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Harmer CJ, Hall RM. IS 26 and the IS 26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024; 88:e0011922. [PMID: 38436262 DOI: 10.1128/mmbr.00119-22] [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] [Indexed: 03/05/2024] Open
Abstract
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Dulyayangkul P, Beavis T, Lee WWY, Ardagh R, Edwards F, Hamilton F, Head I, Heesom KJ, Mounsey O, Murarik M, Pinweha P, Reding C, Satapoomin N, Shaw JM, Takebayashi Y, Tooke CL, Spencer J, Williams PB, Avison MB. Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics. PLoS Pathog 2024; 20:e1012235. [PMID: 38843111 PMCID: PMC11156391 DOI: 10.1371/journal.ppat.1012235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/30/2024] [Indexed: 06/09/2024] Open
Abstract
Amikacin and piperacillin/tazobactam are frequent antibiotic choices to treat bloodstream infection, which is commonly fatal and most often caused by bacteria from the family Enterobacterales. Here we show that two gene cassettes located side-by-side in and ancestral integron similar to In37 have been "harvested" by insertion sequence IS26 as a transposon that is widely disseminated among the Enterobacterales. This transposon encodes the enzymes AAC(6')-Ib-cr and OXA-1, reported, respectively, as amikacin and piperacillin/tazobactam resistance mechanisms. However, by studying bloodstream infection isolates from 769 patients from three hospitals serving a population of 1.2 million people in South West England, we show that increased enzyme production due to mutation in an IS26/In37-derived hybrid promoter or, more commonly, increased transposon copy number is required to simultaneously remove these two key therapeutic options; in many cases leaving only the last-resort antibiotic, meropenem. These findings may help improve the accuracy of predicting piperacillin/tazobactam treatment failure, allowing stratification of patients to receive meropenem or piperacillin/tazobactam, which may improve outcome and slow the emergence of meropenem resistance.
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Affiliation(s)
- Punyawee Dulyayangkul
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Thomas Beavis
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Winnie W. Y. Lee
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Robbie Ardagh
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Frances Edwards
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- North Bristol NHS Trust, Bristol, United Kingdom
| | | | - Ian Head
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Somerset NHS Foundation Trust, Taunton, United Kingdom
| | - Kate J. Heesom
- Bristol University Proteomics Facility, University of Bristol, Bristol, United Kingdom
| | - Oliver Mounsey
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Marek Murarik
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Peechanika Pinweha
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Carlos Reding
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Naphat Satapoomin
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - John M. Shaw
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Catherine L. Tooke
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - James Spencer
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Philip B. Williams
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Matthew B. Avison
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
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Babiker A, Lohsen S, Van Riel J, Hjort K, Weiss DS, Andersson DI, Satola S. Heteroresistance to piperacillin/tazobactam in Klebsiella pneumoniae is mediated by increased copy number of multiple β-lactamase genes. JAC Antimicrob Resist 2024; 6:dlae057. [PMID: 38601791 PMCID: PMC11004786 DOI: 10.1093/jacamr/dlae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Background Piperacillin/tazobactam is a β-lactam/β-lactamase inhibitor combination with a broad spectrum of activity that is often used as empirical and/or targeted therapy among hospitalized patients. Heteroresistance (HR) is a form of antibiotic resistance in which a minority population of resistant cells coexists with a majority susceptible population that has been found to be a cause of antibiotic treatment failure in murine models. Objectives To determine the prevalence of HR and mechanisms of HR to piperacillin/tazobactam among Klebsiella pneumoniae bloodstream infection (BSI) isolates. Materials From July 2018 to June 2021, K. pneumoniae piperacillin/tazobactam-susceptible BSI isolates were collected from two tertiary hospitals in Atlanta, GA, USA. Only first isolates from each patient per calendar year were included. Population analysis profiling (PAP) and WGS were performed to identify HR and its mechanisms. Results Among 423 K. pneumoniae BSI isolates collected during the study period, 6% (25/423) were found to be HR with a subpopulation surviving above the breakpoint. WGS of HR isolates grown in the presence of piperacillin/tazobactam at concentrations 8-fold that of the MIC revealed copy number changes of plasmid-located β-lactamase genes blaCTX-M-15, blaSHV33, blaOXA-1 and blaTEM-1 by tandem gene amplification or plasmid copy number increase. Conclusions Prevalence of HR to piperacillin/tazobactam among bloodstream isolates was substantial. The HR phenotype appears to be caused by tandem amplification of β-lactamase genes found on plasmids or plasmid copy number increase. This raises the possibility of dissemination of HR through horizontal gene transfer and requires further study.
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Affiliation(s)
- Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Lohsen
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Julia Van Riel
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - David S Weiss
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sarah Satola
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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Shropshire WC, Amiji H, Bremer J, Selvaraj Anand S, Strope B, Sahasrabhojane P, Gohel M, Aitken S, Spitznogle S, Zhan X, Kim J, Greenberg DE, Shelburne SA. Genetic determinants underlying the progressive phenotype of β-lactam/β-lactamase inhibitor resistance in Escherichia coli. Microbiol Spectr 2023; 11:e0222123. [PMID: 37800937 PMCID: PMC10715226 DOI: 10.1128/spectrum.02221-23] [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: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE The increased feasibility of whole-genome sequencing has generated significant interest in using such molecular diagnostic approaches to characterize difficult-to-treat, antimicrobial-resistant (AMR) infections. Nevertheless, there are current limitations in the accurate prediction of AMR phenotypes based on existing AMR gene database approaches, which primarily correlate a phenotype with the presence/absence of a single AMR gene. Our study utilized a large cohort of cephalosporin-susceptible Escherichia coli bacteremia samples to determine how increasing the dosage of narrow-spectrum β-lactamase-encoding genes in conjunction with other diverse β-lactam/β-lactamase inhibitor (BL/BLI) genetic determinants contributes to progressively more severe BL/BLI phenotypes. We were able to characterize the complexity of the genetic mechanisms underlying progressive BL/BLI resistance including the critical role of β-lactamase encoding gene amplification. For the diverse array of AMR phenotypes with complex mechanisms involving multiple genomic factors, our study provides an example of how composite risk scores may improve understanding of AMR genotype/phenotype correlations.
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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, Texas, USA
| | - Hatim Amiji
- Frank H. Netter MD School of Medicine, Quinnipiac University, Hamden, Connecticut, USA
| | - Jordan Bremer
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Selvalakshmi Selvaraj Anand
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Benjamin Strope
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marc Gohel
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel Aitken
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Spitznogle
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David E. Greenberg
- Department of Microbiology, UT Southwestern, Dallas, Texas, USA
- Department of Internal Medicine, UT Southwestern, Dallas, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Wang Y, He J, Sun L, Jiang Y, Hu L, Leptihn S, Zhu P, Fu X, Yu Y, Hua X. IS26 mediated bla CTX-M-65 amplification in Escherichia coli increase the antibiotic resistance to cephalosporin in vivo. J Glob Antimicrob Resist 2023; 35:202-209. [PMID: 37802302 DOI: 10.1016/j.jgar.2023.09.018] [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: 10/21/2022] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023] Open
Abstract
OBJECTIVES To characterize two Escherichia coli strains isolated from a patient pre- and post-treatment, using β-lactams and β-lactam/β-lactamase inhibitor combinations (BLBLIs). METHODS A combination of antibiotic susceptibility testing (AST) with whole genome sequencing using Illumina and Oxford Nanopore platforms. Long-read sequencing and reverse transcription-quantitative PCR were performed to determine the copy numbers and expression levels of antibiotic resistance genes (ARGs), respectively. Effect on fitness costs were assessed by growth rate determination. RESULTS The strain obtained from the patient after the antibiotic treatment (XH989) exhibited higher resistance to cefepime, BLBLIs and quinolones compared with the pre-treatment strain (XH987). Sequencing revealed IS26-mediated duplications of a IS26-fosA3-blaCTX-M-65 plasmid-embedded element in strain XH989. Long-read sequencing (7.4 G data volume) indicated a variation in copy numbers of blaCTX-M-65 within one single culture of strain XH989. Increased copy numbers of the IS26-fosA3-blaCTX-M-65 element were correlated with higher CTX-M-65 expression level and did not impose fitness costs, while facilitating faster growth under high antibiotic concentrations. CONCLUSION Our study is an example from the clinic how BLBLIs and β-lactams exposure in vivo possibly promoted the amplification of an IS26-multiple drug resistance (MDR) region. The observation of a copy number variation seen with the blaCTX-M-65 gene in the plasmid of the post-treatment strain expands our knowledge of insertion sequence dynamics and evolution during treatment.
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Affiliation(s)
- Yinping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Long Sun
- Department of Clinical Laboratory, Hangzhou Women's Hospital, Hangzhou Maternity and Child Health Care Hospital, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lihua Hu
- Department of Critical Care Medicine, Hangzhou General Hospital of Chinese People's Armed Police, Hangzhou, People's Republic of China
| | - Sebastian Leptihn
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; University of Edinburgh Medical School, Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Pengfei Zhu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; Qingdao Single-Cell Biotech Co. Ltd., Qingdao, Shandong, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; Qingdao Single-Cell Biotech Co. Ltd., Qingdao, Shandong, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China.
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Gálvez-Benítez L, de la Rosa JMO, Rodriguez-Villodres A, Casimiro-Soriguer CS, Molina-Panadero I, Alvarez-Marin R, Bonnin RA, Naas T, Pachón J, Cisneros JM, Lepe JA, Smani Y. Role of bla TEM and OmpC in the piperacillin-tazobactam resistance evolution by E. coli in patients with complicated intra-abdominal infection. J Infect 2023; 87:220-229. [PMID: 37442373 DOI: 10.1016/j.jinf.2023.07.005] [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: 04/20/2023] [Revised: 06/30/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
Piperacillin-tazobactam resistance (P/T-R) is increasingly reported among Escherichia coli isolates. Although in vitro experiments have suggested that blaTEM gene plays a key role in the P/T-R acquisition, no clinical in vivo study has yet confirmed the role of blaTEM or other genes. Therefore, we aimed to identify the mechanisms underlying P/T-R by following up patients with E. coli complicated intra-abdominal infections (cIAI) who experienced P/T treatment failure. Four pairs of strains, clonally related from four patients, were isolated both before and after treatment with P/T dosed at 4 g/0.5 g intravenously. The P/T MIC was tested using broth microdilution, and β-lactamase activity was determined in these isolates. Whole-genome sequencing (WGS) was performed to decipher the role of blaTEM and other genes associated with P/T-R. Changes in the outer membrane protein (OMP) profile were analyzed using SDS-PAGE, and blaTEM and ompC transcription levels were measured by RT-qPCR. In addition, in vitro competition fitness was performed between each pairs of strains (P/T-susceptible vs. P/T-resistant). We found a higher copy number of blaTEM gene in P/T-R isolates, generated by three different genetic events: (1) IS26-mediated duplication of the blaTEM gene, (2) generation of a small multicopy plasmid (ColE-like) carrying blaTEM, and (3) adaptive evolution via reduction of plasmid size, leading to a higher plasmid copy number. Moreover, two P/T-R strains showed reduced expression of OmpC. This study describes the mechanisms involved in the acquisition of P/T-R by E. coli in patients with cIAI. The understanding of P/T-R evolution is crucial for effectively treating infected patients and preventing the spread of resistant microorganisms.
