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Li P, Xu Q, Ding L, Zhang X, Li D, Wang L, Xu X, Lin D, Wang M. Q48K mutation in the type IB nitroreductase NrmA is responsible for nitrofurantoin resistance in Enterococcus faecium. Int J Antimicrob Agents 2024; 64:107277. [PMID: 39032672 DOI: 10.1016/j.ijantimicag.2024.107277] [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: 12/11/2023] [Revised: 06/16/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
OBJECTIVES Nitrofurantoin is recommended as first-line therapy for the optimal treatment of uncomplicated urinary tract infections (UTIs) caused by enterococci and Escherichia coli. However, the mechanisms of nitrofurantoin resistance in enterococci have not been elucidated. This study aimed to investigate the mechanisms of nitrofurantoin resistance in E. faecium, focusing on the role of the nitroreductase NrmA. METHODS Enterococcus strains isolated from the urinary tract samples were collected and were tested for nitrofurantoin susceptibility. Potential genes associated with nitrofurantoin resistance were screened in the NCBI nucleotide database and by polymerase chain reaction (PCR). Complementation assays and enzyme kinetic tests were performed to assess the impact of the Q48K mutation in NrmA on nitrofurantoin resistance. RESULTS Of the 128 E. faecium isolates tested, 59 (46.1%) were resistant to nitrofurantoin. Analysis revealed the presence of a type IB nitroreductase, designated NrmA, in all E. faecium strains studied, shared 18.7% sequence identity with nitroreductase NfsB in E. coli. Different from NrmA in nitrofurantoin-susceptible E. faecium, nitrofurantoin-resistant strains had a single amino acid substitution, i.e., a lysine instead of a glutamine at position 48 (Q48K mutation). Complementation assays of nitrofurantoin-resistant E. faecium HS17-112 showed that the nitrofurantoin minimal inhibitory concentration of the complemented strain HS17-112: pIB166-nrmA (wild type [WT]) decreased from 128 mg/L to 4 mg/L. Compared with NrmA (WT), NrmA (Q48K) showed significantly reduced catalytic efficiency, with a kcat/Km value decreasing from 0.122 µM-1 s-1 to 0.000042 µM-1 s-1. CONCLUSION The Q48K mutation in nitroreductase NrmA is responsible for nitrofurantoin resistance in E. faecium.
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Affiliation(s)
- Pei Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Qingqing Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Xuefei Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Dongfang Lin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China.
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García-Díez J, Moura D, Grispoldi L, Cenci-Goga B, Saraiva S, Silva F, Saraiva C, Ausina J. Salmonella spp. in Domestic Ruminants, Evaluation of Antimicrobial Resistance Based on the One Health Approach-A Systematic Review and Meta-Analysis. Vet Sci 2024; 11:315. [PMID: 39057999 PMCID: PMC11281391 DOI: 10.3390/vetsci11070315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Salmonella spp. pose a global threat as a leading cause of foodborne illnesses, particularly prevalent in the European Union (EU), where it remains the second cause of foodborne outbreaks. The emergence of antimicrobial resistance (AMR) in Salmonella spp. has become a critical concern, complicating treatment strategies and escalating the risk of severe infections. The study focuses on large and small ruminants, identifying a prevalence of Salmonella spp. in slaughterhouses and revealing varied AMR rates across antimicrobial families throughout a meta-analysis. Also, comparison with AMR in human medicine was carried out by a systematic review. The results of the present meta-analysis displayed a prevalence of Salmonella spp. in large and small ruminants at slaughterhouses of 8.01% (8.31%, cattle; 7.04%, goats; 6.12%, sheep). According to the AMR of Salmonella spp., 20, 14, and 13 out of 62 antimicrobials studied were classified as low (<5%), high (>5% but <10%), and very high (>10%), respectively. Salmonella spp. did not display AMR against aztreonam, mezlocillin, ertapenem, meropenem, cefoxitin, ceftazidime, levofloxacin, tilmicosin, linezolid, fosfomycin, furazolidone, quinupristin, trimethoprim and spectinomycin. In contrast, a prevalence of 100% of AMR has been described against ofloxacin, lincomycin, and cloxacillin. In the context of the main antibiotics used in the treatment of human salmonellosis, azithromycin was shown to have the highest resistance among Salmonella spp. isolates from humans. Regarding cephalosporins, which are also used for the treatment of salmonellosis in humans, the prevalence of Salmonella spp. resistance to this class of antibiotics was similar in both human and animal samples. Concerning quinolones, despite a heightened resistance profile in Salmonella spp. isolates from ruminant samples, there appears to be no discernible compromise to the efficacy of salmonellosis treatment