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Mushtaq S, Vickers A, Woodford N, Livermore DM. Activity of aztreonam/avibactam and ceftazidime/avibactam against Enterobacterales with carbapenemase-independent carbapenem resistance. Int J Antimicrob Agents 2024; 63:107081. [PMID: 38176458 DOI: 10.1016/j.ijantimicag.2023.107081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/01/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Enterobacterales with carbapenemase-independent resistance to carbapenems are sometimes selected during therapy and, on rare occasions, cause outbreaks. Most have extended-spectrum or AmpC β-lactamases, together with changes to permeability or penicillin-binding proteins (PBPs). Newer β-lactam-β-lactamase inhibitor combinations may present useful options for infections due to these organisms. Accordingly, Clinical and Laboratory Standards Institute/European Committee on Antimicrobial Susceptibility Testing broth-microdilution was used to measure the minimum inhibitory concentrations (MICs) of ceftazidime/avibactam and aztreonam/avibactam for 51 carbapenemase-negative Enterobacterales with resistance or reduced susceptibility to carbapenems: genomic sequencing of the least-susceptible organisms was also undertaken. MICs of the two avibactam combinations cross-correlated closely, but with fewer MICs (2/51 vs. 10/51) exceeding 8+4 mg/L in the case of ceftazidime/avibactam. Raised MICs for Escherichia coli were associated with PBP3 inserts together with CMY-42 β-lactamase; correlates among Enterobacter cloacae complex isolates remain elusive, with AmpC and PBP3 sequences found to be species specific. In the case of Klebsiella spp., no MICs exceeding 2 mg/L were seen for either combination. It appears that these avibactam combinations have potential against Enterobacterales with carbapenemase-independent carbapenem resistance or reduced susceptibility, with ceftazidime/avibactam being more reliably active than aztreonam/avibactam.
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Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Anna Vickers
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
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Kawai A, Shropshire WC, Suzuki M, Borjan J, Aitken SL, Bachman WC, McElheny CL, Bhatti MM, Shields RK, Shelburne SA, Doi Y. Structural insights into the molecular mechanism of high-level ceftazidime-avibactam resistance conferred by CMY-185. mBio 2024; 15:e0287423. [PMID: 38179965 PMCID: PMC10865806 DOI: 10.1128/mbio.02874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
β-Lactamases can accumulate stepwise mutations that increase their resistance profiles to the latest β-lactam agents. CMY-185 is a CMY-2-like β-lactamase and was identified in an Escherichia coli clinical strain isolated from a patient who underwent treatment with ceftazidime-avibactam. CMY-185, possessing four amino acid substitutions of A114E, Q120K, V211S, and N346Y relative to CMY-2, confers high-level ceftazidime-avibactam resistance, and accumulation of the substitutions incrementally enhances the level of resistance to this agent. However, the functional role of each substitution and their interplay in enabling ceftazidime-avibactam resistance remains unknown. Through biochemical and structural analysis, we present the molecular basis for the enhanced ceftazidime hydrolysis and impaired avibactam inhibition conferred by CMY-185. The substituted Y346 residue is a major driver of the functional evolution as it rejects primary avibactam binding due to the steric hindrance and augments oxyimino-cephalosporin hydrolysis through a drastic structural change, rotating the side chain of Y346 and then disrupting the H-10 helix structure. The other substituted residues E114 and K120 incrementally contribute to rejection of avibactam inhibition, while S211 stimulates the turnover rate of the oxyimino-cephalosporin hydrolysis. These findings indicate that the N346Y substitution is capable of simultaneously expanding the spectrum of activity against some of the latest β-lactam agents with altered bulky side chains and rejecting the binding of β-lactamase inhibitors. However, substitution of additional residues may be required for CMY enzymes to achieve enhanced affinity or turnover rate of the β-lactam agents leading to clinically relevant levels of resistance.IMPORTANCECeftazidime-avibactam has a broad spectrum of activity against multidrug-resistant Gram-negative bacteria including carbapenem-resistant Enterobacterales including strains with or without production of serine carbapenemases. After its launch, emergence of ceftazidime-avibactam-resistant strains that produce mutated β-lactamases capable of efficiently hydrolyzing ceftazidime or impairing avibactam inhibition are increasingly reported. Furthermore, cross-resistance towards cefiderocol, the latest cephalosporin in clinical use, has been observed in some instances. Here, we clearly demonstrate the functional role of the substituted residues in CMY-185, a four amino-acid variant of CMY-2 identified in a patient treated with ceftazidime-avibactam, for high-level resistance to this agent and low-level resistance to cefiderocol. These findings provide structural insights into how β-lactamases may incrementally alter their structures to escape multiple advanced β-lactam agents.
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Affiliation(s)
- Akito Kawai
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
| | - William C. Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
| | - Jovan Borjan
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel L. Aitken
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - William C. Bachman
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Micah M. Bhatti
- Division of Pathology/Lab Medicine, Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake, Aichi, Japan
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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3
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Shropshire WC, Endres BT, Borjan J, Aitken SL, Bachman WC, McElheny CL, Wu CT, Egge SL, Khan A, Miller WR, Bhatti MM, Saharasbhojane P, Kawai A, Shields RK, Shelburne SA, Doi Y. High-level ceftazidime/avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated β-lactamase CMY-185 variant. J Antimicrob Chemother 2023; 78:2442-2450. [PMID: 37574665 PMCID: PMC10545501 DOI: 10.1093/jac/dkad249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023] Open
Abstract
OBJECTIVES To characterize a blaCMY variant associated with ceftazidime/avibactam resistance from a serially collected Escherichia coli isolate. METHODS A patient with an intra-abdominal infection due to recurrent E. coli was treated with ceftazidime/avibactam. On Day 48 of ceftazidime/avibactam therapy, E. coli with a ceftazidime/avibactam MIC of >256 mg/L was identified from abdominal drainage. Illumina and Oxford Nanopore Technologies WGS was performed on serial isolates to identify potential resistance mechanisms. Site-directed mutants of CMY β-lactamase were constructed to identify amino acid residues responsible for ceftazidime/avibactam resistance. RESULTS WGS revealed that all three isolates were E. coli ST410. The ceftazidime/avibactam-resistant strain uniquely acquired a novel CMY β-lactamase gene, herein called blaCMY-185, harboured on an IncI-γ/K1 conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2, including A114E, Q120K, V211S and N346Y, and conferred high-level ceftazidime/avibactam resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced ceftazidime/avibactam susceptibility. However, double and triple mutants containing N346Y previously associated with ceftazidime/avibactam resistance in other AmpC enzymes, conferred ceftazidime/avibactam MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to steric hindrance between the side chain of Y346 and the sulphate group of avibactam. CONCLUSIONS We identified ceftazidime/avibactam resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer ceftazidime/avibactam resistance.
