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Hurwitz JS, Newton-Foot M, Nel van Zyl K, Nel P. Fosfomycin susceptibility testing and resistance mechanisms in Enterobacterales in South Africa. Afr J Lab Med 2024; 13:2252. [PMID: 38629086 PMCID: PMC11019110 DOI: 10.4102/ajlm.v13i1.2252] [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: 07/05/2023] [Accepted: 12/18/2023] [Indexed: 04/19/2024] Open
Abstract
Background Fosfomycin treatment of urinary tract infections is increasingly attractive due to escalating antibiotic resistance rates among urinary pathogens. Standard antibiotic susceptibility testing methods perform poorly for fosfomycin as there is poor correlation between susceptibility results and clinical outcomes in urinary pathogens other than Escherichia coli. Objective We evaluated the performance of fosfomycin susceptibility testing in E. coli and Klebsiella pneumoniae to determine whether fosfomycin susceptibility is associated with molecular resistance mechanisms. Methods Forty-six each of E. coli and K. pneumoniae clinical isolates were obtained from a tertiary hospital in South Africa, from 01 June 2017 to 31 January 2018. Agar dilution, disk diffusion, and gradient diffusion were performed and interpreted using the Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing guidelines. Molecular resistance mechanisms were identified by whole genome sequence analysis. Results Disk diffusion and gradient diffusion were accurate alternatives for fosfomycin susceptibility testing in E. coli (98% categorical agreement), but not in K. pneumoniae (47% categorical agreement). All E. coli isolates contained at least one resistance mechanism, but only one isolate with a fosA gene was resistant. In K. pneumoniae, 63% (29/46) and 70% (32/46) of isolates were susceptible to fosfomycin, using Clinical Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing breakpoints, respectively, despite all isolates containing a fosA gene and a uhpT mutation. Conclusion A better understanding of fosfomycin susceptibility and improved antibiotic susceptibility testing tools could improve diagnostic capability and clinical guidelines for fosfomycin treatment of urinary tract infections. What this study adds This study highlights the importance of adhering to interpretive guidelines when performing antimicrobial susceptibility testing and the need for simplified, accurate and standardised susceptibility testing methodology and interpretation for fosfomycin in Enterobacterales organisms.
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Affiliation(s)
- Jessica S. Hurwitz
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mae Newton-Foot
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
| | - Kristien Nel van Zyl
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Pieter Nel
- Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Tygerberg Hospital, National Health Laboratory Service, Cape Town, South Africa
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Grilo T, Freire S, Miguel B, Martins LN, Menezes MF, Nordmann P, Poirel L, Sousa MJR, Aires-de-Sousa M. Occurrence of plasmid-mediated fosfomycin resistance (fos genes) among Escherichia coli isolates, Portugal. J Glob Antimicrob Resist 2023; 35:342-346. [PMID: 37553021 DOI: 10.1016/j.jgar.2023.08.001] [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: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
OBJECTIVES To evaluate the occurrence of plasmid-mediated fos genes among fosfomycin-resistant Escherichia coli isolates collected from patients in Lisbon, Portugal, and characterize the fos-positive strains. METHODS A total of 19 186 E. coli isolates were prospectively collected between April 2022 and January 2023 from inpatients and outpatients at a private laboratory in Lisbon. Fosfomycin resistance was initially assessed by semi-automated systems and further confirmed by the disc diffusion method. Resistant isolates were investigated for plasmid-mediated fos genes (fosA1-fosA10, fosC and fosL1-fosL2) and extended-spectrum beta-lactamases (ESBLs) by PCR and sequencing. Multilocus sequence typing was performed to evaluate the clonal relationship among fos-carrying isolates. RESULTS Out of the 19 186 E. coli isolates, 100 were fosfomycin-resistant (0.5%), out of which 15 carried a fosA-like gene (15%). The most prevalent fosfomycin-resistant determinant was fosA3 (n = 11), followed by fosA4 (n = 4). Among the 15 FosA-producing isolates, 10 co-produced an ESBL (67%), being either of CTX-M-15 (n = 8) or CTX-M-14 (n = 2) types. The fosA3 gene was carried on IncFIIA-, IncFIB-, and IncY-type plasmids, whereas fosA4 was always located on IncFIB-type plasmids. Most FosA4-producing isolates belonged to a single sequence type ST2161, whereas isolates carrying the fosA3 gene were distributed into nine distinct genetic backgrounds. CONCLUSION The prevalence of fosfomycin-resistant E. coli isolates is still low in Portugal. Notably, 15% of fosfomycin-resistant isolates harbour a transferable fosA gene, among which there is a high rate of ESBL producers, turning traditional empirical therapeutical options used in Portugal (fosfomycin and amoxicillin-clavulanic acid) ineffective.