in humans since lower prevalences of AMR in Salmonella spp. isolated from human specimens were observed. Although the resistance of Salmonella spp. indicates some degree of concern, most antibiotics are not used in veterinary medicine. Thus, the contribution of cattle, sheep and goats to the rise of antibiotic resistance of Salmonella spp. and its potential impact on public health appears to be relatively insignificant, due to their low prevalence in carcasses and organs. Nevertheless, the observed low prevalence of Salmonella spp. in ruminants at slaughterhouse and the correspondingly low AMR rates of Salmonella spp. to key antibiotics employed in human medicine do not indicate that ruminant livestock poses a substantial public health risk concerning the transmission of AMR. Thus, the results observed in both the meta-analysis and systematic review suggests that AMR is not solely attributed to veterinary antibiotic use but is also influenced by factors such as animal health management (i.e., biosecurity measures, prophylactic schemes) and human medicine.
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Affiliation(s)
- Juan García-Díez
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal; (S.S.); (F.S.); (C.S.)
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Dina Moura
- Divisão de Intervenção de Alimentação e Veterinária de Vila Real e Douro Sul, Direção de Serviços de Alimentação e Veterinária da Região Norte, Direção Geral de Alimentação e Veterinária, Lugar de Codessais, 5000 Vila Real, Portugal;
| | - Luca Grispoldi
- Dipartamento di Medicina Veterinaria, Universitá degli Studi di Perugia, 06126 Perugia, Italy; (L.G.); (B.C.-G.)
| | - Beniamino Cenci-Goga
- Dipartamento di Medicina Veterinaria, Universitá degli Studi di Perugia, 06126 Perugia, Italy; (L.G.); (B.C.-G.)
- Faculty of Veterinary Science, Department of Paraclinical Sciences, University of Pretoria, Onderstepoort 0110, South Africa
| | - Sónia Saraiva
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal; (S.S.); (F.S.); (C.S.)
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
| | - Filipe Silva
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal; (S.S.); (F.S.); (C.S.)
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Cristina Saraiva
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal; (S.S.); (F.S.); (C.S.)
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 1300-477 Lisboa, Portugal
- Department of Veterinary Sciences, School of Agricultural and Veterinary Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Juan Ausina
- Social Psychology and Methodology Department, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain;
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Whelan S, Bottacini F, Buttimer C, Finn K, Lucey B. Whole genome sequencing of uropathogenic E. coli from Ireland reveals diverse resistance mechanisms and strong correlation with phenotypic (EUCAST) susceptibility testing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105600. [PMID: 38692501 DOI: 10.1016/j.meegid.2024.105600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/04/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Urinary tract infections (UTI) caused by uropathogenic Escherichia coli (UPEC) pose a global health concern. Resistance mechanisms, including genetic mutations in antimicrobial target genes, efflux pumps, and drug deactivating enzymes, hinder clinical treatment. These resistance factors often spread through mobile genetic elements. Molecular techniques like whole genome sequencing (WGS), multilocus sequence typing (MLST), and phylotyping help decode bacterial genomes and categorise resistance genes. In this study, we analysed 57 UPEC isolates from different UTI patients following EUCAST guidelines. A selection of 17 representative strains underwent WGS, phylotyping, MLST, and comparative analysis to connect laboratory susceptibility data with predictive genomics based on key resistance genes and chromosomal mutations in antimicrobial targets. Trimethoprim resistance consistently correlated with dfr genes, with six different alleles detected among the isolates. These dfr genes often coexisted with class 1 integrons, with the most common gene cassette combining dfr and aadA. Furthermore, 52.9% of isolates harboured the blaTem-1 gene, rendering resistance to ampicillin and amoxicillin. Ciprofloxacin-resistant strains exhibited mutations in GyrA, GyrB and ParC, plasmid-mediated quinolone resistance genes (qnrb10), and aac(6')-Ib-cr5. Nitrofurantoin resistance in one isolate stemmed from a four amino acid deletion in NfsB. These findings illustrate the varied strategies employed by UPEC to resist antibiotics and the correlation between clinical susceptibility testing and molecular determinants. As molecular testing gains prominence in clinical applications, understanding key resistance determinants becomes crucial for accurate susceptibility testing and guiding effective antimicrobial therapy.
