAC.01260-17. [PMID: 29061750 DOI: 10.1128/aac.01260-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022] Open
Abstract
The diversity of OXA-48-like carbapenemases is continually expanding. In this study, we describe the dissemination and characteristics of a novel carbapenem-hydrolyzing class D β-lactamase (CHDL) named OXA-436. In total, six OXA-436-producing Enterobacteriaceae isolates, including Enterobacter asburiae (n = 3), Citrobacter freundii (n = 2), and Klebsiella pneumoniae (n = 1), were identified in four patients in the period between September 2013 and April 2015. All three species of OXA-436-producing Enterobacteriaceae were found in one patient. The amino acid sequence of OXA-436 showed 90.4 to 92.8% identity to the amino acid sequences of other acquired OXA-48-like variants. Expression of OXA-436 in Escherichia coli and kinetic analysis of purified OXA-436 revealed an activity profile similar to that of OXA-48 and OXA-181, with activity against penicillins, including temocillin; limited or no activity against extended-spectrum cephalosporins; and activity against carbapenems. The blaOXA-436 gene was located on a conjugative ∼314-kb IncHI2/IncHI2A plasmid belonging to plasmid multilocus sequence typing sequence type 1 in a region surrounded by chromosomal genes previously identified to be adjacent to blaOXA genes in Shewanella spp. In conclusion, OXA-436 is a novel CHDL with functional properties similar to those of OXA-48-like CHDLs. The described geographical spread among different Enterobacteriaceae and the plasmid location of blaOXA-436 illustrate its potential for further dissemination.
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19
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Bogaerts P, Naas T, Saegeman V, Bonnin RA, Schuermans A, Evrard S, Bouchahrouf W, Jove T, Tande D, de Bolle X, Huang TD, Dortet L, Glupczynski Y. OXA-427, a new plasmid-borne carbapenem-hydrolysing class D β-lactamase in Enterobacteriaceae. J Antimicrob Chemother 2017; 72:2469-2477. [DOI: 10.1093/jac/dkx184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/18/2017] [Indexed: 12/12/2022] Open
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20
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Coppi M, Antonelli A, Giani T, Spanu T, Liotti FM, Fontana C, Mirandola W, Gargiulo R, Barozzi A, Mauri C, Principe L, Rossolini GM. Multicenter evaluation of the RAPIDEC® CARBA NP test for rapid screening of carbapenemase-producing Enterobacteriaceae and Gram-negative nonfermenters from clinical specimens. Diagn Microbiol Infect Dis 2017; 88:207-213. [PMID: 28502395 DOI: 10.1016/j.diagmicrobio.2017.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/21/2022]
Abstract
The rapid diagnosis of carbapenemase-producing (CP) bacteria is essential for the management of therapy and infection control. In this study, RAPIDEC® CARBA NP (RCNP) was evaluated for the rapid screening of CP Enterobacteriaceae, Acinetobacter baumannii complex, and Pseudomonas aeruginosa from clinical specimens collected at five Italian hospitals. Firstly, each site tested 20 well-characterized strains in a blinded fashion. Secondly, each center prospectively tested 25 isolates from blood cultures processed with a rapid workflow (6h after subculture) and 25 isolates from other specimens processed after an overnight culture. The presence of carbapenemases was confirmed by multiplex real-timePCRs targeting carbapenemase genes. RCNP presented an overall sensitivity, specificity, positive predictive value, and negative predictive value of 70%, 94%, 82%, and 89%, respectively, with a higher performance in detection of CP Enterobacteriaceae and a poorer performance in detection of CP A. baumannii complex. With isolates from blood cultures, RCNP could significantly reduce the time required for identification of CP Enterobacteriaceae (less than 9h since the positivization of blood cultures).
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Affiliation(s)
- Marco Coppi
- Department of Experimental and Clinical Medicine, University of Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Italy
| | - Tommaso Giani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Teresa Spanu
- Institute of Microbiology, Catholic University of the Sacred Heart, Agostino Gemelli Hospital, Rome, Italy
| | - Flora Marzia Liotti
- Institute of Microbiology, Catholic University of the Sacred Heart, Agostino Gemelli Hospital, Rome, Italy
| | - Carla Fontana
- Department of Experimental Medicine and Surgery, Tor Vergata University of Rome, Rome, Italy; Clinical Microbiology Laboratories, Polyclinic of Tor Vergata Foundation, Rome, Italy
| | - Walter Mirandola
- Clinical Microbiology Laboratories, Polyclinic of Tor Vergata Foundation, Rome, Italy
| | - Raffaele Gargiulo
- Provincial Laboratory of Clinical Microbiology, S. Agostino-Estense Hospital, Modena, Italy
| | - Agostino Barozzi
- Provincial Laboratory of Clinical Microbiology, S. Agostino-Estense Hospital, Modena, Italy
| | - Carola Mauri
- Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Luigi Principe
- Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Italy; Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
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Sun F, Zhou D, Sun Q, Luo W, Tong Y, Zhang D, Wang Q, Feng W, Chen W, Fan Y, Xia P. Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata. Sci Rep 2016; 6:33982. [PMID: 27658354 PMCID: PMC5034289 DOI: 10.1038/srep33982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/06/2016] [Indexed: 02/04/2023] Open
Abstract
We previously reported the complete sequence of the resistance plasmid pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL (conferring bleomycin resistance), which is recovered from a clinical Leclercia adecarboxylata isolate P10164 from China. This follow-up work disclosed that there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3 coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and shown to carry a wealth of resistance genes, which encoded the resistance to at least 10 classes of antibiotics (β-lactams. macrolides, quinolones, aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds, sulphonamides, trimethoprim, and rifampicin) and 7 kinds of heavy mental (mercury, silver, copper, nickel, chromate, arsenic, and tellurium). All of these antibiotic resistance genes are associated with mobile elements such as transposons, integrons, and insertion sequence-based transposable units, constituting a total of three novel MDR regions, two in pP10164-2 and the other one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2 and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively drug-resistant.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.,College of Food Science and Project Engineering, Bohai University, Jinzhou 121013, China
| | - Qian Wang
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yahan Fan
- Transfusion Department, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
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22
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Hamdi S, Rousseau GM, Labrie SJ, Kourda RS, Tremblay DM, Moineau S, Slama KB. Characterization of Five Podoviridae Phages Infecting Citrobacter freundii. Front Microbiol 2016; 7:1023. [PMID: 27446058 PMCID: PMC4925675 DOI: 10.3389/fmicb.2016.01023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus.
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Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Geneviève M Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Simon J Labrie
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Rim S Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Denise M Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Karim B Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
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23
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Antonelli A, D'Andrea MM, Montagnani C, Bartolesi AM, Di Pilato V, Fiorini P, Torricelli F, Galli L, Rossolini GM. Newborn bacteraemia caused by an Aeromonas caviae producing the VIM-1 and SHV-12 β-lactamases, encoded by a transferable plasmid. J Antimicrob Chemother 2015; 71:272-4. [PMID: 26410172 DOI: 10.1093/jac/dkv304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Alberto Antonelli
- Department of Medical Biotechnologies, University of Siena, Siena, Italy Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Carlotta Montagnani
- Department of Health Sciences, University of Florence, Florence, Italy Paediatric Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Anna Maria Bartolesi
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vincenzo Di Pilato
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Patrizio Fiorini
- Neonatal Intensive Care Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | | | - Luisa Galli
- Department of Health Sciences, University of Florence, Florence, Italy Paediatric Infectious Diseases Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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