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Affiliation(s)
- Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Bruno Miguel
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal
| | | | - Maria Favila Menezes
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal; Hospital CUF Descobertas, Lisboa, Portugal
| | - Patrice Nordmann
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Maria José Rego Sousa
- Centro Medicina Laboratorial - Germano de Sousa, Lisboa, Portugal; Hospital CUF Descobertas, Lisboa, Portugal
| | - Marta Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa - Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Loras C, Pérez-Vázquez M, González Prieto A, Oteo-Iglesias J, Alós JI. Prevalence of fosA3 Gene in Fosfomycin-Resistant Proteus mirabilis in the Autonomous Community of Madrid (Spain) and Characterization of Two Positive Strains. Microb Drug Resist 2023; 29:444-447. [PMID: 37023411 DOI: 10.1089/mdr.2022.0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Plasmid-mediated resistance to fosfomycin has been seldom described in Proteus mirabilis. We report two strains harboring fosA3 gene. Whole-genome sequencing revealed a plasmid that encoded fosA3 gene flanked by two insertion sequence (IS)26 mobile elements. Both strains also produced the blaCTX-M-65 gene that was located in the same plasmid. The sequence detected was IS1182-blaCTX-M-65-orf1-orf2-IS26-IS26-fosA3-orf1-orf2-orf3-IS26. The importance of this transposon lies in its ability to spread in Enterobacterales, therefore, epidemiological surveillance should be carried out.
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Affiliation(s)
- Cristina Loras
- Servicio de Microbiología, Hospital Universitario de Getafe, Getafe, Spain
| | - María Pérez-Vázquez
- Laboratorio de Resistencia a Antibióticos, Centro Nacional de Microbiología, ISCIII, Majadahonda, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | | | - Jesús Oteo-Iglesias
- Laboratorio de Resistencia a Antibióticos, Centro Nacional de Microbiología, ISCIII, Majadahonda, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Juan-Ignacio Alós
- Servicio de Microbiología, Hospital Universitario de Getafe, Getafe, Spain
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Mattioni Marchetti V, Hrabak J, Bitar I. Fosfomycin resistance mechanisms in Enterobacterales: an increasing threat. Front Cell Infect Microbiol 2023; 13:1178547. [PMID: 37469601 PMCID: PMC10352792 DOI: 10.3389/fcimb.2023.1178547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is well-known to be a global health and development threat. Due to the decrease of effective antimicrobials, re-evaluation in clinical practice of old antibiotics, as fosfomycin (FOS), have been necessary. FOS is a phosphonic acid derivate that regained interest in clinical practice for the treatment of complicated infection by multi-drug resistant (MDR) bacteria. Globally, FOS resistant Gram-negative pathogens are raising, affecting the public health, and compromising the use of the antibiotic. In particular, the increased prevalence of FOS resistance (FOSR) profiles among Enterobacterales family is concerning. Decrease in FOS effectiveness can be caused by i) alteration of FOS influx inside bacterial cell or ii) acquiring antimicrobial resistance genes. In this review, we investigate the main components implicated in FOS flow and report specific mutations that affect FOS influx inside bacterial cell and, thus, its effectiveness. FosA enzymes were identified in 1980 from Serratia marcescens but only in recent years the scientific community has started studying their spread. We summarize the global epidemiology of FosA/C2/L1-2 enzymes among Enterobacterales family. To date, 11 different variants of FosA have been reported globally. Among acquired mechanisms, FosA3 is the most spread variant in Enterobacterales, followed by FosA7 and FosA5. Based on recently published studies, we clarify and represent the molecular and genetic composition of fosA/C2 genes enviroment, analyzing the mechanisms by which such genes are slowly transmitting in emerging and high-risk clones, such as E. coli ST69 and ST131, and K. pneumoniae ST11. FOS is indicated as first line option against uncomplicated urinary tract infections and shows remarkable qualities in combination with other antibiotics. A rapid and accurate identification of FOSR type in Enterobacterales is difficult to achieve due to the lack of commercial phenotypic susceptibility tests and of rapid systems for MIC detection.