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Affiliation(s)
- Shane Whelan
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
| | - Francesca Bottacini
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Karen Finn
- Department of Analytical, Biopharmaceutical and Medical Sciences, Atlantic Technological University Galway City, Dublin Road, Galway, Ireland.
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
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Nasrollahian S, Graham JP, Halaji M. A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli. Front Cell Infect Microbiol 2024; 14:1387497. [PMID: 38638826 PMCID: PMC11024256 DOI: 10.3389/fcimb.2024.1387497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.
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Affiliation(s)
- Sina Nasrollahian
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jay P. Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, United States
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Microbiology and Biotechnology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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5
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Rahman Z, McLaws M, Thomas T. Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia. Microbiologyopen 2024; 13:e1403. [PMID: 38488803 PMCID: PMC10941799 DOI: 10.1002/mbo3.1403] [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: 10/05/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.
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Affiliation(s)
- Zillur Rahman
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
| | - Mary‐Louise McLaws
- School of Population HealthUNSW SydneySydneyNew South WalesAustralia
- UNSW Global Water InstituteUNSW SydneySydneyNew South WalesAustralia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
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6
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Hussein M, Sun Z, Hawkey J, Allobawi R, Judd LM, Carbone V, Sharma R, Thombare V, Baker M, Rao GG, Li J, Holt KE, Velkov T. High-level nitrofurantoin resistance in a clinical isolate of Klebsiella pneumoniae: a comparative genomics and metabolomics analysis. mSystems 2024; 9:e0097223. [PMID: 38078757 PMCID: PMC10805014 DOI: 10.1128/msystems.00972-23] [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: 09/21/2023] [Accepted: 11/02/2023] [Indexed: 01/24/2024] Open
Abstract
Nitrofurantoin is a commonly used chemotherapeutic agent in the treatment of uncomplicated urinary tract infections caused by the problematic multidrug resistant Gram-negative pathogen Klebsiella pneumoniae. The present study aims to elucidate the mechanism of nitrofurantoin action and high-level resistance in K. pneumoniae using whole-genome sequencing (WGS), qPCR analysis, mutation structural modeling and untargeted metabolomic analysis. WGS profiling of evolved highly resistant mutants (nitrofurantoin minimum inhibitory concentrations > 256 mg/L) revealed modified expression of several genes related to membrane transport (porin ompK36 and efflux pump regulator oqxR) and nitroreductase activity (ribC and nfsB, involved in nitrofurantoin reduction). Untargeted metabolomics analysis of total metabolites extracted at 1 and 4 h post-nitrofurantoin treatment revealed that exposure to the drug caused a delayed effect on the metabolome which was most pronounced after 4 h. Pathway enrichment analysis illustrated that several complex interrelated metabolic pathways related to nitrofurantoin bacterial killing (aminoacyl-tRNA biosynthesis, purine metabolism, central carbohydrate metabolism, and pantothenate and CoA biosynthesis) and the development of nitrofurantoin resistance (riboflavin metabolism) were significantly perturbed. This study highlights for the first time the key role of efflux pump regulator oqxR in nitrofurantoin resistance and reveals global metabolome perturbations in response to nitrofurantoin, in K. pneumoniae.IMPORTANCEA quest for novel antibiotics and revitalizing older ones (such as nitrofurantoin) for treatment of difficult-to-treat Gram-negative bacterial infections has become increasingly popular. The precise antibacterial activity of nitrofurantoin is still not fully understood. Furthermore, although the prevalence of nitrofurantoin resistance remains low currently, the drug's fast-growing consumption worldwide highlights the need to comprehend the emerging resistance mechanisms. Here, we used multidisciplinary techniques to discern the exact mechanism of nitrofurantoin action and high-level resistance