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Affiliation(s)
- Lydia Gálvez-Benítez
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - José Manuel Ortiz de la Rosa
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Angel Rodriguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII), Madrid, Spain
| | - Carlos S Casimiro-Soriguer
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Irene Molina-Panadero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
| | - Rocío Alvarez-Marin
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII), Madrid, Spain
| | - Rémy A Bonnin
- Team ReSIST, INSERM U1184, Université Paris-Saclay, CEA, Inserm, Immunologie des Maladies Virales, Auto-Immunes, Hématologiques et Bactériennes (IMVA-HB/IDMIT), 94270 Le Kremlin Bicêtre, France; Service de Bactériologie-Hygiène, Hôpital Bicêtre, AP-HP, 94270 Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriales, 94270 Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, Université Paris-Saclay, CEA, Inserm, Immunologie des Maladies Virales, Auto-Immunes, Hématologiques et Bactériennes (IMVA-HB/IDMIT), 94270 Le Kremlin Bicêtre, France; Service de Bactériologie-Hygiène, Hôpital Bicêtre, AP-HP, 94270 Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriales, 94270 Le Kremlin-Bicêtre, France
| | - Jerónimo Pachón
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Department of Medicine, School of Medicine, University of Seville, Seville, Spain
| | - José Miguel Cisneros
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII), Madrid, Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Seville, Spain; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III (CIBERINFEC, ISCIII), Madrid, Spain
| | - Younes Smani
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain; Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain; Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain.
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Tsai CH, Chen YC, Chen PY, Lai CC, Tang HJ, Chuang YC, Chen CC, Ho CH, Hsu WY, Chang TH. Antimicrobial Susceptibility of E. coli Isolates from Intra-Abdominal Infections in the Asia-Pacific Region: Trends in Ciprofloxacin, Ceftriaxone, Cefepime, and Piperacillin/Tazobactam Susceptibility. Infect Drug Resist 2023; 16:5599-5611. [PMID: 37650005 PMCID: PMC10464894 DOI: 10.2147/idr.s422203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023] Open
Abstract
Purpose To investigate the antibiotic susceptibility of Escherichia coli isolates in patients diagnosed with intra-abdominal infections (IAIs) in the Asia-Pacific region. Patients and Methods This study was conducted at 50 medical hospitals across 9 countries/regions as part of the Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program from 2014 to 2018. Nonduplicate isolates of aerobic and facultative gram-negative bacilli were collected and processed for further antimicrobial susceptibility testing. Results A total of 10,709 isolates were collected, with E. coli (n=4737, 44.2%) being the leading pathogen causing IAIs, followed by Klebsiella pneumoniae (n=2429, 22.7%) and Pseudomonas aeruginosa (n=931, 8.7%). Community-associated (CA) E. coli isolates generally exhibited higher susceptibility rates for most antibiotics than hospital-associated (HA) isolates. In countries/regions other than Hong Kong, South Korea, and Singapore, HA isolates displayed lower susceptibility rates for multiple classes (≥4) of antibiotics. Among the commonly used antibiotics in IAIs, the overall susceptibility rate for ciprofloxacin was low, with an average of 41.3%. Ceftriaxone susceptibility rates in all selected countries were below 80% starting in 2018, ranging from 23.3% to 75.8%. The cefepime susceptibility rates varied across regions, with consistently reduced susceptibility ranging from 45.5% to 57.8% in India, Thailand, and Vietnam. Piperacillin/tazobactam demonstrated effectiveness against E. coli isolates in almost all countries except India, with a downward trend observed in the Philippines and Taiwan. Carbapenems remained effective against more than 90% of E. coli isolates, except in India. Conclusion Prudent use of fluoroquinolones and ceftriaxone is advised when treating both CA and HA IAIs in the Asia-Pacific region. The low susceptibility rate of cefepime in India, Thailand, and Vietnam needs careful consideration in its administration. Moreover, the increase in nonsusceptibility to piperacillin/tazobactam in the Philippines and Taiwan poses a potential risk that should be closely monitored.
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Affiliation(s)
- Chia-Hung Tsai
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Yu-Chin Chen
- Department of Pediatrics, Chi Mei Medical Center, Chiali, Tainan, Taiwan
| | - Po-Yu Chen
- Department of Nursing, Min-Hwei College of Health Care Management, Tainan, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hung-Jen Tang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Yin-Ching Chuang
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
| | - Chi-Chung Chen
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
- Department of Food Science, National Chiayi University, Chiayi, Taiwan
| | - Chung-Han Ho
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
- Department of Information Management, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Wei-Yun Hsu
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Tu-Hsuan Chang
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
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8
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RecA inactivation as a strategy to reverse the heteroresistance phenomenon in clinical isolates of Escherichia coli. Int J Antimicrob Agents 2023; 61:106721. [PMID: 36642235 DOI: 10.1016/j.ijantimicag.2023.106721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/25/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
RecA inhibition could be an important strategy to combat antimicrobial resistance because of its key role in the SOS response, DNA repair and homologous recombination contributing to bacterial survival. This study evaluated the impact of RecA inactivation on heteroresistance in clinical isolates of Escherichia coli and their corresponding recA-deficient isogenic strains to multiple classes of antimicrobial agents. A high frequency (>30%) of heteroresistance was observed in this collection of clinical isolates. Deletion of the recA gene led to a marked reduction in heteroresistant subpopulations, especially against quinolones or β-lactams. The molecular basis of heteroresistance was associated with an increase in copy number of plasmid-borne resistance genes (blaTEM-1B) or tandem gene amplifications (qnrA1). Of note, in the absence of the recA gene, the increase in copy number of resistance genes was suppressed. This makes the recA gene a promising target for combating heteroresistance.
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9
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Wagner TM, Howden BP, Sundsfjord A, Hegstad K. Transiently silent acquired antimicrobial resistance: an emerging challenge in susceptibility testing. J Antimicrob Chemother 2023; 78:586-598. [PMID: 36719135 PMCID: PMC9978586 DOI: 10.1093/jac/dkad024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acquisition and expression of antimicrobial resistance (AMR) mechanisms in bacteria are often associated with a fitness cost. Thus, evolutionary adaptation and fitness cost compensation may support the advance of subpopulations with a silent resistance phenotype when the antibiotic selection pressure is absent. However, reports are emerging on the transient nature of silent acquired AMR, describing genetic alterations that can change the expression of these determinants to a clinically relevant level of resistance, and the association with breakthrough infections causing treatment failures. This phenomenon of transiently silent acquired AMR (tsaAMR) is likely to increase, considering the overall expansion of acquired AMR in bacterial pathogens. Moreover, the augmented use of genotypic methods in combination with conventional phenotypic antimicrobial susceptibility testing (AST) will increasingly enable the detection of genotype and phenotype discrepancy. This review defines tsaAMR as acquired antimicrobial resistance genes with a corresponding phenotype within the wild-type distribution or below the clinical breakpoint for susceptibility for which genetic alterations can mediate expression to a clinically relevant level of resistance. References to in vivo resistance development and therapeutic failures caused by selected resistant subpopulations of tsaAMR in Gram-positive and Gram-negative pathogens are given. We also describe the underlying molecular mechanisms, including alterations in the expression, reading frame or copy number of AMR determinants, and discuss the clinical relevance concerning challenges for conventional AST.
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Affiliation(s)
- Theresa Maria Wagner
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Benjamin Peter Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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10
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Shropshire WC, Konovalova A, McDaneld P, Gohel M, Strope B, Sahasrabhojane P, Tran CN, Greenberg D, Kim J, Zhan X, Aitken S, Bhatti M, Savidge TC, Treangen TJ, Hanson BM, Arias CA, Shelburne SA. Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections. mSystems 2022; 7:e0047622. [PMID: 36036505 PMCID: PMC9601100 DOI: 10.1128/msystems.00476-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 01/25/2023] Open
Abstract
Noncarbapenemase-producing carbapenem-resistant Enterobacterales (non-CP-CRE) are increasingly recognized as important contributors to prevalent carbapenem-resistant Enterobacterales (CRE) infections. However, there is limited understanding of mechanisms underlying non-CP-CRE causing invasive disease. Long- and short-read whole-genome sequencing was used to elucidate carbapenem nonsusceptibility determinants in Enterobacterales bloodstream isolates at MD Anderson Cancer Center in Houston, Texas. We investigated carbapenem nonsusceptible Enterobacterales (CNSE) mechanisms (i.e., isolates with carbapenem intermediate resistance phenotypes or greater) through a combination of phylogenetic analysis, antimicrobial resistance gene detection/copy number quantification, porin assessment, and mobile genetic element (MGE) characterization. Most CNSE isolates sequenced were non-CP-CRE (41/79; 51.9%), whereas 25.3% (20/79) were Enterobacterales with intermediate susceptibility to carbapenems (CIE), and 22.8% (18/79) were carbapenemase-producing Enterobacterales (CPE). Statistically significant copy number variants (CNVs) of extended-spectrum β-lactamase (ESBL) genes (Wilcoxon Test; P-value < 0.001) were present in both non-CP-CR E. coli (median CNV = 2.6×; n = 17) and K. pneumoniae (median CNV = 3.2×, n = 17). All non-CP-CR E. coli and K. pneumoniae had predicted reduced expression of at least one outer membrane porin gene (i.e., ompC/ompF or ompK36/ompK35). Completely resolved CNSE genomes revealed that IS26 and ISEcp1 structures harboring blaCTX-M variants along with other antimicrobial resistance elements were associated with gene amplification, occurring in mostly IncFIB/IncFII plasmid contexts. MGE-mediated β-lactamase gene amplifications resulted in either tandem arrays, primarily mediated by IS26 translocatable units, or segmental duplication, typically due to ISEcp1 transposition units. Non-CP-CRE strains were the most common cause of CRE bacteremia with carbapenem nonsusceptibility driven by concurrent porin loss and MGE-mediated amplification of blaCTX-M genes. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) are considered urgent antimicrobial resistance (AMR) threats. The vast majority of CRE research has focused on carbapenemase-producing Enterobacterales (CPE) even though noncarbapenemase-producing CRE (non-CP-CRE) comprise 50% or more of isolates in some surveillance studies. Thus, carbapenem resistance mechanisms in non-CP-CRE remain poorly characterized. To address this problem, we applied a combination of short- and long-read sequencing technologies to a cohort of CRE bacteremia isolates and used these data to unravel complex mobile genetic element structures mediating β-lactamase gene amplification. By generating complete genomes of 65 carbapenem nonsusceptible Enterobacterales (CNSE) covering a genetically diverse array of isolates, our findings both generate novel insights into how non-CP-CRE overcome carbapenem treatments and provide researchers scaffolds for characterization of their own non-CP-CRE isolates. Improved recognition of mechanisms driving development of non-CP-CRE could assist with design and implementation of future strategies to mitigate the impact of these increasingly recognized AMR pathogens.