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Affiliation(s)
- Vittoria Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
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Mattioni Marchetti V, Kraftova L, Finianos M, Sourenian T, Hrabak J, Bitar I. Polyclonal Spread of Fosfomycin Resistance among Carbapenemase-Producing Members of the Enterobacterales in the Czech Republic. Microbiol Spectr 2023; 11:e0009523. [PMID: 37098942 PMCID: PMC10269928 DOI: 10.1128/spectrum.00095-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/31/2023] [Indexed: 04/27/2023] Open
Abstract
Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 μg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.
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Affiliation(s)
- V. Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - L. Kraftova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - M. Finianos
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - T. Sourenian
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - J. Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - I. Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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Lysitsas M, Chatzipanagiotidou I, Billinis C, Valiakos G. Fosfomycin Resistance in Bacteria Isolated from Companion Animals (Dogs and Cats). Vet Sci 2023; 10:vetsci10050337. [PMID: 37235420 DOI: 10.3390/vetsci10050337] [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: 03/31/2023] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Fosfomycin is an old antibacterial agent, which is currently used mainly in human medicine, in uncomplicated Urinary Tract Infections (UTIs). The purpose of this review is to investigate the presence and the characteristics of Fosfomycin resistance in bacteria isolated from canine or feline samples, estimate the possible causes of the dissemination of associated strains in pets, and underline the requirements of prospective relevant studies. Preferred Reporting Items for Systematic Reviews (PRISMA) guidelines were used for the search of current literature in two databases. A total of 33 articles were finally included in the review. Relevant data were tracked down, assembled, and compared. Referring to the geographical distribution, Northeast Asia was the main area of origin of the studies. E. coli was the predominant species detected, followed by other Enterobacteriaceae, Staphylococci, and Pseudomonas spp. FosA and fosA3 were the more frequently encountered Antimicrobial Resistance Genes (ARGs) in the related Gram-negative isolates, while fosB was regularly encountered in Gram-positive ones. The majority of the strains were multidrug-resistant (MDR) and co-carried resistance genes against several classes of antibiotics and especially β-Lactams, such as blaCTX-M and mecA. These results demonstrate the fact that the cause of the spreading of Fosfomycin-resistant bacteria among pets could be the extended use of other antibacterial agents, that promote the prevalence of MDR, epidemic strains among an animal population. Through the circulation of these strains into a community, a public health issue could arise. Further research is essential though, for the comprehensive consideration of the issue, as the current data are limited.
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Affiliation(s)
- Marios Lysitsas
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
| | | | | | - George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece
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7
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Freire S, Grilo T, Nordmann P, Poirel L, Aires-de-Sousa M. Multiplex PCR for detection of acquired plasmid-borne fosfomycin resistance fos genes in Escherichia coli. Diagn Microbiol Infect Dis 2023; 105:115864. [PMID: 36502596 DOI: 10.1016/j.diagmicrobio.2022.115864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
A rapid (<3 hours) and reliable multiplex PCR was developed for detecting simultaneously known plasmid-mediated fos genes conferring acquired resistance to fosfomycin. Our technique was tested on a collection of Escherichia coli isolates previously identified as bearing the fosA-, fosC- and fosL-like genes, showing a sensitivity and a specificity of 100%.