in Klebsiella pneumoniae, a common cause of urinary tract infections for which nitrofurantoin is the recommended treatment. We found that the expression of multiple genes related to membrane transport (including active efflux and passive diffusion of drug molecules) and nitroreductase activity was modified in nitrofurantoin-resistant strains, including oqxR, the transcriptional regulator of the oqxAB efflux pump. Furthermore, complex interconnected metabolic pathways that potentially govern the nitrofurantoin-killing mechanisms (e.g., aminoacyl-tRNA biosynthesis) and nitrofurantoin resistance (riboflavin metabolism) were significantly inhibited following nitrofurantoin treatment. Our study could help inform the improvement of nitrofuran derivatives, the development of new pharmacophores, or drug combinations to support the resurgence of nitrofurantoin in the management of multidrug resistant K. pneumouniae infection.
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Affiliation(s)
- Maytham Hussein
- Department of Pharmacology, Monash Biomedicine Discovery Institute,Monash University, Clayton, Victoria, Australia
| | - Zetao Sun
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Rafah Allobawi
- Department of Pharmacology, Monash Biomedicine Discovery Institute,Monash University, Clayton, Victoria, Australia
| | - Louise M. Judd
- Doherty Applied Microbial Genomics (DAMG), 12 Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Vincenzo Carbone
- AgResearch Limited, Grasslands Research Center, Tennent Drive, Palmerston North, New Zealand
| | - Rajnikant Sharma
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Varsha Thombare
- Department of Pharmacology, Monash Biomedicine Discovery Institute,Monash University, Clayton, Victoria, Australia
| | - Mark Baker
- Discipline of Biological 17 Sciences, Priority Research Center in Reproductive Biology, Faculty of Science and IT, University of Newcastle, University Drive, Callaghan, New South Wales, Australia
| | - Gauri G. Rao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jian Li
- Department of Pharmacology, Monash Biomedicine Discovery Institute,Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Tony Velkov
- Department of Pharmacology, Monash Biomedicine Discovery Institute,Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Guy RL, Rudman J, Higgins H, Carter E, Henderson KL, Demirjian A, Gerver SM. Nitrofurantoin resistance as an indicator for multidrug resistance: an assessment of Escherichia coli urinary tract specimens in England, 2015-19. JAC Antimicrob Resist 2023; 5:dlad122. [PMID: 38021038 PMCID: PMC10655056 DOI: 10.1093/jacamr/dlad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Objectives To determine whether MDR occurs more frequently in nitrofurantoin-resistant Escherichia coli urinary isolates in England, compared with nitrofurantoin-susceptible isolates. Methods Using routine E. coli urine isolate antibiotic susceptibility laboratory surveillance data for England, 2015-19 inclusive, the percentage of MDR or XDR phenotype was estimated for nitrofurantoin-susceptible and nitrofurantoin-resistant laboratory-reported urinary tract samples by region, patient sex and age group. Results Resistance to nitrofurantoin among E. coli urinary samples decreased slightly year on year from 2.9% in 2015 to 2.3% in 2019. Among E. coli UTIs tested for nitrofurantoin susceptibility and ≥3 additional antibiotics, the percentage that were MDR was consistently 15%-20% percentage points higher for nitrofurantoin-resistant isolates compared with nitrofurantoin-susceptible isolates. Similarly, the percentage of isolates with an XDR phenotype was higher among nitrofurantoin-resistant versus -susceptible isolates (8.7% versus 1.4%, respectively, in 2019); this disparity was greater in male patients, although variation was seen by age group in both sexes. Regional variation was also noted, with the highest MDR percentage amongst nitrofurantoin-resistant E. coli urinary samples in the London region (36.7% in 2019); the lowest was in the North East (2019: 16.9%). Conclusions MDR and XDR phenotypes occur more frequently in nitrofurantoin-resistant E. coli urinary isolates in England, compared with nitrofurantoin-susceptible isolates. However, nitrofurantoin resistance is low (<3%) overall. This latest study provides important insights into trends in nitrofurantoin resistance and MDR, which is of particular concern for patients ≥75 years old and those who are male. It also emphasises geographical heterogeneities within England in nitrofurantoin resistance and MDR.