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Affiliation(s)
- William C Shropshire
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jovan Borjan
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samuel L Aitken
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William C Bachman
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chin-Ting Wu
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, TX, USA
| | - Stephanie L Egge
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
| | - Ayesha Khan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
| | - Micah M Bhatti
- Department of Laboratory Medicine, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pranoti Saharasbhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akito Kawai
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ryan K Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Huang Z, Liu H, Zhang X, Tang M, Lin Y, Feng L, Ye J, Zhou T, Chen L. Ceftazidime-Decorated Gold Nanoparticles: a Promising Strategy against Clinical Ceftazidime-Avibactam-Resistant Enterobacteriaceae with Different Resistance Mechanisms. Antimicrob Agents Chemother 2023; 67:e0026223. [PMID: 37358468 PMCID: PMC10353462 DOI: 10.1128/aac.00262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023] Open
Abstract
Nanoparticle-based antibiotic delivery systems are essential in combating antibiotic-resistant bacterial infections arising from acquired resistance and/or biofilm formation. Here, we report that the ceftazidime-decorated gold nanoparticles (CAZ_Au NPs) can effectively kill clinical ceftazidime-avibactam-resistant Enterobacteriaceae with various resistance mechanisms. Further study of underlying antibacterial mechanisms suggests that CAZ_Au NPs can damage the bacterial cell membrane and increase the level of intracellular reactive oxygen species. Moreover, CAZ_Au NPs show great potential in inhibiting biofilm formation and eradicating mature biofilms via crystal violet and scanning electron microscope assays. In addition, CAZ_Au NPs demonstrate excellent performance in improving the survival rate in the mouse model of abdominal infection. In addition, CAZ_Au NPs show no significant toxicity at bactericidal concentrations in the cell viability assay. Thus, this strategy provides a simple way to drastically improve the potency of ceftazidime as an antibiotic and its use in further biomedical applications.
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Affiliation(s)
- Zeyu Huang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haifeng Liu
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaotuan Zhang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Miran Tang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuzhan Lin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Luozhu Feng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijiang Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Shropshire WC, Endres BT, Borjan J, Aitken SL, Bachman WC, McElheny CL, Khan A, Bhatti MM, Saharasbhojane P, Kawai A, Shields RK, Shelburne SA, Doi Y. High-level ceftazidime-avibactam resistance in Escherichia coli conferred by the novel plasmid-mediated beta-lactamase CMY-185 variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527067. [PMID: 36778324 PMCID: PMC9915728 DOI: 10.1101/2023.02.03.527067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objectives To characterize a bla CMY variant associated with ceftazidime-avibactam (CZA) resistance from a serially collected Escherichia coli isolate. Methods A patient with an intra-abdominal infection due to recurrent E. coli was treated with CZA. On day 48 of CZA therapy, E. coli with a CZA MIC of >256 mg/L was identified from abdominal drainage. Illumina WGS was performed on all isolates to identify potential resistance mechanisms. Site-directed mutants of CMY β-lactamase were constructed to identify amino acid residues responsible for CZA resistance. Results WGS revealed that all three isolates were E. coli ST410. The CZA-resistant strain uniquely acquired a novel CMY β-lactamase gene, herein called bla CMY-185 , harbored on an IncIγ-type conjugative plasmid. The CMY-185 enzyme possessed four amino acid substitutions relative to CMY-2 including A114E, Q120K, V211S, and N346Y and conferred high-level CZA resistance with an MIC of 32 mg/L. Single CMY-2 mutants did not confer reduced CZA susceptibility. However, double and triple mutants containing N346Y previously associated with CZA resistance in other AmpC enzymes, conferred CZA MICs ranging between 4 and 32 mg/L as well as reduced susceptibility to the newly developed cephalosporin, cefiderocol. Molecular modelling suggested that the N346Y substitution confers the reduction of avibactam inhibition due to the steric hindrance between the side chain of Y346 and the sulfate group of avibactam. Conclusion We identified CZA resistance in E. coli associated with a novel CMY variant. Unlike other AmpC enzymes, CMY-185 appears to require an additional substitution on top of N346Y to confer CZA resistance.
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Pharmacokinetic/Pharmacodynamic Evaluation of Aztreonam/Amoxicillin/Clavulanate Combination against New Delhi Metallo-β-Lactamase and Serine-β-Lactamase Co-Producing Escherichia coli and Klebsiella pneumoniae. Pharmaceutics 2023; 15:pharmaceutics15010251. [PMID: 36678879 PMCID: PMC9865866 DOI: 10.3390/pharmaceutics15010251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/04/2023] [Accepted: 01/08/2023] [Indexed: 01/12/2023] Open
Abstract
This study aimed to examine specific niches and usage for the aztreonam/amoxicillin/clavulanate combination and to use population pharmacokinetic simulations of clinical dosing regimens to predict the impact of this combination on restricting mutant selection. The in vitro susceptibility of 19 New-Delhi metallo-β-lactamase (NDM)-producing clinical isolates to amoxicillin/clavulanate and aztreonam alone and in co-administration was determined based on the minimum inhibitory concentration (MIC) and mutant prevention concentration (MPC). The fractions of a 24-h duration that the free drug concentration was within the mutant selection window (fTMSW) and above the MPC (fT>MPC) in both plasma and epithelial lining fluid were determined from simulations of 10,000 subject profiles based on regimens by renal function categories. This combination reduced the MIC of aztreonam and amoxicillin/clavulanate to values below their clinical breakpoint in 7/9 K. pneumoniae and 8/9 E. coli, depending on the β-lactamase genes detected in the isolate. In the majority of the tested isolates, the combination resulted in fT>MPC > 90% and fTMSW < 10% for both aztreonam and amoxicillin/clavulanate. Clinical dosing regimens of aztreonam and amoxicillin/clavulanate were sufficient to provide mutant restriction coverage for MPC and MIC ≤ 4 mg/L. This combination has limited coverage against NDM- and extended-spectrum β-lactamase co-producing E. coli and K. pneumoniae and is not effective against isolates carrying plasmid-mediated AmpC and KPC-2. This study offers a potential scope and limitations as to where the aztreonam/amoxicillin/clavulanate combination may succeed or fail.