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Affiliation(s)
- Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Patrice Nordmann
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal; Escola Superior de Saúde da Cruz Vermelha Portuguesa - Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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8
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1286-1295. [DOI: 10.1093/jac/dkac061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/01/2022] [Indexed: 11/14/2022] Open
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Selective screening culture medium for fosfomycin resistance in Enterobacterales. J Clin Microbiol 2021; 60:e0206321. [PMID: 34669459 DOI: 10.1128/jcm.02063-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A selective medium for screening fosfomycin (FOS)-resistant Enterobacterales was developed. Performances of this medium were first evaluated by using cultures of a collection of 84 enterobacterial clinical strains (42 FOS-susceptible and 42 FOS-resistant). The SuperFOS medium showed excellent sensitivity and specificity of detection (100%) in those conditions. Then, by testing spiked stool and spiked urine specimens, it revealed excellent performances, with lower limits of identification ranging from 101 to 102 CFU/ml. This screening medium allows easy and accurate detection of FOS-resistant isolates regardless of their resistance mechanisms.
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Wong CP, Delate T, Hudson E, Nguyen JK, Yang SJ, Abraham M. Retrospective assessment of antimicrobial stewardship initiative in outpatient use of ertapenem for uncomplicated extended spectrum beta lactamase Enterobacteriaceae urinary tract infections. BMC Infect Dis 2021; 21:823. [PMID: 34399680 PMCID: PMC8369658 DOI: 10.1186/s12879-021-06458-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/18/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Urinary tract infections (UTI) are often over-diagnosed and over-treated, which can induce and select for resistant pathogens. After observing wide-spread outpatient use of ertapenem, a broad-spectrum antibiotic, a structured antimicrobial stewardship initiative (ASI) to improve appropriate antimicrobial prescribing was undertaken. ASI objectives were to achieve a goal of reducing ertapenem utilization for extended spectrum beta lactamase Enterobacteriaceae (ESBL-EB) UTI by 10% and evaluate the clinical outcomes associated with the ASI. METHODS A pre-to-post cohort study was conducted at a single-center integrated healthcare system between November 1, 2014 and February 26, 2017. An intensive, 90-day, pharmacist-driven, structured ASI was implemented between November 1, 2015 and January 29, 2016. Female patients aged ≥18 years who were treated for an uncomplicated, ESBL-EB urinary tract infection (UTI) were included. Primary outcome was clinical resolution defined as cure, persistence, relapse and recurrence. Secondary outcome measured was monthly ertapenem use expressed as number of days of therapy (DOT)/1000 adjusted patient days (APD). Segmented regression analysis for interrupted time series was performed to estimate ASI intervention effect. RESULTS A total of 184 patients were included in the study. Ertapenem utilization decreased from 0.0145 DOT/1000 APD in Nov. 2014 to 0.0078 DOT/1000 APD Feb. 2017(p < 0.01). The mean ertapenem DOT declined 19% overall from the pre vs. post intervention periods (32 vs 26, p < 0.01). Frequency of recurrent UTIs between treatments did not significantly differ and no adverse effects were reported in patients treated with aminoglycosides. CONCLUSIONS A structured ASI for uncomplicated ESBL-EB UTI was associated with a clinically meaningful decrease in ertapenem utilization and once-daily, 5-day aminoglycoside treatment was well-tolerated.