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Affiliation(s)
- W. C. Shropshire
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - A. Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - P. McDaneld
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - M. Gohel
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - B. Strope
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - P. Sahasrabhojane
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - C. N. Tran
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - D. Greenberg
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - J. Kim
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - X. Zhan
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - S. Aitken
- Division of Pharmacy, Michigan Medicine at University of Michigan, Ann Arbor, Michigan, USA
| | - M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - T. C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - T. J. Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - B. M. Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - C. A. Arias
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. A. Shelburne
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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11
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Harmer CJ, Lebreton F, Stam J, McGann PT, Hall RM. Mechanisms of IS 26-Mediated Amplification of the aphA1 Gene Leading to Tobramycin Resistance in an Acinetobacter baumannii Isolate. Microbiol Spectr 2022; 10:e0228722. [PMID: 36073931 PMCID: PMC9602291 DOI: 10.1128/spectrum.02287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/19/2022] [Indexed: 01/04/2023] Open
Abstract
Enhanced levels of resistance to antibiotics arising from amplification of an antibiotic resistance gene that impact therapeutic options are increasingly observed. Amplification can also disclose novel phenotypes leading to treatment failure. However, the mechanism is poorly understood. Here, the route to amplification of the aphA1 kanamycin and neomycin resistance gene during tobramycin treatment of an Acinetobacter baumannii clinical isolate, leading to tobramycin resistance and treatment failure, was investigated. In the tobramycin-susceptible parent isolate, MRSN56, a single copy of aphA1 is present in the pseudocompound transposon PTn6020, bounded by directly oriented copies of IS26. For two clinical resistant isolates, new long-read sequence data were combined with available short-read data to complete the genomes. Comparison to the completed genome of MRSN56 revealed that, in both cases, IS26 had generated a circular translocatable unit (TU) containing PTn6020 and additional adjacent DNA. In one case, this TU was reincorporated into the second product generated by the deletion that formed the TU via the targeted conservative route and amplified about 7 times. In the second case, the TU was incorporated at a new location via the copy-in route and amplified about 65 times. Experimental amplification ex vivo by subjecting MRSN56 to tobramycin selection pressure yielded different TUs, which were incorporated at either the original location or a new location and amplified many times. The outcomes suggest that when IS26 is involved, amplification occurs via rolling circle replication of a newly formed TU coupled to the IS26-mediated TU formation or reincorporation step. IMPORTANCE Heteroresistance, a significant issue that is known to impact antibiotic treatment outcomes, is caused by the presence of spontaneously arising cells with elevated levels of resistance to therapeutically important antibiotics in a population of susceptible cells. Gene amplification is one well-documented cause of heteroresistance, but precisely how extensive amplification occurs is not understood. Here, we establish the case for the direct involvement of IS26 activity in the amplification of the aphA1 gene to disclose resistance to tobramycin. The aphA1 gene is usually found associated with IS26 in Gram-negative pathogens and is commonly found in extensively resistant Acinetobacter baumannii strains. IS26 and related IS cause adjacent deletions, forming a nonreplicating circular molecule known as a translocatable unit (TU), and amplification via a rolling circle mechanism appears to be coupled to either IS26-mediated TU formation or reincorporation. Related IS found in Gram-positive pathogens may play a similar role.
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Affiliation(s)
- Christopher J. Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Francois Lebreton
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason Stam
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T. McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ruth M. Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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12
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Mondragón-Quiguanas A, Villaquirán-Muriel MÁ, Rivera SP, Rosero-García D, Aranaga C, Correa A, Falco A. Beta-Lactam-Resistant Enterobacterales Isolated from Landfill Leachates. Pathogens 2022; 11:1077. [PMID: 36297134 PMCID: PMC9609224 DOI: 10.3390/pathogens11101077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2023] Open
Abstract
Antibiotic resistance is one of the main challenges worldwide due to the high morbidity and mortality caused by infections produced by resistant bacteria. In Colombia, this problem has been studied mainly from the clinical perspective; however, it is scarcely studied in the leachates produced in landfills. The objective of this study was to detect, identify and determine the antibiotic sensitivity profile of Enterobacterales isolated from a leachate treatment plant located in Cali, Colombia. Detection was performed using selective culture media, bacterial identification using Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF, bioMérieux) and by sequencing the gene coding for the 16S ribosomal RNA subunit when discrepancies were observed between phenotypic characteristics and MALDI-TOF. Antibiotic sensitivity profiling was determined using the automated VITEK®2 system (bioMérieux). Twenty-one isolates were obtained, of which Klebsiella pneumoniae was the most frequent (23.8%), and 34% of the isolates showed decreased sensitivity to beta-lactam antibiotics such as cefoxitin, ampicillin/sulbactam and piperacillin/tazobactam. These findings suggest that leachates from landfills could be a reservoir of pathogenic bacteria carrying antibiotic resistance determinants, so periodic microbiological characterization of these effluents should be performed, promoting the One Health approach.
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Affiliation(s)
- Alejandra Mondragón-Quiguanas
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
| | - Miguel Ángel Villaquirán-Muriel
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
| | - Sandra Patricia Rivera
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
- Laboratorio de Salud Pública Departamental, Secretaria Departamental de Salud del Valle del Cauca, Gobernación del Valle del Cauca, Cali 760045, Colombia
| | - Doris Rosero-García
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
| | - Carlos Aranaga
- Universidad Santiago de Cali, Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Cali 760035, Colombia
| | - Adriana Correa
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
- Clínica Imbanaco, Cali 760042, Colombia
| | - Aura Falco
- Universidad Santiago de Cali, Grupo de Investigación en Microbiología, Industria y Ambiente (GIMIA), Facultad de Ciencias Básicas, Cali 760035, Colombia
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Pharmacodynamics of Piperacillin-Tazobactam/Amikacin Combination versus Meropenem against Extended-Spectrum β-Lactamase-Producing Escherichia coli in a Hollow Fiber Infection Model. Antimicrob Agents Chemother 2022; 66:e0016222. [PMID: 35924928 PMCID: PMC9487465 DOI: 10.1128/aac.00162-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Carbapenems are recommended for the treatment of urosepsis caused by extended-spectrum β-lactamase (ESBL)-producing, multidrug-resistant Escherichia coli; however, due to selection of carbapenem resistance, there is an increasing interest in alternative treatment regimens including the use of β-lactam-aminoglycoside combinations. We compared the pharmacodynamic activity of piperacillin-tazobactam and amikacin as mono and combination therapy versus meropenem monotherapy against extended-spectrum β-lactamase (ESBL)-producing, piperacillin-tazobactam resistant E. coli using a dynamic hollow fiber infection model (HFIM) over 7 days. Broth-microdilution was performed to determine the MIC of E. coli isolates. Whole genome sequencing was conducted. Four E. coli isolates were tested in HFIM with an initial inoculum of ~107 CFU/mL. Dosing regimens tested were piperacillin-tazobactam 4.5 g, 6-hourly, plus amikacin 30 mg/kg, 24-hourly, as combination therapy, and piperacillin-tazobactam 4.5 g, 6-hourly, amikacin 30 mg/kg, 24-hourly, and meropenem 1 g, 8-hourly, each as monotherapy. We observed that piperacillin-tazobactam and amikacin monotherapy demonstrated initial rapid bacterial killing but then led to amplification of resistant subpopulations. The piperacillin-tazobactam/amikacin combination and meropenem experiments both attained a rapid bacterial killing (~4-5 log10) within 24 h and did not result in any emergence of resistant subpopulations. Genome sequencing demonstrated that all ESBL-producing E. coli clinical isolates carried multiple antibiotic resistance genes including blaCTX-M-15, blaOXA-1, blaEC, blaTEM-1, and aac(6')-Ib-cr. These results suggest that the combination of piperacillin-tazobactam/amikacin may have a potential role as a carbapenem-sparing regimen, which should be tested in future urosepsis clinical trials.
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14
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Villodres AR, Benítez LG, Arroyo MJ, Méndez G, Mancera L, Domínguez AV, Jímenez JAL, Smani Y. Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistant Escherichia coli by the MALDIpiptaz test. Emerg Microbes Infect 2022; 11:2034-2044. [PMID: 35972021 PMCID: PMC9423838 DOI: 10.1080/22221751.2022.2113746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Background The excessive use of piperacillin/tazobactam (P/T) has promoted the emergence of P/T-resistant Enterobacterales. We reported that in Escherichia coli, P/T contributes to the development of extended-spectrum resistance to β-lactam/β-lactamase inhibitor (BL/BLI) (ESRI) in isolates that are P/T susceptible but have low-level resistance to BL/BLI. Currently, the detection of P/T resistance relying on conventional methods is time-consuming. To overcome this issue, we developed a cost-effective test based on MALDI-MS technology, called MALDIpiptaz, which aims to detect P/T resistance and ESRI developers in E. coli. Methods We used automated Clover MS Data Analysis software to analyse the protein profile spectra obtained by MALDI-MS from a collection of 248 E. coli isolates (91 P/T-resistant, 81 ESRI developers and 76 P/T-susceptible). This software allowed to preprocess all the spectra to build different peak matrices that were analysed by machine learning algorithms. Results We demonstrated that MALDIpiptaz can efficiently and rapidly (15 min) discriminate between P/T-resistant, ESRI developer and P/T-susceptible isolates and allowed the correct classification between ESRI developers from their isogenic resistance to P/T. Conclusion The combination of excellent performance and cost-effectiveness are all desirable attributes, allowing the MALDIpiptaz test to be a useful tool for the rapid determination of P/T resistance in clinically relevant E. coli isolates.