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Affiliation(s)
- Rebecca L Guy
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
| | - Jamie Rudman
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
| | - Hannah Higgins
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
| | - Emma Carter
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
| | - Katherine L Henderson
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
| | - Alicia Demirjian
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, London, SE1 7EH, UK
- Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | - Sarah M Gerver
- Healthcare-Associated Infection, Fungal, Antimicrobial Resistance, Antimicrobial Use & Sepsis Division, United Kingdom Health Security Agency (UKHSA), Colindale, London, UK
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Wan Y, Sabnis A, Mumin Z, Potterill I, Jauneikaite E, Brown CS, Ellington MJ, Edwards A, Sriskandan S. IS 1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli. Microb Genom 2023; 9:001102. [PMID: 37672334 PMCID: PMC10569738 DOI: 10.1099/mgen.0.001102] [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: 04/04/2023] [Accepted: 08/16/2023] [Indexed: 09/07/2023] Open
Abstract
Nitrofurantoin is a broad-spectrum first-line antimicrobial used for managing uncomplicated urinary tract infection (UTI). Loss-of-function mutations in chromosomal genes nfsA, nfsB and ribE of Escherichia coli are known to reduce nitrofurantoin susceptibility. Here, we report the discovery of nitrofurantoin heteroresistance in E. coli clinical isolates and a novel genetic mechanism associated with this phenomenon. Subpopulations with lower nitrofurantoin susceptibility than major populations (hereafter, nitrofurantoin-resistant subpopulations) in two E. coli blood isolates (previously whole-genome sequenced) were identified using population analysis profiling. Each isolate was known to have a loss-of-function mutation in nfsA. From each isolate, four nitrofurantoin-resistant isolates were derived at a nitrofurantoin concentration of 32 mg l-1, and a comparator isolate was obtained without any nitrofurantoin exposure. Genomes of derived isolates were sequenced on Illumina and Nanopore MinION systems. Genetic variation between isolates was determined based on genome assemblies and read mapping. Nitrofurantoin minimum inhibitory concentrations (MICs) of both blood isolates were 64 mg l-1, with MICs of major nitrofurantoin-susceptible populations varying from 4 to 8 mg l-1. Two to 99 c.f.u. per million demonstrated growth at the nitrofurantoin concentration of 32 mg l-1, which is distinct from that of a homogeneously susceptible or resistant isolate. Derived nitrofurantoin-resistant isolates had 11-66 kb deletions in chromosomal regions harbouring nfsB, and all deletions were immediately adjacent to IS1-family insertion sequences. Our findings demonstrate that the IS1-associated large-scale genetic deletion is a hitherto unrecognized mechanism of nitrofurantoin heteroresistance and could compromise UTI management. Further, frequencies of resistant subpopulations from nitrofurantoin-heteroresistant isolates may challenge conventional nitrofurantoin susceptibility testing in clinical settings.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Akshay Sabnis
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Zaynab Mumin
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Isabelle Potterill
- Reference Services Division, National Infection Service, UK Health Security Agency, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - Colin S. Brown
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Andrew Edwards
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