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Affiliation(s)
- Carrie P Wong
- Kaiser Permanente Northern California Ambulatory Care Pharmacy, Kaiser Permanente Santa Clara Medical Center, 700 Lawrence Expy, Santa Clara, CA, 95051, USA.
| | - Thomas Delate
- Pharmacy Outcomes Research Group, Kaiser Permanente National Pharmacy, Aurora, CO, USA
- Department of Clinical Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Elizabeth Hudson
- Kaiser Permanente Southern California Infectious Diseases Clinic, Panorama City Specialty Medical Office, Panorama City, CA, USA
| | - Julia K Nguyen
- Kaiser Permanente Southern California Outpatient Infusion Pharmacy, Kaiser Permanente Panorama City Medical Center, 13652 Cantara St, Bldg 4, LL, Rm L21, Panorama City, CA, 91402, USA.
| | - Su-Jau Yang
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Mariana Abraham
- Kaiser Permanente Southern California Outpatient Infusion Pharmacy, Kaiser Permanente Panorama City Medical Center, 13652 Cantara St, Bldg 4, LL, Rm L21, Panorama City, CA, 91402, USA
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Paganini JA, Plantinga NL, Arredondo-Alonso S, Willems RJL, Schürch AC. Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data. Microorganisms 2021; 9:1613. [PMID: 34442692 PMCID: PMC8400445 DOI: 10.3390/microorganisms9081613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
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Abbott IJ, Dekker J, van Gorp E, Wijma RA, Raaphorst MN, Klaassen CHW, Meletiadis J, Mouton JW, Peleg AY. Impact of bacterial species and baseline resistance on fosfomycin efficacy in urinary tract infections. J Antimicrob Chemother 2021; 75:988-996. [PMID: 31873748 DOI: 10.1093/jac/dkz519] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/17/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To assess the antibacterial effects of a single 3 g oral fosfomycin dose on Escherichia coli and Klebsiella pneumoniae clinical isolates within a dynamic bladder infection model. METHODS An in vitro model simulating dynamic urinary fosfomycin concentrations was used. Target fosfomycin exposure (Cmax = 1984 mg/L and Tmax = 7.5 h) was validated by LC-MS/MS. Pharmacodynamic responses of 24 E. coli and 20 K. pneumoniae clinical isolates were examined (fosfomycin MIC ≤0.25-128 mg/L). Mutant prevention concentration (MPC), fosfomycin heteroresistance, fosfomycin resistance genes and fosA expression were examined. Pathogen kill and emergence of high-level resistance (HLR; MIC >1024 mg/L) were quantified. RESULTS Following fosfomycin exposure, 20 of 24 E. coli exhibited reductions in bacterial counts below the lower limit of quantification without regrowth, despite baseline fosfomycin MICs up to 128 mg/L. Four E. coli regrew (MIC = 4-32 mg/L) with HLR population replacement. At baseline, these isolates had detectable HLR subpopulations and MPC >1024 mg/L. All E. coli isolates were fosA negative. In contrast, 17 of 20 K. pneumoniae regrew post exposure, 6 with emergence of HLR (proportion = 0.01%-100%). The three isolates without regrowth did not have a detectable HLR subpopulation after dynamic drug-free incubation. All K. pneumoniae had MPC >1024 mg/L and were fosA positive. WGS analysis and fosA expression failed to predict fosfomycin efficacy. CONCLUSIONS E. coli and K. pneumoniae isolates demonstrate discrepant responses to a single fosfomycin dose in a dynamic bladder infection in vitro model. Treatment failure against E. coli was related to an HLR subpopulation, not identified by standard MIC testing. Activity against K. pneumoniae appeared limited, regardless of MIC testing, due to universal baseline heteroresistance.