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Ma K, Zong Z. Resistance to aztreonam-avibactam due to CTX-M-15 in the presence of penicillin-binding protein 3 with extra amino acids in Escherichia coli. Front Microbiol 2022; 13:1047109. [PMID: 36406430 PMCID: PMC9674307 DOI: 10.3389/fmicb.2022.1047109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Aztreonam-avibactam is a promising combination to treat carbapenem-resistant Enterobacterales including coverage for metallo-β-lactamases. Escherichia coli strains resistant to aztreonam-avibactam have emerged but resistance mechanisms remain to be elucidated. We performed a study to investigate the mechanism for aztreonam-avibactam in a carbapenem-resistant Escherichia coli clinical strain. This strain was resistant to aztreonam-avibactam (aztreonam MIC, 16 mg/L in the presence of 4 mg/L avibactam). Whole genome sequencing revealed that the strain carried metallo-β-lactamase gene blaNDM-4 and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15 and had a YRIK four amino acid insertion in penicillin-binding protein 3 (PBP3). blaCTX-M-15 was cloned into pET-28a(+), followed by the transformation, with the gene, of E. coli strain 035125∆pCMY42 possessing the YRIK insertion in PBP3 and strain BL21 with the wildtype PBP3. blaCTX-M-14, another common ESBL gene, and blaCTX-M-199, a hybrid of blaCTX-M-14 and blaCTX-M-15 were also individually cloned into both E. coli strains for comparison. Aztreonam-avibactam resistance was only observed in the E. coli strains with the YRIK insertion in PBP3 that produced CTX-M-15 or its hybrid enzyme CTX-M-199. Checkerboard titration assays were performed to determine the synergistic effects between aztreonam-avibactam and ceftazidime or meropenem. Doubling avibactam concentration in vitro reversed aztreonam-avibactam resistance, while the combination of aztreonam-avibactam and ceftazidime or meropenem did not. In conclusion, CTX-M enzymes with activity against aztreonam, (e.g., CTX-M-15 and CTX-M-199), can confer resistance in the combination of PBP3 with YRIK insertions in metallo-β-lactamase-producing carbapenem-resistant E. coli. Doubling the concentration of avibactam may overcome such resistance.
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Affiliation(s)
- Ke Ma
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- *Correspondence: Zhiyong Zong,
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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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Ajayi AO, Perry B, Yost CK, Jamieson R, Truelstrup Hansen L, Rahube T. Comparative Genomic Analyses of the β-lactamase (blaCMY-42) Encoding Plasmids Isolated from Wastewater Treatment Plants in Canada. Can J Microbiol 2021; 67:737-748. [PMID: 34077692 DOI: 10.1139/cjm-2021-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Wastewater treatment plants are useful environments for investigating the occurrence, diversity, and evolution of plasmids encoding clinically relevant antibiotic resistance genes. Our objective was to isolate and sequence plasmids encoding meropenem resistance from bacterial hosts within Canadian WWTPs. We used two enrichment culture approaches for primary plasmid isolation, followed by screening of antibiotic resistance, conjugative mobility, and stability in enteric bacteria. Isolated plasmids were sequenced using Illumina MiSeq and Sanger sequencing methods. Bioinformatics analyses resolved a multi-resistance IncF/MOBF12 plasmid, pFEMG (209,357 bp), harbouring resistance genes to beta-lactam (blaCMY-42, blaTEM-1β, and blaNDM-5), macrolide (mphA-mrx-mphR), tetracycline (tetR-tetB-tetC-tetD), trimethoprim (dfrA12), aminoglycoside (aadA2), and sulfonamide (sul1) antibiotic classes. We also isolated an IncI1/MOBP12 plasmid pPIMR (172,280 bp), carrying similar beta-lactamase and a small multidrug efflux resistance gene cluster (blaCMY-42-blc-sugE) to pFEMG. The co-occurrence of different ARGs within a single 24,552 bp cluster in pFEMG - intersperced with transposons, insertion sequence elements, and a class 1 integron - maybe of significant interest to human and veterinary medicine. Additionally, the presence of conjugative and plasmid maintenance genes in the studied plasmids corresponds to the observed high conjugative transfer frequencies and stable maintenance. Extensive investigation is required to further understand the fitness trade offs of plasmids having differing types of conjugative transfer and maintenance modules.
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Affiliation(s)
| | - Ben Perry
- University of Regina, 6846, Regina, Saskatchewan, Canada;
| | | | - Rob Jamieson
- Dalhousie University, 3688, Halifax, Nova Scotia, Canada;
| | - Lisbeth Truelstrup Hansen
- Dalhousie University, 3688, Department of Process Engineering and Applied Science, Halifax, Canada.,Technical University of Denmark, 5205, Department of Process Engineering and Applied Science, Lyngby, Denmark;
| | - Teddie Rahube
- University of Regina, 6846, Biology Department, Regina, Canada, S4S 0A2.,Botswana International University of Science and Technology, 357305, Biology Department, Palapye, Botswana;
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Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India. Antibiotics (Basel) 2020; 9:antibiotics9110826. [PMID: 33227950 PMCID: PMC7699290 DOI: 10.3390/antibiotics9110826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 01/21/2023] Open
Abstract
Antibiotic resistance is one of the major current global health crises. Because of increasing contamination with antimicrobials, pesticides, and heavy metals, the aquatic environment has become a hotspot for emergence, maintenance, and dissemination of antibiotic and heavy metal resistance genes among bacteria. The aim of the present study was to determine the co-resistance to quinolones, ampicillin, and heavy metals among the bacterial isolates harboring extended-spectrum β-lactamases (ESBLs) genes. Among 73 bacterial strains isolated from a highly polluted stretch of the Yamuna River in Delhi, those carrying blaCTX-M, blaTEM, or blaSHV genes were analyzed to detect the genetic determinants of resistance to quinolones, ampicillin, mercury, and arsenic. The plasmid-mediated quinolone resistance (PMQR) gene qnrS was found in 22 isolates; however, the qnrA, B, C, and qnrD genes could not be detected in any of the bacteria. Two variants of CMY, blaCMY-2 and blaCMY-42, were identified among eight and seven strains, respectively. Furthermore, merB, merP, merT, and arsC genes were detected in 40, 40, 44, and 24 bacterial strains, respectively. Co-transfer of different resistance genes was also investigated in a transconjugation experiment. Successful transconjugants had antibiotic and heavy metal resistance genes with similar tolerance toward antibiotics and heavy metals as did their donors. This study indicates that the aquatic environment is a major reservoir of bacteria harboring resistance genes to antibiotics and heavy metals and emphasizes the need to study the genetic basis of resistant microorganisms and their public health implications.
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Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism. mSystems 2020; 5:5/6/e00821-20. [PMID: 33144312 PMCID: PMC7646527 DOI: 10.1128/msystems.00821-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aztreonam-avibactam is a promising antimicrobial combination against multidrug-resistant organisms, such as carbapenemase-producing Enterobacterales Resistance to aztreonam-avibactam has been found, but the resistance mechanism remains poorly studied. We recovered three Escherichia coli isolates of an almost identical genome but exhibiting varied aztreonam-avibactam resistance. The isolates carried a cephalosporinase gene, bla CMY-42, on IncIγ plasmids with a single-nucleotide variation in an antisense RNA-encoding gene, inc, of the replicon. The isolates also had four extra amino acids (YRIK) in penicillin-binding protein 3 (PBP3) due to a duplication of a 12-nucleotide (TATCGAATTAAC) stretch in pbp3 By cloning and plasmid-curing experiments, we found that elevated CMY-42 cephalosporinase production or amino acid insertions in PBP3 alone mediated slightly reduced susceptibility to aztreonam-avibactam, but their combination conferred aztreonam-avibactam resistance. We show that the elevated CMY-42 production results from increased plasmid copy numbers due to mutations in inc We also verified the findings using in vitro mutation assays, in which aztreonam-avibactam-resistant mutants also had mutations in inc and elevated CMY-42 production compared with the parental strain. This choir of target modification, hydrolyzing enzyme, and plasmid expression represents a novel, coordinated, complex antimicrobial resistance mechanism and also reflects the struggle of bacteria to survive under selection pressure imposed by antimicrobial agents.IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) is a serious global challenge with limited therapeutic options. Aztreonam-avibactam is a promising antimicrobial combination with activity against CPE producing serine-based carbapenemases and metallo-β-lactamases and has the potential to be a major option for combatting CPE. Aztreonam-avibactam resistance has been found, but resistance mechanisms remain largely unknown. Understanding resistance mechanisms is essential for optimizing treatment and developing alternative therapies. Here, we found that either penicillin-binding protein 3 modification or the elevated expression of cephalosporinase CMY-42 due to increased plasmid copy numbers does not confer resistance to aztreonam-avibactam, but their combination does. We demonstrate that increased plasmid copy numbers result from mutations in antisense RNA-encoding inc of the IncIγ replicon. The findings reveal that antimicrobial resistance may be due to concerted combinatorial effects of target alteration, hydrolyzing enzyme, and plasmid expression and also highlight that resistance to any antimicrobial combination will inevitably emerge.