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Affiliation(s)
- Angel Rodríguez Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Lydia Gálvez Benítez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Manuel J Arroyo
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Gema Méndez
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Luis Mancera
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016 Granada, Spain
| | - Andrea Vila Domínguez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - José Antonio Lepe Jímenez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Younes Smani
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Andalusian Center of Developmental Biology, CSIC, University of Pablo de Olavide, Seville, Spain
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Yang F, Zhao Q, Wang L, Wu J, Jiang L, Sheng L, Zhang L, Xue Z, Yi M. Diminished Susceptibility to Cefoperazone/Sulbactam and Piperacillin/Tazobactam in Enterobacteriaceae Due to Narrow-Spectrum β-Lactamases as Well as Omp Mutation. Pol J Microbiol 2022; 71:251-256. [PMID: 35716168 PMCID: PMC9252146 DOI: 10.33073/pjm-2022-023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/30/2022] [Indexed: 11/05/2022] Open
Abstract
Cefoperazone/sulbactam (CSL) and piperacillin/tazobactam (TZP) are commonly used in clinical practice in China because of their excellent antimicrobial activity. CSL and TZP-nonsusceptible Enterobacteriaceae are typically resistant to extended-spectrum cephalosporins such as ceftriaxone (CRO). However, 11 nonrepetitive Enterobacteriaceae strains, which were resistant to CSL and TZP yet susceptible to CRO, were collected from January to December 2020. Antibiotic susceptibility tests and whole-genome sequencing were conducted to elucidate the mechanism for this rare phenotype. Antibiotic susceptibility tests showed that all isolates were amoxicillin/clavulanic-acid resistant and sensitive to ceftazidime, cefepime, cefepime/tazobactam, cefepime/zidebactam, ceftazidime/avibactam, and ceftolozane/tazobactam. Whole-genome sequencing revealed three of seven Klebsiella pneumoniae strains harbored bla SHV-1 only, and four harbored bla SHV-1 and bla TEM-1B. Two Escherichia coli strains carried bla TEM-1B only, while two Klebsiella oxytoca isolates harbored bla OXY-1-3 and bla OXY-1-1, respectively. No mutation in the β-lactamase gene and promoter sequence was found. Outer membrane protein (Omp) gene detection revealed that numerous missense mutations of OmpK36 and OmpK37 were found in all strains of K. pneumoniae. Numerous missense mutations of OmpK36 and OmpK35 and OmpK37 deficiency were found in one K. oxytoca strain, and no OmpK gene was found in the other. No Omp mutations were found in E. coli isolates. These results indicated that narrow spectrum β-lactamases, TEM-1, SHV-1, and OXY-1, alone or in combination with Omp mutation, contributed to the resistance to CSL and TZP in CRO-susceptible Enterobacteriaceae. Antibiotic susceptibility tests Antibiotics Breakpoint, (μg/ml) Klebsiella pneumoniae Escherichia cou Klebriehd axyoca E1 E3 E4 E7 E9 E10 E11 E6 E8 E2 E5 CRO ≤1≥4 ≤0.5 ≤0.5 ≤0.5 ≤0.5 1 ≤0.5 1 ≤0.5 ≤0.5 1 1 CAZ 4 ≥16 1 2 1 4 4 4 4 2 4 1 1 FEP ≤2 216 1 1 0.25 1 2 2 2 0.5 2 1 1 AMC ≤8 ≥32 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 ≥128 CSL ≤16 ≥64 64 64 64 64 ≥128 128 ≥128 64 128 128 ≥128 TZP ≤16 ≥128 ≥256 ≥256 ≥256 ≥256 2256 2256 ≥256 ≥256 ≥256 ≥256 ≥256 FPT ≤2 ≥16 1 0.5 0.06 0.125 2 1 2 0.25 1 0.125 0.25 FPZ ≤2 216 0.25 0.25 0.06 0.125 0.25 0.25 1 0.125 0.25 0.125 0.125 CZA ≤8 216 1 0.5 0.25 0.25 1 0.25 1 0.5 0.5 0.5 0.25 CZT ≤2 28 2 1 0.5 1 2 2 2 1 1 2 2 CROceftriaxone, CAZceftazidime, FEPcefepime, AMC:amoxicillin clavulanic-acid, CSLcefoperazone/sulbactam, TZP:piperadllin/tazobactam, FPT:cefepime tazobactam, FPZ:cefepime/zidebactam, CZA:ceftazidime/avibactam, CZTceftolozane/tazobactam Gene sequencing results Number Strain ST p-Lactamase gene Promoter sequence mutation Omp mutation El Kpn 45 blaSHV-1, blaTEM-lB none OmpK36, OmpK3 7 E3 Kpn 45 blaSHV-1, blaTEM-lB none OmpK36. OmpK3 7 E4 Kpn 2854 blaSHV-1 none OmpK36, OmpK3 7 E7 Kpn 2358 blaSHV-1 - blaTEM-lB none OmpK36, OmpK3 7 E9 Kpn 2358 blaSHV-1. blaTEM-lB none OmpK36. OmpK3 7 E10 Kpn 18 9 blaSHV-1 none OmpK36. OmpK3 7 Ell Kpn 45 blaSHV-1 none OmpK36, OmpK3 7 E6 Eco 88 blaTEM-lB none none ES Eco 409 blaTEM-1B none none E2 Kox 194 blaOXY-1-3 none OmpK36 mutations. OmpK35 and OmpK 37 deficiency E5 Kox 11 blaOXY-1-1 none no OmpK (OmpK3 5, OmpK36 and OmpK37) gene found.
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Affiliation(s)
- Fengzhen Yang
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Qi Zhao
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Lipeng Wang
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Jinying Wu
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Lihua Jiang
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Li Sheng
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Leyan Zhang
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Zhaoping Xue
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
| | - Maoli Yi
- Department of Laboratory Medicine, Qingdao University Medical College Affiliated Yantai Yuhuangding Hospital, Yantai, China
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Evolutionary Trajectories toward High-Level β-Lactam/β-Lactamase Inhibitor Resistance in the Presence of Multiple β-Lactamases. Antimicrob Agents Chemother 2022; 66:e0029022. [PMID: 35652643 DOI: 10.1128/aac.00290-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
β-Lactam antibiotics are the first choice for the treatment of most bacterial infections. However, the increased prevalence of β-lactamases, in particular extended-spectrum β-lactamases, in pathogenic bacteria has severely limited the possibility of using β-lactam treatments. Combining β-lactam antibiotics with β-lactamase inhibitors can restore treatment efficacy by negating the effect of the β-lactamase and has become increasingly important against infections caused by β-lactamase-producing strains. Not surprisingly, bacteria with resistance to even these combinations have been found in patients. Studies on the development of bacterial resistance to β-lactam/β-lactamase inhibitor combinations have focused mainly on the effects of single, chromosomal or plasmid-borne, β-lactamases. However, clinical isolates often carry more than one β-lactamase in addition to multiple other resistance genes. Here, we investigate how the evolutionary trajectories of the development of resistance to three commonly used β-lactam/β-lactamase inhibitor combinations, ampicillin-sulbactam, piperacillin-tazobactam, and ceftazidime-avibactam, were affected by the presence of three common β-lactamases, TEM-1, CTX-M-15, and OXA-1. First-step resistance was due mainly to extensive gene amplifications of one or several of the β-lactamase genes where the amplification pattern directly depended on the respective drug combination. Amplifications also served as a stepping-stone for high-level resistance in combination with additional mutations that reduced drug influx or mutations in the β-lactamase gene blaCTX-M-15. This illustrates that the evolutionary trajectories of resistance to β-lactam/β-lactamase inhibitor combinations are strongly influenced by the frequent and transient nature of gene amplifications and how the presence of multiple β-lactamases shapes the evolution to higher-level resistance.
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Ruppé E, d'Humières C, Armand-Lefèvre L. Inferring antibiotic susceptibility from metagenomic data: dream or reality? Clin Microbiol Infect 2022; 28:1225-1229. [PMID: 35551982 DOI: 10.1016/j.cmi.2022.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48h after sampling, at best. Recently, clinical metagenomics (CMg), the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. CMg indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality. OBJECTIVES The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data. SOURCES We conducted a narrative review using published articles available in the NCBI Pubmed database. CONTENT We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host. IMPLICATIONS Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.
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Affiliation(s)
- Etienne Ruppé
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France.
| | - Camille d'Humières
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Laurence Armand-Lefèvre
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
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Baaity Z, von Loewenich FD, Nagy E, Orosz L, Burián K, Somogyvári F, Sóki J. Phenotypic and Molecular Characterization of Carbapenem-Heteroresistant Bacteroides fragilis Strains. Antibiotics (Basel) 2022; 11:antibiotics11050590. [PMID: 35625234 PMCID: PMC9138018 DOI: 10.3390/antibiotics11050590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 12/29/2022] Open
Abstract
Carbapenem-resistant Bacteroides fragilis strains usually emerge by an insertion sequence (IS) jump into the upstream region of the cfiA carbapenemase gene. However, intermediate or fully resistant cfiA-positive strains also exist. These do not have such IS element activations, but usually have heterogeneous resistance (HR) phenotypes, as detected by a disc diffusion or gradient tests. Heteroresistance is a serious antibiotic resistance problem, whose molecular mechanisms are not fully understood. We aim to characterize HR and investigate diagnostic issues in the set of cfiA-positive B. fragilis strains using phenotypic and molecular methods. Of the phenotypic methods used, the population analysis profile (PAP) and area under curve (AUC) measurements were the best prognostic markers for HR. PAP AUC, imipenem agar dilution and imipenemase production corresponded well with each other. We also identified a saturation curve parameter (quasi-PAP curves), which correlated well with these phenotypic traits, implying that HR is a stochastic process. The genes, on a previously defined ‘cfiA element’, act in a complex manner to produce the HR phenotype, including a lysine-acetylating toxin and a lysine-rich peptide. Furthermore, imipenem HR is triggered by imipenem. The two parameters that most correlate with the others are imipenemase production and ‘GNAT’ expression, which prompted us to suspect that carbapenem heteroresistance of the B. fragilis strains is stochastically regulated and is mediated by the altered imipenemase production.
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Affiliation(s)
- Zain Baaity
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
| | | | - Elisabeth Nagy
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
| | - László Orosz
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
| | - Katalin Burián
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
| | - Ferenc Somogyvári
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
| | - József Sóki
- Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and School of Medicine, University of Szeged, H-6725 Szeged, Hungary; (Z.B.); (E.N.); (L.O.); (K.B.); (F.S.)
- Correspondence: author:
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19
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Edwards T, Heinz E, van Aartsen J, Howard A, Roberts P, Corless C, Fraser AJ, Williams CT, Bulgasim I, Cuevas LE, Parry CM, Roberts AP, Adams ER, Mason J, Hubbard ATM. Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types. Microb Genom 2022; 8. [PMID: 35404783 PMCID: PMC9453079 DOI: 10.1099/mgen.0.000789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Resistance to piperacillin/tazobactam (TZP) in Escherichia coli has predominantly been associated with mechanisms that confer resistance to third-generation cephalosporins. Recent reports have identified E. coli strains with phenotypic resistance to piperacillin/tazobactam but susceptibility to third-generation cephalosporins (TZP-R/3GC-S). In this study we sought to determine the genetic diversity of this phenotype in E. coli (n=58) isolated between 2014–2017 at a single tertiary hospital in Liverpool, UK, as well as the associated resistance mechanisms. We compare our findings to a UK-wide collection of invasive E. coli isolates (n=1509) with publicly available phenotypic and genotypic data. These data sets included the TZP-R/3GC-S phenotype (n=68), and piperacillin/tazobactam and third-generation cephalosporin-susceptible (TZP-S/3GC-S, n=1271) phenotypes. The TZP-R/3GC-S phenotype was displayed in a broad range of sequence types, which was mirrored in the same phenotype from the UK-wide collection, and the overall diversity of invasive E. coli isolates. The TZP-R/3GC-S isolates contained a diverse range of plasmids, indicating multiple acquisition events of TZP resistance mechanisms rather than clonal expansion of a particular plasmid or sequence type. The putative resistance mechanisms were equally diverse, including hyperproduction of TEM-1, either via strong promoters or gene amplification, carriage of inhibitor-resistant β-lactamases, and an S133G blaCTX-M-15 mutation detected for the first time in clinical isolates. Several of these mechanisms were present at a lower abundance in the TZP-S/3GC-S isolates from the UK-wide collection, but without the associated phenotypic resistance to TZP. Eleven (19%) of the isolates had no putative mechanism identified from the genomic data. Our findings highlight the complexity of this cryptic phenotype and the need for continued phenotypic monitoring, as well as further investigation to improve detection and prediction of the TZP-R/3GC-S phenotype from genomic data.