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Affiliation(s)
- Iain J Abbott
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jordy Dekker
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Elke van Gorp
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Rixt A Wijma
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands.,Department of Hospital Pharmacy, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Merel N Raaphorst
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Corné H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Haidari, Athens, Greece
| | - Johan W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Anton Y Peleg
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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13
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Prevalence, detection and characterisation of fosfomycin-resistant Escherichia coli strains carrying fosA genes in Community of Madrid, Spain. J Glob Antimicrob Resist 2021; 25:137-141. [PMID: 33757820 DOI: 10.1016/j.jgar.2021.02.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES The aim of this this study was to describe the presence of different variants of the fosA gene in fosfomycin-resistant Escherichia coli strains in Madrid, Spain. METHODS fos genes were searched for in 55 E. coli strains collected from seven representative hospitals located in Madrid. A phenotypic screening test was performed following the disk diffusion method with sodium phosphonoformate added as described by Nakamura et al. Additionally, a molecular study based on PCR was used to confirm the screening results. Positive strains for fos genes were further subjected to whole-genome sequencing (WGS). RESULTS Phenotypic screening was positive in 9/55 strains (16.4%), although genotypic detection was positive in only 3 (fosA3, fosA4 and fosA6). Thus, the prevalence of fos genes in Madrid was 5.5% (3/55). WGS data were not available for the fosA6-positive strain. One isolate with fosA3 (ST69) carried a blaCTX-M-55 gene and seven virulence genes (air, eilA, iha, iss, lpfA, sat and senB). The fosA4-positive isolate (ST4038) carried the virulence genes iss, lpfA, iroN and mchF. Both fos genes were located between two IS26 mobile elements of a plasmid. CONCLUSION We detected the presence of different variants of plasmid-mediated fosA genes in fosfomycin-resistant E. coli strains in Madrid, Spain. Despite the few reports in Europe, it would be of interest to monitor the spread of these acquired resistance genes.
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14
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Identification and Characterization of a Novel FosA7 Member from Fosfomycin-Resistant Escherichia coli Clinical Isolates from Canadian Hospitals. Antimicrob Agents Chemother 2020; 65:AAC.00865-20. [PMID: 33077665 DOI: 10.1128/aac.00865-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/16/2020] [Indexed: 11/20/2022] Open
Abstract
Here, we characterize the fosA genes from three Escherichia coli clinical isolates recovered from Canadian patients. Each fosA sequence was individually overexpressed in E. coli BW25113, and antimicrobial susceptibility testing was performed to assess their role in fosfomycin resistance. The findings from this study identify and functionally characterize FosA3, FosA8, and novel FosA7 members and highlight the importance of phenotypic characterization of fosA genes.
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15
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Zurfluh K, Treier A, Schmitt K, Stephan R. Mobile fosfomycin resistance genes in Enterobacteriaceae-An increasing threat. Microbiologyopen 2020; 9:e1135. [PMID: 33128341 PMCID: PMC7755807 DOI: 10.1002/mbo3.1135] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance is one of the major threats to the health and welfare of both humans and animals. The shortage of new antimicrobial agents has led to the re-evaluation of old antibiotics such as fosfomycin as a potential regimen for treating multidrug-resistant bacteria especially extended-spectrum-beta-lactamase- and carbapenemase-producing Enterobacteriaceae. Fosfomycin is a broad-spectrum bactericidal antibiotic that inhibits the initial step of the cell wall biosynthesis. Fosfomycin resistance can occur due to mutation in the drug uptake system or by the acquisition of fosfomycin-modifying enzymes. In this review, we focus on mobile fosfomycin-resistant genes encoding glutathione-S-transferase which are mainly responsible for fosfomycin resistance in Enterobacteriaceae, that is, fosA and its subtypes, fosC2, and the recently described fosL1-L2. We summarized the proposed origins of the different resistance determinants and highlighted the different plasmid types which are attributed to the dissemination of fosfomycin-modifying enzymes. Thereby, IncF and IncN plasmids play a predominant role. The detection of mobile fosfomycin-resistant genes in Enterobacteriaceae has increased in recent years. Similar to the situation in (East) Asia, the most frequently detected fosfomycin-resistant gene in Europe is fosA3. Mobile fosfomycin-resistant genes have been detected in isolates of human, animal, food, and environmental origin which leads to a growing concern regarding the risk of spread of such bacteria, especially Escherichia coli and Salmonella, at the human-animal-environment interface.