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Genome-based insights into the resistomes and mobilomes of two Providencia rettgeri strains isolated from wound infections in Madagascar. J Glob Antimicrob Resist 2020; 20:178-182. [DOI: 10.1016/j.jgar.2019.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 11/24/2022] Open
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San N, Aung MS, Urushibara N, San T, Maw WW, Lwin MM, Mar TT, Myint YY, Thu PP, Hlaing MS, Ganesh B, Kobayashi N. Genetic Diversity of CMY Beta-Lactamase Genes in Clinical Isolates of Escherichia coli in Myanmar: Identification of Three Novel Types and Updated Phylogenetic Classification of blaCMY. Microb Drug Resist 2019; 26:497-504. [PMID: 31738628 DOI: 10.1089/mdr.2019.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The dissemination of CMY-type enzymes, one of the plasmid-mediated AmpC beta-lactamases, among Enterobacteriaceae has become an important public health concern. In this study, genetic diversity of CMY beta-lactamase genes was investigated for 50 blaCMY-positive isolates detected from 426 clinical isolates of Escherichia coli in Yangon, Myanmar. CMY genes were differentiated into 9 types, with blaCMY-42 being predominant (22 isolates, 44%), followed by blaCMY-2, blaCMY-6, blaCMY-146, and included three novel types (CMY-156, CMY-158, CMY-159). Among E. coli harboring blaCMY, phylogenetic group D-sequence type (ST)405 and A-ST410 were the most common genotypes, and blaCTX-M-15 was detected in 72% (36/50) of isolates. blaCMY-42 was distributed to phylogenetic groups A, B1, and D E. coli with 11 STs, which included 10 isolates harboring carbapenemase genes (blaNDM-4, blaNDM-5, or blaNDM-7). Phylogenetic analysis of all the blaCMY genes reported to date, including the three novel types in the present study, revealed the presence of at least four distinct genetic groups, that is, CMY-1, CMY-2, CMY-70, and CMY-98 group, showing less than 91% nucleotide sequence identities among different groups. CMY-2 group beta-lactamase genes, which contained by far the largest number of CMY types (89.7%) with extensive diversity, were divided into two clusters (I and II). While eight CMY types identified in the present study were classified into CMY-2 group cluster I, novel type CMY-159 was assigned into CMY-98 group with a Citrobacter freundii strain in Thailand.
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Affiliation(s)
- Nilar San
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Thida San
- Yangon Children's Hospital, Ministry of Health and Sports, Yangon, Myanmar
| | - Win Win Maw
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Mya Mya Lwin
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Thin Thin Mar
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Yi Yi Myint
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Pyae Phyo Thu
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Myat Su Hlaing
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | | | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective. Clin Microbiol Infect 2019; 26:643.e1-643.e7. [PMID: 31586657 DOI: 10.1016/j.cmi.2019.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Predicting the antibiotic susceptibility phenotype from genomic data is challenging, especially for some specific antibiotics in the order Enterobacterales. Here we aimed to assess the performance of whole genomic sequencing (WGS) for predicting the antibiotic susceptibility in various Enterobacterales species using the detection of antibiotic resistance genes (ARGs), specific mutations and a knowledge-based decision algorithm. METHODS We sequenced (Illumina MiSeq, 2×250 bp) 187 clinical isolates from species possessing (n = 98) or not (n = 89) an intrinsic AmpC-type cephalosporinase. Phenotypic antibiotic susceptibility was performed by the disc diffusion method. Reads were assembled by A5-miseq and ARGs were identified from the ResFinder database using Diamond. Mutations on GyrA and ParC topoisomerases were studied. Piperacillin, piperacillin-tazobactam, ceftazidime, cefepime, meropenem, amikacin, gentamicin and ciprofloxacin were considered for prediction. RESULTS A total of 1496 isolate/antibiotic combinations (187 isolates × 8 antibiotics) were considered. In 230 cases (15.4%), no attempt of prediction was made because it could not be supported by current knowledge. Among the 1266 attempts, 1220 (96.4%) were correct (963 for predicting susceptibility and 257 for predicting resistance), 24 (1.9%) were major errors (MEs) and 22 (1.7%) were very major errors (VMEs). Concordance were similar between non-AmpC and AmpC-producing Enterobacterales (754/784 (96.2%) vs 466/482 (96.7%), chi-square test p 0.15), but more VMEs were observed in non-AmpC producing strains than in those producing an AmpC (19/784 (2.4%) vs 3/466 (0.6%), chi-square test p 0.02). The majority of VMEs were putatively due to the overexpression of chromosomal genes. CONCLUSIONS In conclusion, the inference of antibiotic susceptibility from genomic data showed good performances for non-AmpC and AmpC-producing Enterobacterales species. However, more knowledge about the mechanisms underlying the derepression of AmpC are needed.
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15
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Simoni S, Caucci S, Brenciani A, Morroni G, Giovanetti E, Menzo S, Facinelli B, Mingoia M. Increase and diversity of carbapenemase-producing Escherichia coli isolates, Italy. Future Microbiol 2019; 14:1035-1042. [DOI: 10.2217/fmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study reports on a surveillance in an Italian hospital focused on carbapenemase-producing Escherichia coli (CP-Ec). Materials & methods: Eighteen isolates (nine from clinical specimens and nine from rectal swab) were characterized for antibiotic susceptibilities, typing features, main carbapenemase, extended-spectrum ß-lactamases (ESBLs) and other bla genes, and their transferability by conjugation and transformation. Results: An increase in CP-Ec isolates was observed during 3-year surveillance period. Compared with the clinical isolates, all belonging to one sequence type (ST), ST131, those from rectal swab were very heterogeneous and belonged to eight STs. Transfer data confirmed the role of conjugative plasmids in the spreading of carbapenemase genes. Conclusion: The prevalence of CP-Ec in Italy has risen, with a substantial increase over the last year.