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Affiliation(s)
- Thomas Edwards
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jon van Aartsen
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alex Howard
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Paul Roberts
- Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton WV1 1LY, UK
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Caroline Corless
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alice J. Fraser
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christopher T. Williams
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Issra Bulgasim
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Luis E. Cuevas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christopher M. Parry
- Alder Hey Children’s NHS Foundation Trust, Liverpool, L12 2AP, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily R. Adams
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jenifer Mason
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alasdair T. M. Hubbard
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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20
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Leopold SR, Abdelraouf K, Nicolau DP, Agresta H, Johnson J, Teter K, Dunne WM, Broadwell D, van Belkum A, Schechter LM, Sodergren EJ, Weinstock GM. Murine Model for Measuring Effects of Humanized-Dosing of Antibiotics on the Gut Microbiome. Front Microbiol 2022; 13:813849. [PMID: 35250930 PMCID: PMC8892246 DOI: 10.3389/fmicb.2022.813849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/13/2022] [Indexed: 11/29/2022] Open
Abstract
There is a current need for enhancing our insight in the effects of antimicrobial treatment on the composition of human microbiota. Also, the spontaneous restoration of the microbiota after antimicrobial treatment requires better understanding. This is best addressed in well-defined animal models. We here present a model in which immune-competent or neutropenic mice were administered piperacillin-tazobactam (TZP) according to human treatment schedules. Before, during and after the TZP treatment, fecal specimens were longitudinally collected at established intervals over several weeks. Gut microbial taxonomic distribution and abundance were assessed through culture and molecular means during all periods. Non-targeted metabolomics analyses of stool samples using Quadrupole Time of Flight mass spectrometry (QTOF MS) were also applied to determine if a metabolic fingerprint correlated with antibiotic use, immune status, and microbial abundance. TZP treatment led to a 5–10-fold decrease in bacterial fecal viability counts which were not fully restored during post-antibiotic follow up. Two distinct, relatively uniform and reproducible restoration scenarios of microbiota changes were seen in post TZP-treatment mice. Post-antibiotic flora could consist of predominantly Firmicutes or, alternatively, a more diverse mix of taxa. In general, the pre-treatment microbial communities were not fully restored within the screening periods applied. A new species, closely related to Eubacterium siraeum, Mageeibacillus indolicus, and Saccharofermentans acetigenes, became predominant post-treatment in a significant proportion of mice, identified by 16S rRNA gene sequencing. Principal component analysis of QTOF MS of mouse feces successfully distinguished treated from non-treated mice as well as immunocompetent from neutropenic mice. We observe dynamic but distinct and reproducible responses in the mouse gut microbiota during and after TZP treatment and propose the current murine model as a useful tool for defining the more general post-antibiotic effects in the gastro-intestinal ecosystem where humanized antibiotic dosing may ultimately facilitate extrapolation to humans.
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Affiliation(s)
- Shana R. Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Kamilia Abdelraouf
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, United States
| | - David P. Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, United States
| | - Hanako Agresta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Jethro Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Kathleen Teter
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | - Alex van Belkum
- BioMérieux SA, Clinical Unit, Grenoble, France
- *Correspondence: Alex van Belkum,
| | | | - Erica J. Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
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21
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Hertz FB, Andreasen MR, Almind SR, Nielsen KL, Hansen KH, Jelsbak L, Frimodt-Møller N, Schønning K. Efficacy of piperacillin-tazobactam and cefotaxime against Escherichia coli hyperproducing TEM-1 in a mouse peritonitis infection model. Int J Antimicrob Agents 2022; 59:106543. [DOI: 10.1016/j.ijantimicag.2022.106543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/08/2022] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
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22
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Seo S, Disney-McKeethen S, Prabhakar RG, Song X, Mehta HH, Shamoo Y. Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics. ACS Infect Dis 2022; 8:242-254. [PMID: 34962128 PMCID: PMC10022597 DOI: 10.1021/acsinfecdis.1c00564] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In vitro experimental evolution of pathogens to antibiotics is commonly used for the identification of clinical biomarkers associated with antibiotic resistance. Microdroplet emulsions allow exquisite control of spatial structure, species complexity, and selection microenvironments for such studies. We investigated the use of monodisperse microdroplets in experimental evolution. Using Escherichia coli adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.
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Affiliation(s)
- Seokju Seo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | | | | | - Xinhao Song
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Heer H Mehta
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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23
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Emergence of Ceftazidime- and Avibactam-Resistant Klebsiella pneumoniae Carbapenemase-Producing Pseudomonas aeruginosa in China. mSystems 2021; 6:e0078721. [PMID: 34726488 PMCID: PMC8562488 DOI: 10.1128/msystems.00787-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC)-producing Pseudomonas aeruginosa (KPC-PA) has been reported sporadically. However, epidemiological and antimicrobial susceptibility data specific for KPC-PA are lacking. We collected 374 carbapenem-resistant P. aeruginosa (CRPA) isolates from seven hospitals in China from June 2016 to February 2019 and identified the blaKPC-2 gene in 40.4% (n = 151/374) of the isolates. Approximately one-half of all KPC-PA isolates (n = 76/151; 50.3%) were resistant to ceftazidime-avibactam (CAZ-AVI). Combining Kraken2 taxonomy identification and Nanopore sequencing, we identified eight plasmid types, five of which carried blaKPC-2, and 13 combination patterns of these plasmid types. In addition, we identified IS26-ΔTn6296 and Tn1403-like–ΔTn6296 as the two mobile genetic elements that mediated blaKPC-2 transmission. blaKPC-2 plasmid curing in 28 strains restored CAZ-AVI susceptibility, suggesting that blaKPC-2 was the mediator of CAZ-AVI resistance. Furthermore, the blaKPC-2 copy number was found to correlate with KPC expression and, therefore, CAZ-AVI resistance. Taken together, our results suggest that KPC-PA is becoming a clinical threat and that using CAZ-AVI to treat this specific pathogen should be done with caution. IMPORTANCE Previous research has reported several cases of KPC-PA strains and three KPC-encoding P. aeruginosa plasmid types in China. However, the prevalence and clinical significance of KPC-PA are not available. In addition, the susceptibility of the strains to CAZ-AVI remains unknown. Samples in this study were collected from seven tertiary hospitals prior to CAZ-AVI clinical approval in China. Therefore, our results represent a retrospective study establishing the baseline efficacy of the novel β-lactam/β-lactamase combination agent for treating KPC-PA infections. The observed correlation between the blaKPC copy number and CAZ-AVI resistance suggests that close monitoring of the susceptibility of the strain during treatment is required. It would also be beneficial to screen for the blaKPC gene in CRPA strains for antimicrobial surveillance purposes.
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24
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Wang Z, Chen Q, Zhang J, Yan H, Chen Y, Chen C, Chen X. High prevalence of unstable antibiotic heteroresistance in cyanobacteria causes resistance underestimation. WATER RESEARCH 2021; 202:117430. [PMID: 34298276 DOI: 10.1016/j.watres.2021.117430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Both cyanobacterial bloom and antibiotic resistance have aggravated worldwide and posed a global threat to public health in recent years. Cyanobacteria can exhibit discrepancy between their resistance genotype and susceptible phenotype due to antibiotic heteroresistance, which leads to difficulties in unambiguously classifying cyanobacterial strains as susceptible or resistant. Here we profiled the prevalence and mechanisms of antibiotic heteroresistance in cyanobacterial strains isolated from 50 sites across four eutrophicated lakes in China. Among 300 cyanobacterial isolates tested against 19 different antibiotics, over 90% of cyanobacterial isolates exhibited HR to multiple antibiotics and 19.5% of isolate/antibiotic interactions classified as susceptible by traditional minimum inhibitory concentration (MIC) estimates were designated heteroresistant. Over 97% of these monoclonal HR cases were unstable, with an increased resistance of subpopulations due to amplification of known resistance genes with high fitness cost. Wide-type cyanobacterial isolates of Synechococcus, Synechocystis, Anabaena and Microcystis aeruginosa exposed to sub-MIC level of four antibiotics evolved high-level resistance with little fitness cost, resulting in stable polyclonal HR. Both stable polyclonal HR and unstable monoclonal HR observed in different cyanobacterial strains can be promoted under environmental levels of antibiotic pressure. The highly prevalent and unstable monoclonal HR with the potential for susceptibility misclassification highlighted underestimation of cyanobacteria-derived antibiotic resistance. Cost-effective strategies should be developed to identify heteroresistance in cyanobacteria and to avoid false positive or negative results in traditional susceptibility testing.
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Affiliation(s)
- Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China
| | - Qiuwen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China.
| | - Jianyun Zhang
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Yangtze Institute for Conservation and Green Development, Hohai University, Nanjing 210098, China.
| | - Hanlu Yan
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Yuchen Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Cheng Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - Xiaoxue Chen
- State Key Laboratory of Hydrology-Water Resources & Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210098, China; Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
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25
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Single-molecule nanopore sequencing reveals extreme target copy number heterogeneity in arylomycin-resistant mutants. Proc Natl Acad Sci U S A 2021; 118:2021958118. [PMID: 33443214 PMCID: PMC7817135 DOI: 10.1073/pnas.2021958118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genetic heterogeneity is a significant driver of antibiotic resistance in bacteria. Understanding copy number (CN) heterogeneity is important because minority subclones with increased CN can drive resistance during antibiotic exposure, but revert and escape detection during clinical susceptibility testing. Despite its clinical relevance, CN variation has eluded quantification at single-molecule resolution. Here, we report nanopore sequencing of arylomycin-resistant mutants carrying tandem repeats ranging in size from 4.8 to 50.0 kb and encompassing the arylomycin target gene lepB. Reads spanning individual repeat arrays show vast differences in CN, underscoring the importance of amplifications in driving the emergence of genetic heterogeneity. This is a direct observation of cell-to-cell CN differences in an antibiotic-resistant bacterial population. Tandem gene amplification is a frequent and dynamic source of antibiotic resistance in bacteria. Ongoing expansions and contractions of repeat arrays during population growth are expected to manifest as cell-to-cell differences in copy number (CN). As a result, a clonal bacterial culture could comprise subpopulations of cells with different levels of antibiotic sensitivity that result from variable gene dosage. Despite the high potential for misclassification of heterogenous cell populations as either antibiotic-susceptible or fully resistant in clinical settings, and the concomitant risk of inappropriate treatment, CN distribution among cells has defied analysis. Here, we use the MinION single-molecule nanopore sequencer to uncover CN heterogeneity in clonal populations of Escherichia coli and Acinetobacter baumannii grown from single cells isolated while selecting for resistance to an optimized arylomycin, a member of a recently discovered class of Gram-negative antibiotic. We found that gene amplification of the arylomycin target, bacterial type I signal peptidase LepB, is a mechanism of unstable arylomycin resistance and demonstrate in E. coli that amplification instability is independent of RecA. This instability drives the emergence of a nonuniform distribution of lepB CN among cells with a range of 1 to at least 50 copies of lepB identified in a single clonal population. In sum, this remarkable heterogeneity, and the evolutionary plasticity it fuels, illustrates how gene amplification can enable bacterial populations to respond rapidly to novel antibiotics. This study establishes a rationale for further nanopore-sequencing studies of heterogeneous cell populations to uncover CN variability at single-molecule resolution.