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Affiliation(s)
- Katrin Zurfluh
- Institute for Food Safety and HygieneVetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Andrea Treier
- Institute for Food Safety and HygieneVetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Kira Schmitt
- Institute for Food Safety and HygieneVetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Roger Stephan
- Institute for Food Safety and HygieneVetsuisse FacultyUniversity of ZurichZurichSwitzerland
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16
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Huang Y, Lin Q, Zhou Q, Lv L, Wan M, Gao X, Wang C, Liu JH. Identification of fosA10, a Novel Plasmid-Mediated Fosfomycin Resistance Gene of Klebsiella pneumoniae Origin, in Escherichia coli. Infect Drug Resist 2020; 13:1273-1279. [PMID: 32431524 PMCID: PMC7200238 DOI: 10.2147/idr.s251360] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/07/2020] [Indexed: 11/24/2022] Open
Abstract
Purpose Several subtypes of plasmid-mediated fosfomycin resistance gene fosA in Enterobacteriaceae have been reported worldwide and have caused concern. The present study characterized a novel member of fosA gene located on a plasmid from Escherichia coli. Materials and Methods A fosfomycin-resistant E. coli isolate PK9 was recovered from a chicken meat sample in 2018. The presence of fosA genes was detected by PCR and sequencing. Whole-genome sequencing (WGS), conjugation, and cloning were performed to identify the mechanism responsible for fosfomycin resistance. Oxford Nanopore MinION sequencing was carried out to characterize the plasmid carrying fosfomycin resistance gene and the genetic context of the novel fosA variant. Results A novel fosA gene with significant homology (>98%) with fosA6 and fosA5 genes was identified by WGS and was named fosA10. FosA10 shared 56.1% to 98.6% amino acid sequence identity with other reported plasmid-mediated FosA enzymes. Fosfomycin resistance and fosA10 gene were successfully transferred to E. coli C600 by conjugation. Cloning confirmed that FosA10 could confer fosfomycin resistance (MIC > 128 μg/mL). The fosA10 gene was localized on a 53kb IncFII (F35:A-:B-) plasmid. The ∆lysR-fosA10-∆hp fragment (4328 bp), located between two copies of IS10R, showed 100% identity with the chromosomal sequences of 17 Klebsiella pneumoniae strains of ST664 and one of ST3821 in GenBank. Conclusion Our findings indicated that the fosA10 gene of E. coli might be captured from the chromosome of K. pneumoniae by IS10, which further demonstrated that K. pneumoniae might act as a reservoir of fosA-like genes acquired by E. coli.
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Affiliation(s)
- Ying Huang
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Qingqing Lin
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Qiaoli Zhou
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Luchao Lv
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Miao Wan
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Xun Gao
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Chengzhen Wang
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Jian-Hua Liu
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People's Republic of China
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Characterization of FosL1, a Plasmid-Encoded Fosfomycin Resistance Protein Identified in Escherichia coli. Antimicrob Agents Chemother 2020; 64:AAC.02042-19. [PMID: 31932373 DOI: 10.1128/aac.02042-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/21/2019] [Indexed: 02/05/2023] Open
Abstract
Fosfomycin is gaining renewed interest for treating urinary tract infections. Monitoring fosfomycin resistance is therefore important in order to detect the emergence of novel resistance mechanisms. Here, we used the Rapid Fosfomycin NP test to screen a collection of extended-spectrum-β-lactamase-producing Escherichia coli isolates from Switzerland and found a fosfomycin-resistant isolate in which a novel plasmid-mediated fosfomycin resistance gene, named fosL1, was identified. The FosL1 protein is a putative glutathione S-transferase enzyme conferring high-level resistance to fosfomycin and sharing between 57% to 63% amino acid identity with other FosA-like family members. Genetic analyses showed that the fosL1 gene was embedded in a mobile insertion cassette and had likely been acquired by transposition through a Tn7-related mechanism. In silico analysis over GenBank databases identified the FosL1-encoding gene in addition to another variant (fosL1 and fosL2, respectively) in two Salmonella enterica isolates from the United States. Our study further highlights the necessity of monitoring fosfomycin resistance in Enterobacteriaceae to identify the emergence of novel mechanisms of resistance.
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