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Affiliation(s)
- Serena Simoni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life & Environmental Sciences Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Bruna Facinelli
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
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Lorme F, Maataoui N, Rondinaud E, Esposito-Farèse M, Clermont O, Ruppe E, Arlet G, Genel N, Matheron S, Andremont A, Armand-Lefevre L. Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics. PLoS One 2018; 13:e0206909. [PMID: 30562395 PMCID: PMC6298645 DOI: 10.1371/journal.pone.0206909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/22/2018] [Indexed: 12/31/2022] Open
Abstract
Travelers are at high risk of acquiring multi-drug resistant Enterobacteriaceae (MRE) while traveling abroad. Acquisition of extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) while traveling has been extensively described, but not that of plasmid-mediated cephalosporinase producing Enterobacteriaceae (pAmpC-E). Here, we characterized the pAmpC-E acquired in 574 French travelers to tropical areas enrolled in the VOYAG-R study. Among the 526 MRE isolated at return, 57 (10.8%) from 49 travelers were pAmpC-E. The acquisition rate of pAmpC-E was 8.5% (49/574) ranging from 12.8% (25/195) in Asia, 7.6% (14/184) in Latin America to 5.1% (10/195) in Africa. The highest acquisition rates were observed in Peru (21.9%), India (21.4%) and Vietnam (20%). The carriage of pAmpC-E decreased quickly after return with 92.5% of colonized travelers being negative at one month. Most enzymes were CMY types (96.5%, n = 55, only met in Escherichia coli), including 40 CMY-2 (70.2%), 12 CMY-42 (21.1%), 1 CMY-6 and two new CMY-2 variants. The remaining were two DHA observed in Klebsiella pneumoniae. CMY-2 producing strains were acquired worldwide whereas CMY-42, except for one, were all acquired in Asia. BlaCMY-2 genes were associated with different plasmid types, including IncI1 (45. 2%), IncF (10%), IncF-IncI (7.5%), IncA/C (5%) and IncR (2.5%) whereas blaCMY-42 were all associated with IncI1 plasmids. Even though the pAmpC-E acquisition rate was much lower than that of ESBL-E, it was significant, especially in Asia, showing that pAmpC-E, especially CMY-type producing E. coli have spread in the community settings of tropical regions.
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Affiliation(s)
- Florian Lorme
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Naouale Maataoui
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Emilie Rondinaud
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Marina Esposito-Farèse
- AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- INSERM, CIC 1425-EC, UMR1123, Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Etienne Ruppe
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Guillaume Arlet
- AP-HP, Groupe Hospitalier des Hôpitaux Universitaires de l'Est Parisien, Département de Bactériologie, Paris, France
- INSERM U1135, CIMI, Team E13, Paris, France, Sorbonne Université, UPMC Université Paris, Paris, France
| | - Nathalie Genel
- AP-HP, Groupe Hospitalier des Hôpitaux Universitaires de l'Est Parisien, Département de Bactériologie, Paris, France
- INSERM U1135, CIMI, Team E13, Paris, France, Sorbonne Université, UPMC Université Paris, Paris, France
| | | | - Sophie Matheron
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- AP-HP, Hôpital Bichat, Maladies Infectieuses et Tropicales, Paris, France
| | - Antoine Andremont
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Laurence Armand-Lefevre
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- * E-mail:
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Dagher C, Salloum T, Alousi S, Arabaghian H, Araj GF, Tokajian S. Molecular characterization of Carbapenem resistant Escherichia coli recovered from a tertiary hospital in Lebanon. PLoS One 2018; 13:e0203323. [PMID: 30188911 PMCID: PMC6126819 DOI: 10.1371/journal.pone.0203323] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
The emergence of carbapenem resistant Escherichia coli represents a serious public health concern. This study investigated the resistome, virulence, plasmids content and clonality of 27 carbapenem resistant E. coli isolated from 27 hospitalized patients at the American University of Beirut Medical Center (AUBMC) in Lebanon between 2012 and 2016. Whole-genome sequencing (WGS) data were used to identify resistance determinants. Multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), phylogenetic grouping and PCR-based replicon typing (PBRT) were also performed. The 27 isolates were distributed into 15 STs, of which ST405 (14.8%; n = 4) was the most prevalent. All of the 27 isolates were carbapenem resistant and 20 (74%) were extended-spectrum β-lactamase (ESBL) gene carriers. The predominant detected carbapenemases were blaOXA-48 (48.1%; n = 13) and blaOXA-181 (7.4%; n = 2), for the ESBLs it was blaCTX-M-15 (55.6%; n = 15) and blaCTX-M-24 (18.5%; n = 5), and for the AmpC-type β-lactamases, blaCMY-42 (40.7%; n = 11) and blaCMY-2 (3.7%; n = 1). Thirteen replicons were identified among the 27 E. coli isolates including: IncL/M, IncFIA, IncFIB, IncFII, IncI1, and IncX3. PFGE revealed a high genetic diversity with the 27 isolates being grouped in 21 different pulsotypes. SNPs analysis and PFGE showed a possible clonal dissemination of ST405, ST1284, ST354 and ST410 and the dominance of certain STs, monitoring of which could help in elucidating routes of transmission. This study represents the first WGS-based in depth analysis of the resistomes and mobilomes of carbapenem resistant E. coli in Lebanon.
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Affiliation(s)
- Christel Dagher
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sahar Alousi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Harout Arabaghian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - George F. Araj
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
- * E-mail:
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18
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Dziri O, Dziri R, Maraoub A, Chouchani C. First Report of SHV-148-Type ESBL and CMY-42-Type AmpC β-Lactamase in Klebsiella pneumoniae Clinical Isolates in Tunisia. Microb Drug Resist 2018; 24:1483-1488. [PMID: 29927719 DOI: 10.1089/mdr.2018.0073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum beta-lactamase producing Enterobacteriaceae present a real problem worldwide. We aimed to investigate the molecular mechanisms of resistance to antibiotics among Klebsiella pneumoniae clinical isolates collected from a Hospital in the southeast of Tunisia. Eighteen cephalosporin-resistant K. pneumoniae were recovered between April 2015 and August 2016. Molecular characterization of antimicrobial resistance encoding genes was performed by PCR and sequencing. Results revealed several types of Ambler class A β-lactamase encoding genes among our isolates: [blaCTXM-15 (15), blaSHV-28 (6), blaSHV-1 (2), blaSHV-148 (1), blaSHV-61 (1), blaSHV-76 (1), blaSHV-186 (1), blaTEM-1 (8)]. The association of blaOXA-1 was observed in nine isolates. However, the class C β-lactamase encoding genes were detected in four isolates [blaCMY-4 (2), blaCMY-42 (1), blaACT-35 (1)]. Molecular typing of K. pneumoniae isolates by pulsed-field gel electrophoresis showed 16 unrelated pulsotypes proving a high diversity among our isolates. Our study provides new epidemiological information showing a huge diversity of β-lactamase encoding genes among our isolates. In fact, this is the first report of SHV-76, SHV-148, and SHV-186 in Tunisia. This is also the first report of CMY-42 and ACT-35 producing K. pneumoniae in our country.