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26
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Rodríguez-Villodres Á, Gil-Marqués ML, Álvarez-Marín R, Bonnin RA, Pachón-Ibáñez ME, Aguilar-Guisado M, Naas T, Aznar J, Pachón J, Lepe JA, Smani Y. Extended-spectrum resistance to β-lactams/β-lactamase inhibitors (ESRI) evolved from low-level resistant Escherichia coli. J Antimicrob Chemother 2021; 75:77-85. [PMID: 31613964 DOI: 10.1093/jac/dkz393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/29/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Escherichia coli is characterized by three resistance patterns to β-lactams/β-lactamase inhibitors (BLs/BLIs): (i) resistance to ampicillin/sulbactam and susceptibility to amoxicillin/clavulanic acid and piperacillin/tazobactam (RSS); (ii) resistance to ampicillin/sulbactam and amoxicillin/clavulanic acid, and susceptibility to piperacillin/tazobactam (RRS); and (iii) resistance to ampicillin/sulbactam, amoxicillin/clavulanic acid and piperacillin/tazobactam (RRR). These resistance patterns are acquired consecutively, indicating a potential risk of developing resistance to piperacillin/tazobactam, but the precise mechanism of this process is not completely understood. METHODS Clinical isolates incrementally pressured by piperacillin/tazobactam selection in vitro and in vivo were used. We determined the MIC of piperacillin/tazobactam in the presence and absence of piperacillin/tazobactam pressure. We deciphered the role of the blaTEM genes in the new concept of extended-spectrum resistance to BLs/BLIs (ESRI) using genomic analysis. The activity of β-lactamase was quantified in these isolates. RESULTS We show that piperacillin/tazobactam resistance is induced in E. coli carrying blaTEM genes. This resistance is due to the increase in copy numbers and transcription levels of the blaTEM gene, thus increasing β-lactamase activity and consequently increasing piperacillin/tazobactam MICs. Genome sequencing of two blaTEM-carrying representative isolates showed that piperacillin/tazobactam treatment produced two types of duplications of blaTEM (8 and 60 copies, respectively). In the clinical setting, piperacillin/tazobactam treatment of patients infected by E. coli carrying blaTEM is associated with a risk of therapeutic failure. CONCLUSIONS This study describes for the first time the ESRI in E. coli. This new concept is very important in the understanding of the mechanism involved in the acquisition of resistance to BLs/BLIs.
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Affiliation(s)
- Ángel Rodríguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - María Luisa Gil-Marqués
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Rocío Álvarez-Marín
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Rémy A Bonnin
- EA7361, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, APHP, Hôpital Bicêtre, EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, Institut Pasteur-APHP-Université Paris-Sud, Le Kremlin-Bicêtre, France
| | - María Eugenia Pachón-Ibáñez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Manuela Aguilar-Guisado
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Thierry Naas
- EA7361, Université Paris-Saclay, LabEx Lermit, Bacteriology-Hygiene unit, APHP, Hôpital Bicêtre, EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, Institut Pasteur-APHP-Université Paris-Sud, Le Kremlin-Bicêtre, France
| | - Javier Aznar
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Department of Microbiology, University of Seville, Seville, Spain
| | - Jerónimo Pachón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Department of Medicine, University of Seville, Seville, Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Younes Smani
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, Seville, Spain.,Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
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Savin M, Bierbaum G, Kreyenschmidt J, Schmithausen RM, Sib E, Schmoger S, Käsbohrer A, Hammerl JA. Clinically Relevant Escherichiacoli Isolates from Process Waters and Wastewater of Poultry and Pig Slaughterhouses in Germany. Microorganisms 2021; 9:microorganisms9040698. [PMID: 33800539 PMCID: PMC8066038 DOI: 10.3390/microorganisms9040698] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli is frequently associated with multiple antimicrobial resistances and a major cause of bacterial extraintestinal infections in livestock and humans. However, data on the epidemiology of (i) multidrug-resistant (MDR) and (ii) extraintestinal pathogenic E. coli (ExPEC) in poultry and pig slaughterhouses in Germany is currently lacking. Selected E. coli isolates (n = 71) with phenotypic resistance to cephalosporins from two poultry and two pig slaughterhouses expressing high MDR rates (combined resistance to piperacillin, cefotaxime and/or ceftazidime, and ciprofloxacin) of 51.4% and 58.3%, respectively, were analyzed by whole-genome sequencing. They constituted a reservoir for 53 different antimicrobial resistance determinants and were assigned various sequence types, including high-risk clones involved in human infections worldwide. An ExPEC pathotype was detected in 17.1% and 5.6% of the isolates from poultry and pig slaughterhouses, respectively. Worryingly, they were recovered from scalding water and eviscerators, indicating an increased risk for cross-contaminations. Uropathogenic E. coli (UPEC) were detected in the effluent of an in-house wastewater treatment plant (WWTP) of a poultry slaughterhouse, facilitating their further dissemination into surface waters. Our study provides important information on the molecular characteristics of (i) MDR, as well as (ii) ExPEC and UPEC regarding their clonal structure, antimicrobial resistance and virulence factors. Based on their clinical importance and pathogenic potential, the risk of slaughterhouse employees’ exposure cannot be ruled out. Through cross-contamination, these MDR E. coli pathotypes may be introduced into the food chain. Moreover, inadequate wastewater treatment may contribute to the dissemination of UPEC into surface waters, as shown for other WWTPs.
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Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, 53113 Bonn, Germany;
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
- Correspondence: (M.S.); (J.A.H.)
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53113 Bonn, Germany;
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, 53113 Bonn, Germany;
- Department of Fresh Produce Logistics, Hochschule Geisenheim University, 65366 Geisenheim, Germany
| | - Ricarda Maria Schmithausen
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
| | - Esther Sib
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
| | - Silvia Schmoger
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
| | - Annemarie Käsbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
- Department for Farm Animals and Veterinary Public Health and Epidemiology, Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
- Correspondence: (M.S.); (J.A.H.)
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28
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Singh NS, Singhal N, Kumar M, Virdi JS. Exploring the genetic mechanisms underlying amoxicillin-clavulanate resistance in waterborne Escherichia coli. INFECTION GENETICS AND EVOLUTION 2021; 90:104767. [PMID: 33581330 DOI: 10.1016/j.meegid.2021.104767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/22/2021] [Accepted: 02/08/2021] [Indexed: 11/28/2022]
Abstract
Escherichia coli is a human commensal and faecal indicator bacteria which is also the etiologic agent of several nosocomial- and community-acquired infections. Amoxicillin-clavulanate (AMC) is a widely prescribed β-lactam/β-lactamase inhibitor which is used against E. coli infections. Resistance to AMC in E. coli has been primarily attributed to point mutations in blaTEM-1 resulting in inhibitor-resistant TEM (IRT) β-lactamases. In this study, we have explored the reasons underlying AMC-resistance in waterborne E. coli. Most of the studies regarding IRT-producing E. coli have been conducted on clinical samples and studies exploring genetic mechanisms underlying AMC-resistance in aquatic E. coli are scarce. Since, blaTEM-1 and several antimicrobial resistance determinants are located on mobile genetic elements they can easily disseminate among other microbes inhabiting urban waterbodies. Thus, it is important to understand the underlying mechanisms to check the dissemination of AMC-resistance in other waterborne pathogens. Our results indicated that AMC-resistant E. coli were susceptible to other β-lactam/β-lactamase inhibitors like, ampicillin/sulbactam and piperacillin/tazobactam. Though, blaTEM-1 was present, none of the strains harbored point mutations which could qualify as IRT and only one strain harbored both blaTEM-1 and blaOXA-1. Hyperproduction of blaTEM-1, presence of plasimd-mediated ampC or promoter/attenuator mutations in the chromososmal ampC might not be related to IRT-like phenotype or AMC-resistance. This suggests that other mechanisms like, increased plasmid copy numbers or gene amplification or deficiency in the expression/function of porins might be responsible for AMC-resistance in waterborne E. coli.
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Affiliation(s)
- Nambram Somendro Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India; Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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29
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Awasthi A, Singh SK, Kumar B, Gulati M, Kumar R, Wadhwa S, Khursheed R, Corrie L, Kr A, Kumar R, Patni P, Kaur J, Vishwas S, Yadav A. Treatment Strategies Against Diabetic Foot Ulcer: Success so Far and the Road Ahead. Curr Diabetes Rev 2021; 17:421-436. [PMID: 33143613 DOI: 10.2174/1573399816999201102125537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Diabetic foot ulcer (DFU) is one of the leading complications of type-2 diabetes mellitus. It is associated with neuropathy and peripheral arterial disease of the lower limb in patients with diabetes. There are four stages of wound healing, namely hemostasis phase, inflammatory phase, proliferative phase and maturation phase. In the case of DFU, all these stages are disturbed which lead to delay in healing and consequently to lower limb amputation. Conventional dosage forms like tablets, creams, ointments, gels and capsules have been used for the treatment of diabetic foot ulcer for many years. INTRODUCTION In this review, the global prevalence as well as etiopathogenesis related to diabetic foot ulcer have been discussed. The potential role of various synthetic and herbal drugs, as well as their conventional dosage forms in the effective management of DFU have been discussed in detail. METHODS Structured search of bibliographic databases from previously published peer-reviewed research papers was explored and data has been represented in terms of various approaches that are used for the treatment of DFU. RESULTS About 148 papers, including both research and review articles, were included in this review to produce a comprehensive as well as a readily understandable article. A series of herbal and synthetic drugs have been discussed along with their current status of treatment in terms of dose and mechanism of action. CONCLUSION DFU has become one of the most common complications in patients having diabetes for more than ten years. Hence, understanding the root cause and its successful treatment is a big challenge because it depends upon multiple factors such as the judicious selection of drugs as well as proper control of blood sugar level. Most of the drugs that have been used so far either belong to the category of antibiotics, antihyperglycaemic or they have been repositioned. In clinical practice, much focus has been given to dressings that have been used to cover the ulcer. The complete treatment of DFU is still a farfetched dream to be achieved and it is expected that combination therapy of herbal and synthetic drugs with multiple treatment pathways could be able to offer better management of DFU.
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Affiliation(s)
- Ankit Awasthi
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Bimlesh Kumar
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Rajesh Kumar
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Sheetu Wadhwa
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Rubiya Khursheed
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Leander Corrie
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Arya Kr
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Rajan Kumar
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Pooja Patni
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Jaskiran Kaur
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Sukriti Vishwas
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
| | - Ankit Yadav
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara, 144411, Punjab, India
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30
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Hubbard ATM, Mason J, Roberts P, Parry CM, Corless C, van Aartsen J, Howard A, Bulgasim I, Fraser AJ, Adams ER, Roberts AP, Edwards T. Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of bla TEM-1B. Nat Commun 2020; 11:4915. [PMID: 33004811 PMCID: PMC7530762 DOI: 10.1038/s41467-020-18668-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the β-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B. The TU re-inserts into the chromosome adjacent to IS26 and forms a tandem array of TUs, which increases the copy number of blaTEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in blaTEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of blaTEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Chromosomes, Bacterial/genetics
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/genetics
- Drug Therapy, Combination/methods
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/isolation & purification
- Escherichia coli Infections/drug therapy
- Escherichia coli Infections/microbiology
- Escherichia coli Proteins/genetics
- Gene Amplification
- Gene Expression Regulation, Bacterial
- Genome, Bacterial/genetics
- Humans
- Microbial Sensitivity Tests
- Piperacillin/pharmacology
- Piperacillin/therapeutic use
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- Tazobactam/pharmacology
- Tazobactam/therapeutic use
- Whole Genome Sequencing
- beta-Lactamases/genetics
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Jenifer Mason
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Paul Roberts
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Building MA, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Christopher M Parry
- Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, L12 2AP, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69 7BE, UK
- Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Caroline Corless
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Jon van Aartsen
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Alex Howard
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Alice J Fraser
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily R Adams
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Thomas Edwards
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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31
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Savin M, Bierbaum G, Hammerl JA, Heinemann C, Parcina M, Sib E, Voigt A, Kreyenschmidt J. Antibiotic-resistant bacteria and antimicrobial residues in wastewater and process water from German pig slaughterhouses and their receiving municipal wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138788. [PMID: 32498197 DOI: 10.1016/j.scitotenv.2020.138788] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Slaughterhouse process- and wastewater are considered as a hotspot for antibiotic-resistant bacteria and antimicrobial residues and may thus play an important role for their dissemination into the environment. In this study, we investigated occurrence and characteristics of ESKAPE bacteria (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.) and ESBL (extended spectrum β-lactamase) -producing E. coli in water samples of different processing stages of two German pig slaughterhouses (S1/S2) as well as their municipal wastewater treatment plants (mWWTPs). Furthermore, residues of various antimicrobials were determined. A total of 103 water samples were taken in delivery and dirty areas of the slaughterhouses S1/S2 (n = 37), their in-house WWTPs (n = 30) and mWWTPs including their receiving water bodies (n = 36). The recovered isolates (n = 886) were characterized for their antimicrobial resistance pattern and its genetic basis. Targeted species were ubiquitous along the slaughtering and wastewater chains. Phenotypic and genotypic analyses revealed a broad variety of resistance phenotypes and β-lactamase genes. Carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE) and healthcare-associated (HA) MRSA were recovered only from mWWTPs and their preflooders. In contrast, the mcr-1 gene was exclusively detected in E. coli from S1/S2. Residues of five antimicrobials were detected in 14.9% (10/67) of S1/S2 samples in low range concentrations (≤1.30 μg/L), whereas 91.7% (33/36) of mWWTPs samples exhibited residues of 22 different antibiotics in concentrations of up to 4.20 μg/L. Target bacteria from S1/S2 and mWWTPs exhibited differences in their abundances, resistance phenotypes and genotypes as well as clonal lineages. S1/S2 samples exhibited bacteria with zoonotic potential (e.g. MRSA of CC398, E. coli of significant clones), whereas ESKAPE bacteria exhibiting resistances of clinical importance were mainly detected in mWWTPs. Municipal WWTPs seem to fail to eliminate these bacteria leading to a discharge into the preflooder and a subsequent dissemination into the surface water.