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Affiliation(s)
- Olfa Dziri
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
| | - Raoudha Dziri
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
| | - Abderrahmen Maraoub
- 2 Hôpital régional Sadok Mkaddem de Djerba, Avenue Habib Bourguiba Houmet Souk Djerba , Tunis, Tunisia
| | - Chedly Chouchani
- 1 Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar , Tunis, Tunisia
- 3 Laboratoire de Recherche Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage , Technopôle de Borj-Cedria, Hammam-Lif, Tunisia
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Shelburne SA, Kim J, Munita JM, Sahasrabhojane P, Shields RK, Press EG, Li X, Arias CA, Cantarel B, Jiang Y, Kim MS, Aitken SL, Greenberg DE. Whole-Genome Sequencing Accurately Identifies Resistance to Extended-Spectrum β-Lactams for Major Gram-Negative Bacterial Pathogens. Clin Infect Dis 2018; 65:738-745. [PMID: 28472260 DOI: 10.1093/cid/cix417] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
Background There is marked interest in using DNA-based methods to detect antimicrobial resistance (AMR), with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole-genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR. Methods Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the 4 most common gram-negative bacteria causing bloodstream infections in neutropenic patients. The WGS data, including both gene presence/absence and detection of mutations in an array of AMR-relevant genes, were used to predict resistance to 4 β-lactams commonly used in the empiric treatment of neutropenic fever. The genotypic predictions were then compared to phenotypic resistance as determined by BMD and by commercial methods during routine patient care. Results Of 133 putative instances of resistance to the β-lactams of interest identified by WGS, only 87 (65%) would have been detected by a typical PCR-based approach. The sensitivity, specificity, and positive and negative predictive values for WGS in predicting AMR were 0.87, 0.98, 0.97, and 0.91, respectively. Using BMD as the gold standard, our genotypic resistance prediction approach had a significantly higher positive predictive value compared to minimum inhibitory concentrations generated by commercial methods (0.97 vs 0.92; P = .025). Conclusions These data demonstrate the potential feasibility of using WGS to guide antibiotic treatment decisions for patients with life-threatening infections for an array of medically important pathogens.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.,Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston
| | - Jiwoong Kim
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School at Houston.,Genomics and Resistant Microbes Group, Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan K Shields
- Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Ellen G Press
- Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Xiqi Li
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center
| | - Cesar A Arias
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School at Houston.,Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston.,Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Brandi Cantarel
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas
| | - Ying Jiang
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Min S Kim
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas
| | - Samuel L Aitken
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Pharmacy, MD Anderson Cancer Center, Houston
| | - David E Greenberg
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Microbiology, University of Texas Southwestern, Dallas
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Singh NS, Singhal N, Virdi JS. Genetic Environment of blaTEM-1, blaCTX-M-15, blaCMY-42 and Characterization of Integrons of Escherichia coli Isolated From an Indian Urban Aquatic Environment. Front Microbiol 2018; 9:382. [PMID: 29563901 PMCID: PMC5845874 DOI: 10.3389/fmicb.2018.00382] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/20/2018] [Indexed: 12/02/2022] Open
Abstract
The presence of antibiotic resistance genes (ARGs) including those expressing ESBLs and AmpC-β-lactamases in Escherichia coli inhabiting the aquatic environments is a serious health problem. The situation is further complicated by the fact that ARGs can be easily transferred among bacterial species with the help of mobile genetic elements – plasmids, integrons, insertion sequences (IS), and transposons. Therefore, the analysis of genetic environment and mobile genetic elements associated with ARGs is important as these provide useful information about the epidemiology of these genes. In our previous study, we had reported presence of various β-lactam resistance genes present in E. coli strains inhabiting the river Yamuna traversing the National Capital Territory of Delhi (India). In the present study, we have analyzed the genetic environment of three ARGs blaTEM-1, blaCTX-M-15, and blaCMY -42 of those E. coli strains. The structure of class 1 integrons and their gene cassettes was also analyzed. Insertion sequence IS26 was present upstream of blaTEM-1, ISEcp1 was present upstream of blaCTXM-15 gene and orf477 was present downstream of blaCTXM-15. ISEcp1 was also present upstream of blaCMY -42 and, blc and sugE genes were present in the downstream region of this gene. Thus, the overall genetic environment surrounding these genes was similar to that reported from E. coli strains isolated globally. Conjugation assays, isolation and analysis of plasmid DNA of the transconjugants indicated that blaTEM-1, blaCTX-M-15, blaCMY -42 and class 1 integron were plasmid-mediated and possibly transmit between genera through horizontal gene transfer (HGT). This might lead to dissemination of antimicrobial resistance genes in aquatic environment. The work embodied in this paper is the first describing the genetic environment of bla and integrons in aquatic E. coli isolated from India.
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Affiliation(s)
- Nambram S Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
| | - Neelja Singhal
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
| | - Jugsharan S Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
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Occurrence of bla CMY-42 on an IncI1 plasmid in multidrug-resistant Escherichia coli from a tertiary referral hospital in India. J Glob Antimicrob Resist 2018; 14:78-82. [PMID: 29505913 DOI: 10.1016/j.jgar.2018.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Plasmids of different replicon types are believed to be associated with the carriage and transmission of antimicrobial resistance genes. The present study was undertaken to examine the association of blaCIT with particular plasmid types and to identify Escherichia coli strains involve in the maintenance of this resistance determinant in the plasmid. METHODS Phenotypic screening of AmpC β-lactamases was performed by the modified three-dimensional extract method, followed by antimicrobial susceptibility testing and determination of minimum inhibitory concentrations (MICs). Genotyping screening of β-lactamase genes was performed by PCR assay, followed by sequencing. Transferability of the blaCMY gene was performed by transformation and conjugation experiments. Plasmid incompatibility typing and DNA fingerprinting by enterobacterial repetitive intergenic consensus (ERIC)-PCR were performed. RESULTS Among 203 E. coli obtained from different clinical specimens (pus, urine, stool and sputum), 37 were detected as harbouring the blaCIT gene and sequencing of this gene showed nucleotide sequence similarity with the blaCMY-42 variant. This study revealed IncI1-type plasmids as carriers of blaCMY-42 and its propagation within E. coli ST5377, ST361 and ST672. According to the stability results, the blaCMY-42-encoding plasmid can be maintained in E. coli strains for a longer duration without any antimicrobial pressure. CONCLUSIONS These finding document blaCMY-42 on IncI1-type plasmids, which are considered to be the main vehicles for the spread of blaCMY-42 in this hospital setting. Thus, a proper strategy should be developed to curb the expansion of IncI1-type plasmids in the hospital and community environment.
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Acquisition of Carbapenem Resistance by Plasmid-Encoded-AmpC-Expressing Escherichia coli. Antimicrob Agents Chemother 2016; 61:AAC.01413-16. [PMID: 27799202 DOI: 10.1128/aac.01413-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/22/2016] [Indexed: 01/06/2023] Open
Abstract
Although AmpC β-lactamases can barely degrade carbapenems, if at all, they can sequester them and prevent them from reaching their targets. Thus, carbapenem resistance in Escherichia coli and other Enterobacteriaceae can result from AmpC production and simultaneous reduction of antibiotic influx into the periplasm by mutations in the porin genes. Here we investigated the route and genetic mechanisms of acquisition of carbapenem resistance in a clinical E. coli isolate carrying blaCMY-2 on a plasmid by selecting for mutants that are resistant to increasing concentrations of meropenem. In the first step, the expression of OmpC, the only porin produced in the strain under laboratory conditions, was lost, leading to reduced susceptibility to meropenem. In the second step, the expression of the CMY-2 β-lactamase was upregulated, leading to resistance to meropenem. The loss of OmpC was due to the insertion of an IS1 element into the ompC gene or to frameshift mutations and premature stop codons in this gene. The blaCMY-2 gene was found to be located on an IncIγ plasmid, and overproduction of the CMY-2 enzyme resulted from an increased plasmid copy number due to a nucleotide substitution in the inc gene. The clinical relevance of these genetic mechanisms became evident from the analysis of previously isolated carbapenem-resistant clinical isolates, which appeared to carry similar mutations.
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Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India. Antimicrob Agents Chemother 2016; 60:2972-80. [PMID: 26953207 DOI: 10.1128/aac.01950-15] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 02/21/2016] [Indexed: 12/30/2022] Open
Abstract
To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The blaNDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: blaNDM-1 in 2 isolates, blaNDM-5 in 7 isolates, and blaNDM-7 in 5 isolates. The blaCTX-M gene was detected in 112 isolates (66.3%): blaCTX-M-15 in 108 isolates and blaCTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the blaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.
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Bajaj P, Singh NS, Virdi JS. Escherichia coli β-Lactamases: What Really Matters. Front Microbiol 2016; 7:417. [PMID: 27065978 PMCID: PMC4811930 DOI: 10.3389/fmicb.2016.00417] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/14/2016] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.
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Affiliation(s)
- Priyanka Bajaj
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
| | - Nambram S Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
| | - Jugsharan S Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus New Delhi, India
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Increased Hydrolysis of Oximino-β-Lactams by CMY-107, a Tyr199Cys Mutant Form of CMY-2 Produced by Escherichia coli. Antimicrob Agents Chemother 2015; 59:7894-8. [PMID: 26438499 DOI: 10.1128/aac.01793-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/29/2015] [Indexed: 01/10/2023] Open
Abstract
The cephalosporinase CMY-107, a Tyr199Cys mutant form of CMY-2 encoded by an IncI self-transferable plasmid carried by an Escherichia coli clinical strain, was characterized. The enzyme hydrolyzed oximino-cephalosporins and aztreonam more efficiently than CMY-2 did.
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Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12. Sci Rep 2015; 5:12275. [PMID: 26194736 PMCID: PMC4508618 DOI: 10.1038/srep12275] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/22/2015] [Indexed: 02/05/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.
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Bajaj P, Singh NS, Kanaujia PK, Virdi JS. Distribution and molecular characterization of genes encoding CTX-M and AmpC β-lactamases in Escherichia coli isolated from an Indian urban aquatic environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 505:350-6. [PMID: 25461036 DOI: 10.1016/j.scitotenv.2014.09.084] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/14/2014] [Accepted: 09/25/2014] [Indexed: 05/21/2023]
Abstract
Aquatic environments harboring antibiotic resistant Escherichia coli constitute an important public health concern. Thus, it is important to characterize the resistance genetic elements of waterborne E. coli. It is also important to identify the predominant clonal groups/phylogroups represented by resistant strains to understand the epidemiology of antibiotic resistant E. coli in natural environments, and to identify the role of well-established genotypes in the spread of resistance in a particular geographical area through natural environments. In the present investigation, E. coli strains (n=126) isolated from various points along the river Yamuna traversing through the National Capital Territory of Delhi (India) were grouped phylogenetically. A collection of 61 strains representing all phylogroups was investigated for extended-spectrum β-lactamase (ESBL) and AmpC production. blaTEM, blaSHV and blaCTX-M genes were detected and analyzed, promoter/attenuator mutations associated with chromosomally-mediated AmpC overexpression were identified, and plasmid-mediated ampC was determined. blaTEM was the most widespread (100%) gene followed by bla(CTX-M) (16%), and plasmid-mediated ampC (3%). bla(CTX-M-15) and bla(CMY-42) were identified as the genes encoding CTX-M type ESBL and CIT type AmpC β-lactamases, respectively. CTX-M-15 ESBL phenotype was most common in phylogroup D (50%), followed by phylogroups B1 (30%), and A (20%). E. coli that produce plasmid-mediated AmpC were rare and present only in phylogroup D. Presence of multi β-lactam resistance, bla(CTX-M-15) and bla(CMY-42) in waterborne E. coli belonging to virulence-associated phylogroup D highlights the need for routine surveillance of resistance determinants in aquatic environments. This is also the first report for the presence of bla(CMY-42) in waterborne E. coli.
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Affiliation(s)
- Priyanka Bajaj
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Nambram Somendro Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Pawan Kumar Kanaujia
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jugsharan Singh Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Barišić I, Mitteregger D, Hirschl AM, Noehammer C, Wiesinger-Mayr H. High diversity of beta-lactamases in the General Hospital Vienna verified by whole genome sequencing and statistical analysis. INFECTION GENETICS AND EVOLUTION 2014; 27:408-17. [PMID: 25159028 DOI: 10.1016/j.meegid.2014.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 08/06/2014] [Accepted: 08/15/2014] [Indexed: 12/26/2022]
Abstract
The detailed analysis of antibiotic resistance mechanisms is essential for understanding the underlying evolutionary processes, the implementation of appropriate intervention strategies and to guarantee efficient treatment options. In the present study, 110 β-lactam-resistant, clinical isolates of Enterobacteriaceae sampled in 2011 in one of Europe's largest hospitals, the General Hospital Vienna, were screened for the presence of 31 β-lactamase genes. Twenty of those isolates were selected for whole genome sequencing (WGS). In addition, the number of β-lactamase genes was estimated using biostatistical models. The carbapenemase genes blaKPC-2, blaKPC-3, and blaVIM-4 were identified in carbapenem-resistant and intermediate susceptible isolates, blaOXA-72 in an extended-spectrum β-lactamase (ESBL)-positive one. Furthermore, the observed high prevalence of the acquired blaDHA-1 and blaCMY AmpC β-lactamase genes (70%) in phenotypically AmpC-positive isolates is alarming due to their capability to become carbapenem-resistant upon changes in membrane permeability. The statistical analyses revealed that approximately 55% of all β-lactamase genes present in the General Hospital Vienna were detected by this study. In summary, this work gives a very detailed picture on the disseminated β-lactamases and other resistance genes in one of Europe's largest hospitals.