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Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, Bonn, Germany.
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Marijo Parcina
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Esther Sib
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Germany
| | - Alexander Voigt
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany; Hochschule Geisenheim University, Department of Fresh Produce Logistics, Geisenheim, Germany
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32
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Ramirez MS, Bonomo RA, Tolmasky ME. Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace. Biomolecules 2020; 10:biom10050720. [PMID: 32384624 PMCID: PMC7277208 DOI: 10.3390/biom10050720] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.
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Affiliation(s)
- Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
| | - Robert A. Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA;
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics; Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- WRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
- Correspondence: ; Tel.: +657-278-5263
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33
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Tagliaferri TL, Guimarães NR, Pereira MDPM, Vilela LFF, Horz HP, Dos Santos SG, Mendes TADO. Exploring the Potential of CRISPR-Cas9 Under Challenging Conditions: Facing High-Copy Plasmids and Counteracting Beta-Lactam Resistance in Clinical Strains of Enterobacteriaceae. Front Microbiol 2020; 11:578. [PMID: 32425894 PMCID: PMC7203346 DOI: 10.3389/fmicb.2020.00578] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/16/2020] [Indexed: 01/21/2023] Open
Abstract
The antimicrobial resistance (AMR) crisis urgently requires countermeasures for reducing the dissemination of plasmid-borne resistance genes. Of particular concern are opportunistic pathogens of Enterobacteriaceae. One innovative approach is the CRISPR-Cas9 system which has recently been used for plasmid curing in defined strains of Escherichia coli. Here we exploited this system further under challenging conditions: by targeting the blaTEM–1 AMR gene located on a high-copy plasmid (i.e., 100–300 copies/cell) and by directly tackling blaTEM–1-positive clinical isolates. Upon CRISPR-Cas9 insertion into a model strain of E. coli harboring blaTEM–1 on the plasmid pSB1A2, the plasmid number and, accordingly, the blaTEM–1 gene expression decreased but did not become extinct in a subpopulation of CRISPR-Cas9 treated bacteria. Sequence alterations in blaTEM–1 were observed, likely resulting in a dysfunction of the gene product. As a consequence, a full reversal to an antibiotic sensitive phenotype was achieved, despite plasmid maintenance. In a clinical isolate of E. coli, plasmid clearance and simultaneous re-sensitization to five beta-lactams was possible. Reusability of antibiotics could be confirmed by rescuing larvae of Galleria mellonella infected with CRISPR-Cas9-treated E. coli, as opposed to infection with the unmodified clinical isolate. The drug sensitivity levels could also be increased in a clinical isolate of Enterobacter hormaechei and to a lesser extent in Klebsiella variicola, both of which harbored additional resistance genes affecting beta-lactams. The data show that targeting drug resistance genes is encouraging even when facing high-copy plasmids. In clinical isolates, the simultaneous interference with multiple genes mediating overlapping drug resistance might be the clue for successful phenotype reversal.
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Affiliation(s)
- Thaysa Leite Tagliaferri
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Natália Rocha Guimarães
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Liza Figueiredo Felicori Vilela
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Simone Gonçalves Dos Santos
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Suzuki Y, Sato T, Fukushima Y, Nakajima C, Suzuki Y, Takahashi S, Yokota SI. Contribution of β-lactamase and efflux pump overproduction to tazobactam-piperacillin resistance in clinical isolates of Escherichia coli. Int J Antimicrob Agents 2020; 55:105919. [PMID: 32062000 DOI: 10.1016/j.ijantimicag.2020.105919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/27/2020] [Accepted: 02/08/2020] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Tazobactam-piperacillin (TZP) is a mixture of a broad-spectrum penicillin and an irreversible β-lactamase inhibitor. TZP is effective against Gram-negative bacteria that produce extended-spectrum β-lactamases, and it is used as a first-line or second-line drug to treat serious infections. METHODS This study identified three TZP-resistant and two TZP-intermediate strains among 514 clinical isolates of Escherichia coli. RESULTS These five isolates possessed one or more β-lactamase genes, blaTEM-1, blaCTX-M-2, blaCTX-M-14, and/or blaCMY-8. The expression levels of β-lactamase genes and acrAB genes in the strains were examined by using real-time reverse transcription PCR. The total enzymatic piperacillin-degrading activity in cells was determined. Two TZP-resistance mechanisms were identified: hyperproduction of TEM-1 in the two resistant strains; and simultaneous high production of β-lactamase and efflux pump AcrAB in the two TZP-intermediate isolates. The latter are an international high-risk clone O25b:H4-ST131-H30R. CONCLUSION TZP resistance is still rare in clinical isolates of E. coli. However, resistance can develop on high production and/or combinations of known antimicrobial resistance mechanisms in different ways.
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Affiliation(s)
- Yuuki Suzuki
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan.
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Piperacillin-Tazobactam-Resistant/Third-Generation Cephalosporin-Susceptible Escherichia coli and Klebsiella pneumoniae Isolates: Resistance Mechanisms and In vitro-In vivo Discordance. Int J Antimicrob Agents 2020; 55:105885. [PMID: 31923568 DOI: 10.1016/j.ijantimicag.2020.105885] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/18/2019] [Accepted: 12/28/2019] [Indexed: 02/06/2023]
Abstract
We previously reported the detection of Escherichia coli and Klebsiella pneumoniae that displayed in vitro piperacillin-tazobactam (TZP) resistance but were susceptible to third-generation cephalosporins (TZP-R/Ceph3-S). In this study, we assessed the phenotypic and genotypic profiles of 12 clinical non-clonal TZP-R/Ceph3-S E. coli and K. pneumoniae isolates derived from bloodstream infections. Whole-genome sequencing revealed that most of the TZP-R/Ceph3-S E. coli and K. pneumoniae isolates examined harbored blaTEM-1 and blaSHV-1 genes, respectively, but none harbored extended-spectrum β-lactamase, AmpC β-lactamase or carbapenemase genes. Increasing the tazobactam concentration from 4 mg/L to 16 mg/L restored TZP in vitro susceptibility among E. coli isolates expressing TEM-1, but had minimal impact on the susceptibility of K. pneumoniae to TZP. Real-time qPCR analysis showed that blaTEM-1 expression was amplified in TZP-R E. coli upon incubation with sub-inhibitory TZP concentrations. Using an immunocompetent murine septicemia model, the efficacy of TZP against TZP-R/Ceph3-S isolates was assessed using TZP doses that mimicked human plasma exposures following intravenous (IV) administration of TZP 4.5 g q6h over 0.5 h for 24 h. Efficacy was assessed by survival through 96 h. There was high mortality in untreated control mice for all tested isolates. Compared with controls, TZP human-simulated exposure significantly improved survival for all TZP-R/Ceph3-S E. coli and K. pneumoniae isolates examined (P < 0.05). Thus, TZP was associated with remarkable in vivo activity against TZP-R/Ceph3-S E. coli and K. pneumoniae despite the observed resistance in vitro.
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Abstract
Resistance to β-lactam antibiotics in Gram-negative bacteria is commonly associated with production of β-lactamases, including extended-spectrum β-lactamases (ESBLs) and carbapenemases belonging to different molecular classes: those with a catalytically active serine and those with at least one active-site Zn2+ to facilitate hydrolysis. To counteract the hydrolytic activity of these enzymes, combinations of a β-lactam with a β-lactamase inhibitor (BLI) have been clinically successful. However, some β-lactam-BLI combinations have lost their effectiveness against prevalent Gram-negative pathogens that produce ESBLs, carbapenemases or multiple β-lactamases in the same organism. In this Review, descriptions are provided for medically relevant β-lactamase families and various BLI combinations that have been developed or are under development. Recently approved inhibitor combinations include the inhibitors avibactam and vaborbactam of the diazabicyclooctanone and boronic acid inhibitor classes, respectively, as new scaffolds for future inhibitor design.
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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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Hansen KH, Andreasen MR, Pedersen MS, Westh H, Jelsbak L, Schønning K. Resistance to piperacillin/tazobactam in Escherichia coli resulting from extensive IS26-associated gene amplification of blaTEM-1. J Antimicrob Chemother 2019; 74:3179-3183. [DOI: 10.1093/jac/dkz349] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
bla TEM-1 encodes a narrow-spectrum β-lactamase that is inhibited by β-lactamase inhibitors and commonly present in Escherichia coli. Hyperproduction of blaTEM-1 may cause resistance to penicillin/β-lactamase inhibitor (P/BLI) combinations.
Objectives
To characterize EC78, an E. coli bloodstream isolate, resistant to P/BLI combinations, which contains extensive amplification of blaTEM-1 within the chromosome.
Methods
EC78 was sequenced using Illumina and Oxford Nanopore Technology (ONT) methodology. Configuration of blaTEM-1 amplification was probed using PCR. Expression of blaTEM-1 mRNA was determined using quantitative PCR and β-lactamase activity was determined spectrophotometrically in a nitrocefin conversion assay. Growth rate was assessed to determine fitness and stability of the gene amplification was assessed by passage in the absence of antibiotics.
Results
Illumina sequencing of EC78 identified blaTEM-1B as the only acquired β-lactamase preceded by the WT P3 promoter and present at a copy number of 182.6 with blaTEM-1B bracketed by IS26 elements. The chromosomal location of the IS26-blaTEM-1B amplification was confirmed by ONT sequencing. Hyperproduction of blaTEM-1 was confirmed by increased transcription of blaTEM-1 and β-lactamase activity and associated with a significant fitness cost; however, the array was maintained at a relatively high copy number for 150 generations. PCR screening for blaTEM amplification of isolates resistant to P/BLI combinations identified an additional strain containing an IS26-associated amplification of a blaTEM gene.