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Affiliation(s)
- Ivan Barišić
- AIT Austrian Institute of Technology, Molecular Diagnostics, Muthgasse 11/2, 1190 Vienna, Austria.
| | - Dieter Mitteregger
- Medical University of Vienna, Department of Laboratory Medicine, Division of Clinical Microbiology, Währinger Gürtel 18-20, 1090 Vienna, Austria.
| | - Alexander M Hirschl
- Medical University of Vienna, Department of Laboratory Medicine, Division of Clinical Microbiology, Währinger Gürtel 18-20, 1090 Vienna, Austria.
| | - Christa Noehammer
- AIT Austrian Institute of Technology, Molecular Diagnostics, Muthgasse 11/2, 1190 Vienna, Austria.
| | - Herbert Wiesinger-Mayr
- AIT Austrian Institute of Technology, Molecular Diagnostics, Muthgasse 11/2, 1190 Vienna, Austria.
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Zhang X, Lou D, Xu Y, Shang Y, Li D, Huang X, Li Y, Hu L, Wang L, Yu F. First identification of coexistence of blaNDM-1 and blaCMY-42 among Escherichia coli ST167 clinical isolates. BMC Microbiol 2013; 13:282. [PMID: 24313961 PMCID: PMC4029178 DOI: 10.1186/1471-2180-13-282] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/28/2013] [Indexed: 11/14/2022] Open
Abstract
Background Emergence of multidrug resistance in Enterobacteriaceae limits the selection of antimicrobials for treatment of infectious diseases. Identification of NDM-1 makes more difficulty in treating multidrug-resistant Enterobacteriaceae infections. Carbapenem-resistant Escherichia coli clinical isolates from a tertiary hospital in Wenzhou, east China, were investigated for NDM-1 production. Results The two tested isolates were negative for modified Hodge test, but positive for a double-disc synergy test used for detecting metallo-β-lactamase production. E. coli WZ33 and WZ51 exhibited discrepant-level resistance to most clinically frequent used antimicrobials, but still susceptible to trimethoprim/sulfamethoxazole, amikacin, fosfomycin, tigecycline and polymyxin B. E. coli WZ33 and WZ51 were positive for blaNDM-1 determined by PCR and DNA sequencing. Other than blaNDM-1, E. coli WZ33 also harbored blaCTX-M-14 and blaCMY-42, while E. coli WZ51 simultaneously harbored blaSHV-12,blaCTX-M-14 and blaCMY-42. Carbapenem resistance for E. coli WZ51 and WZ33 could not be transferred to E. coli recipients through conjugation, but could be transferred to E. coli recipients by chemical transformation. The EcoR1-digested DNA pattern of plasmids from the transformant of E. coli WZ51 was different from that of E. coli WZ51. MLST showed that E. coli WZ33 and WZ51 belonged to an animal-associated clone (ST167). Conclusion The present study is the first report of blaNDM-1 carriage in E. coli ST167 isolates and coexistence of blaNDM-1 and blaCMY-42 in same isolate. Systemic surveillance should focus on the dissemination of blaNDM-1 among Enterobacteriaceae, especially E. coli ST167 clone associated with animal infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Liangxing Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, 2 Fuxue lane, Wenzhou 325000, China.
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Crémet L, Caroff N, Giraudeau C, Reynaud A, Caillon J, Corvec S. Detection of clonally related Escherichia coli isolates producing different CMY β-lactamases from a cystic fibrosis patient. J Antimicrob Chemother 2013; 68:1032-5. [PMID: 23302581 DOI: 10.1093/jac/dks520] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES This study reports details on Escherichia coli isolates recovered from a cystic fibrosis (CF) patient in order to understand how this pathogen adapts to and resists broad-spectrum antipseudomonal therapy in this context. METHODS Five E. coli isolates were obtained from various clinical samples (airways, urine or dialysis catheter) over a 7 month period covering a double-lung transplantation. All isolates were analysed in terms of clonality [enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing], virulence profiles (phylogroup and search for 15 virulence genes), growth patterns (morphotype, biofilm-forming ability and growth rate), hypermutability and antimicrobial susceptibility, with molecular characterization of β-lactamases and porins. RESULTS The five isolates shared similar ERIC-PCR profiles and sequence types (ST1193) and exhibited the same virulence profile. The respiratory isolates were strong mutators, exhibited mucoid or small-colony morphotypes, exhibited strong biofilm-forming ability and grew slowly compared with the others. All isolates were highly resistant to ceftazidime. The respiratory isolates showed reduced susceptibility to cefepime and high resistance to aztreonam. The patient had received a 31 day course of ceftazidime/aztreonam until transplantation. All isolates harboured the same wild-type chromosomal AmpC. A CMY-2 enzyme was detected in the non-respiratory isolates. The respiratory isolates harboured L293S and V211A/L293S new CMY-2 variants, which were designated CMY-94 and CMY-95, respectively. OmpF porin loss was observed in the non-respiratory isolates. CONCLUSIONS Our study shows that, similarly to Pseudomonas aeruginosa, E. coli can undergo phenotypic and genomic changes in the CF context. For the first time, we identified an in vivo expanded-spectrum evolution of the CMY-2 β-lactamase, during bacterial persistence in the CF lung.
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Affiliation(s)
- Lise Crémet
- Service de Bactériologie-Hygiène, CHU de Nantes, 9 quai Moncousu, 44093 Nantes cedex 1, France.
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Interactions of oximino-substituted boronic acids and β-lactams with the CMY-2-derived extended-spectrum cephalosporinases CMY-30 and CMY-42. Antimicrob Agents Chemother 2012; 57:968-76. [PMID: 23229484 DOI: 10.1128/aac.01620-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CMY-30 and CMY-42 are extended-spectrum (ES) derivatives of CMY-2. ES characteristics are due to substitutions of Gly (CMY-30) and Ser (CMY-42) for Val211 in the Ω-loop. To characterize the effects of 211 substitutions, we studied the interactions of CMY-2, -30, and -42 with boronic acid transition state inhibitors (BATSIs) resembling ceftazidime and cefotaxime, assessed thermal stability of the enzymes in their free forms and in complexes with BATSIs and oximino-β-lactams, and simulated, using molecular dynamics (MD), the CMY-42 apoenzyme and the CMY-42 complexes with ceftazidime and the ceftazidime-like BATSI. Inhibition constants showed that affinities between CMY-30 and CMY-42 and the R1 groups of BATSIs were lower than those of CMY-2. ES variants also exhibited decreased thermal stability either as apoenzymes or in covalent complexes with oximino compounds. MD simulations further supported destabilization of the ES variants. Val211Ser increased thermal factors of the Ω-loop backbone atoms, as previously observed for CMY-30. The similar effects of the two substitutions seemed to be due to a less-constrained Tyr221 likely inducing concerted movement of elements at the edges of the active site (Ω-loop-Q120 loop-R2 loop/H10 helix). This inner-protein movement, along with the wider R1 binding cleft, enabled intense vibrations of the covalently bound ceftazidime and ceftazidime-like BATSIs. Increased flexibility of the ES enzymes may assist the productive adaptation of the active site to the various geometries of the oximino substrates during the reaction (higher frequency of near-attack conformations).
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