Conclusions
IS26-associated amplification of blaTEM can cause resistance to P/BLI combinations. This adaptive mechanism of resistance may be overlooked if simple methods of genotypic prediction (e.g. gene presence/absence) are used to predict antimicrobial susceptibility from sequencing data.
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Affiliation(s)
- Katrine Hartung Hansen
- Department of Clinical Microbiology 445, Hvidovre University Hospital, Hvidovre, Denmark
| | - Minna Rud Andreasen
- Department of Clinical Microbiology 445, Hvidovre University Hospital, Hvidovre, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Martin Schou Pedersen
- Department of Clinical Microbiology 445, Hvidovre University Hospital, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology 445, Hvidovre University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Jelsbak
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology 445, Hvidovre University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Mechanisms and clinical relevance of bacterial heteroresistance. Nat Rev Microbiol 2019; 17:479-496. [DOI: 10.1038/s41579-019-0218-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 02/08/2023]
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Williams CT, Musicha P, Feasey NA, Adams ER, Edwards T. ChloS-HRM, a novel assay to identify chloramphenicol-susceptible Escherichia coli and Klebsiella pneumoniae in Malawi. J Antimicrob Chemother 2019; 74:1212-1217. [PMID: 30689880 PMCID: PMC6477986 DOI: 10.1093/jac/dky563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Chloramphenicol is a broad-spectrum antimicrobial widely available in sub-Saharan Africa. With susceptibility re-emerging among Enterobacteriaceae in Blantyre, Malawi, we designed and evaluated a new high-resolution melt (HRM) RT-PCR assay, ChloS-HRM, to identify chloramphenicol-susceptible infections in a hospital setting. METHODS Seventy-two previously whole-genome sequenced isolates of Escherichia coli and Klebsiella pneumoniae from the Queen Elizabeth Central Hospital, Malawi, were subjected to determination of chloramphenicol MICs. Primers were designed to detect 18 chloramphenicol resistance genes that produce seven distinct peaks correlating with different gene groups (catA1, catA2, catA3, catB2, catB group 3, cmlA and floR) following HRM analysis. ChloS-HRM results were compared with MIC and WGS results. RESULTS ChloS-HRM correctly identified 15 of 17 phenotypically susceptible isolates and 54 of 55 resistant isolates, giving an accuracy of 88% in identifying susceptibility and 98% in identifying resistance. WGS identified 16 of 17 susceptible and 54 of 55 resistant isolates, giving an accuracy of 94% in identifying susceptibility and 98% in identifying resistance. The single false-susceptible result had no detectable gene by ChloS-HRM or WGS. Compared with WGS, ChloS-HRM had 100% sensitivity and specificity for catA (catA1-3), cmlA and floR, and 96% specificity for catB; sensitivity could not be estimated due to the lack of catB in the clinical sample collection. The overall agreement between MIC and HRM was 96% and between MIC and WGS it was 97%. CONCLUSIONS ChloS-HRM could support antimicrobial stewardship in enabling de-escalation from third-generation cephalosporins by identifying chloramphenicol-susceptible infections. This would be valuable in areas with chloramphenicol-susceptible MDR and XDR Enterobacteriaceae.
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Affiliation(s)
- Christopher T Williams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Emily R Adams
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Edwards
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
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Zhou K, Tao Y, Han L, Ni Y, Sun J. Piperacillin-Tazobactam (TZP) Resistance in Escherichia coli Due to Hyperproduction of TEM-1 β-Lactamase Mediated by the Promoter Pa/Pb. Front Microbiol 2019; 10:833. [PMID: 31040841 PMCID: PMC6476967 DOI: 10.3389/fmicb.2019.00833] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
TEM-1, mediated by plasmid and transposon, is the most commonly encountered β-lactamase in Gram-negative bacteria. Four different promoters upstream of blaTEM-related genes have been identified: the weak P3 promoter, and the strong promoters Pa/Pb, P4, and P5. In this study, we investigated the genetic basis of a clinical strain of Escherichia coli (RJ904), which was found to be resistant to BLBLIs (β-lactam/β-lactamase inhibitors), including amoxicillin-clavulanate, ticarcillin-clavulanate (TCC), and piperacillin-tazobactam (TZP) but sensitive to third-generation cephalosporins. The conjugation test and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) demonstrated that transfer of this resistance was mediated by a ca. 100 kb plasmid. The transformant with TZP resistance was screened out with the shortgun cloning. Sequence analysis revealed that the recombinant plasmid contained a blaTEM-1b gene with the strong promoter Pa/Pb. Different plasmids were cloned based on the clone vector pACYC184 with the insertion of the blaTEM-1b gene with promoters Pa/Pb or P3. Susceptibility to TZP was determined by the E-test, agar dilution, and broth microdilution. The level of blaTEM-1b-specific transcription was determined by quantitative real-time PCR. Substitution of Pa/Pb for P3 resulted in a 128-fold decline of the MIC value of TZP, from >1024 mg/L to 8 mg/L, and a significantly lower blaTEM-1b expression level. Hyperproduction of TEM-1 β-lactamase mediated by the promoter Pa/Pb was responsible for high resistance to TZP in E. coli. Our data show possible risks of resistance development in association with the clinical use of TZP. The blaTEM promoter modifications should be considered for whole genome whole-genome sequencing-inferred bacterial antimicrobial susceptibility testing.
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Affiliation(s)
- Kaixin Zhou
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Tao
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxing Ni
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat Microbiol 2019; 4:504-514. [PMID: 30742072 DOI: 10.1038/s41564-018-0342-0] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022]
Abstract
When choosing antibiotics to treat bacterial infections, it is assumed that the susceptibility of the target bacteria to an antibiotic is reflected by laboratory estimates of the minimum inhibitory concentration (MIC) needed to prevent bacterial growth. A caveat of using MIC data for this purpose is heteroresistance, the presence of a resistant subpopulation in a main population of susceptible cells. We investigated the prevalence and mechanisms of heteroresistance in 41 clinical isolates of the pathogens Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii against 28 different antibiotics. For the 766 bacteria-antibiotic combinations tested, as much as 27.4% of the total was heteroresistant. Genetic analysis demonstrated that a majority of heteroresistance cases were unstable, with an increased resistance of the subpopulations resulting from spontaneous tandem amplifications, typically including known resistance genes. Using mathematical modelling, we show how heteroresistance in the parameter range estimated in this study can result in the failure of antibiotic treatment of infections with bacteria that are classified as antibiotic susceptible. The high prevalence of heteroresistance with the potential for treatment failure highlights the limitations of MIC as the sole criterion for susceptibility determinations. These results call for the development of facile and rapid protocols to identify heteroresistance in pathogens.
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Bloodstream Infection due to Piperacillin/Tazobactam Non-Susceptible, Cephalosporin-Susceptible Escherichia coli: A Missed Opportunity for De-Escalation of Therapy. Antibiotics (Basel) 2018; 7:antibiotics7040104. [PMID: 30513755 PMCID: PMC6316510 DOI: 10.3390/antibiotics7040104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/29/2018] [Indexed: 11/17/2022] Open
Abstract
An increasing number of reports describing Escherichia coli isolates with piperacillin/tazobactam resistance, despite retained cephalosporin susceptibility, suggest further emergence of this phenotypic resistance pattern. In this report, a patient with metastatic breast cancer presented to medical care after two days of chills, nausea, vomiting, reduced oral intake, and generalized weakness. Blood and urine cultures grew E. coli as identified by rapid diagnostics multiplex PCR and MALDI-TOF, respectively. The patient continued to manifest signs of sepsis with hypotension and tachypnea during the first three days of hospitalization despite empirical antimicrobial therapy with intravenous piperacillin/tazobactam. After in vitro antimicrobial susceptibility testing demonstrated a piperacillin/tazobactam minimal inhibitory concentration (MIC) of 64 and a ceftriaxone MIC of ≤1 mcg/mL, antimicrobial therapy was switched from intravenous piperacillin/tazobactam to ceftriaxone. All symptoms and signs of infection resolved within 48 h of starting ceftriaxone therapy. This report describes the clinical failure of piperacillin/tazobactam in the treatment of a bloodstream infection due to E. coli harboring a phenotypic resistance pattern of isolated piperacillin/tazobactam non-susceptibility. The case demonstrates the role of cephalosporins as potential treatment options and highlights the value of early de-escalation of antimicrobial therapy based on rapid diagnostic testing for microbial identification.
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Baker TM, Rogers W, Chavda KD, Westblade LF, Jenkins SG, Nicolau DP, Kreiswirth BN, Calfee DP, Satlin MJ. Epidemiology of Bloodstream Infections Caused by Escherichia coli and Klebsiella pneumoniae That Are Piperacillin-Tazobactam-Nonsusceptible but Ceftriaxone-Susceptible. Open Forum Infect Dis 2018; 5:ofy300. [PMID: 30568979 PMCID: PMC6290775 DOI: 10.1093/ofid/ofy300] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
Background Piperacillin-tazobactam-nonsusceptible (TZP-NS) Enterobacteriaceae are typically also resistant to ceftriaxone. We recently encountered bacteremias due to Escherichia coli (Ec) and Klebsiella pneumoniae (Kp) that were TZP-NS but ceftriaxone-susceptible (CRO-S). Methods We reviewed all Ec and Kp bacteremias from 2011 to 2015 at our center and assessed the prevalence, antimicrobial susceptibilities, genetic profiles, patient characteristics, treatments, and outcomes of TZP-NS/CRO-S infections. We identified risk factors for TZP-NS/CRO-S infections compared with Ec and Kp bacteremias that were TZP-S and CRO-S (Control Group 1) and compared outcomes of patients with TZP-NS/CRO-S bacteremias, Control Group 1, and patients bacteremic with extended-spectrum β-lactamase (ESBL)–producing Ec and Kp. Results There were 1857 Ec and Kp bacteremia episodes, of which 78 (4.2%) were TZP-NS/CRO-S (Ec: 50/1227 [4.1%]; Kp: 28/630 [4.4%]). All TZP-NS/CRO-S isolates were also ampicillin-sulbactam-NS. Of 32 TZP-NS/CRO-S isolates that were sequenced, 28 (88%) harbored blaTEM-1 or blaSHV-1, none had an ESBL or AmpC β-lactamase gene, and many sequence types were represented. Independent risk factors for TZP-NS/CRO-S bacteremia were exposure to β-lactam/β-lactamase inhibitors (BL/BLIs; adjusted odds ratio [aOR], 5.5; P < .001) and cephalosporins (aOR, 3.0; P = .04). Thirty-day mortality after TZP-NS/CRO-S bacteremia was 25%, which was similar to control groups and was similar in patients treated empirically with BL/BLIs compared with those treated with cephalosporins or carbapenems. Targeted therapy with cephalosporins did not yield a higher 30-day mortality rate than carbapenem therapy. Conclusions TZP-NS/CRO-S Ec and Kp are emerging causes of bacteremia, and further research is needed to better understand the epidemiology, resistance mechanisms, and clinical impact of these strains.
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Affiliation(s)
- Thomas M Baker
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Clinical Immunology, Janssen Research & Development, Spring House, Pennsylvania
| | - Wesley Rogers
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Kalyan D Chavda
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Lars F Westblade
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Stephen G Jenkins
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - David P Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, Connecticut
| | - Barry N Kreiswirth
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey
| | - David P Calfee
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
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