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Whelan S, Lucey B, Finn K. Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment. Microorganisms 2023; 11:2169. [PMID: 37764013 PMCID: PMC10537683 DOI: 10.3390/microorganisms11092169] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections, especially among women and older adults, leading to a significant global healthcare cost burden. Uropathogenic Escherichia coli (UPEC) are the most common cause and accounts for the majority of community-acquired UTIs. Infection by UPEC can cause discomfort, polyuria, and fever. More serious clinical consequences can result in urosepsis, kidney damage, and death. UPEC is a highly adaptive pathogen which presents significant treatment challenges rooted in a complex interplay of molecular factors that allow UPEC to evade host defences, persist within the urinary tract, and resist antibiotic therapy. This review discusses these factors, which include the key genes responsible for adhesion, toxin production, and iron acquisition. Additionally, it addresses antibiotic resistance mechanisms, including chromosomal gene mutations, antibiotic deactivating enzymes, drug efflux, and the role of mobile genetic elements in their dissemination. Furthermore, we provide a forward-looking analysis of emerging alternative therapies, such as phage therapy, nano-formulations, and interventions based on nanomaterials, as well as vaccines and strategies for immunomodulation. This review underscores the continued need for research into the molecular basis of pathogenesis and antimicrobial resistance in the treatment of UPEC, as well as the need for clinically guided treatment of UTIs, particularly in light of the rapid spread of multidrug resistance.
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Affiliation(s)
- Shane Whelan
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland;
| | - Karen Finn
- Department of Analytical, Biopharmaceutical and Medical Sciences, Atlantic Technological University Galway City, Dublin Road, H91 T8NW Galway, Ireland
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10
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Mahdizade Ari M, Dashtbin S, Ghasemi F, Shahroodian S, kiani P, Bafandeh E, Darbandi T, Ghanavati R, Darbandi A. Nitrofurantoin: properties and potential in treatment of urinary tract infection: a narrative review. Front Cell Infect Microbiol 2023; 13:1148603. [PMID: 37577377 PMCID: PMC10414118 DOI: 10.3389/fcimb.2023.1148603] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/23/2023] [Indexed: 08/15/2023] Open
Abstract
Nitrofurantoin (NF), a wide-spectrum antibiotic accessible since 1953, is utilized widely to treat urinary tract infections as it usually stays active against drug-resistant uropathogen. The use of Nitrofurantoin has increased exponentially since new guidelines have repositioned it as first-line therapy for uncomplicated lower urinary tract infection (UTI). To, although fluoroquinolones are usually used to re-evaluate the first- and second-line therapies for treating uncomplicated UTI, their level of utilization is thought to be inappropriately excessive and will eventually have a detrimental impact; thus, we hypothesize that NF might be the best choice for this condition, because of its low frequency of utilization and its high susceptibility in common UTI pathogens. It can be concluded from this review that NF can be considered as the most effective drug in the treatment of acute urinary infection, but due to the long-term side effects of this drug, especially in elderly patients, it is essential to introduce some criteria for prescribing NF in cases of chronic UTI.
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Affiliation(s)
- Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shirin Dashtbin
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Ghasemi
- Department of Pathobiology, Division of Microbiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Shahroodian
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa kiani
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elnaz Bafandeh
- Department of Medical Biotechnology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Talieh Darbandi
- Department of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Roya Ghanavati
- School of Medicine, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Atieh Darbandi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran
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11
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Hung CC, Varga C, Reinhart JM, Maddox CW, Dilger RN, Forsythe L, Stevenson AK, Franklin-Guild RJ, Paul NC, Ramachandran A. Assessing the urinary concentration of nitrofurantoin and its antibacterial activity against Escherichia coli, Staphylococcus pseudintermedius, and Enterococcus faecium isolated from dogs with urinary tract infections. Front Vet Sci 2023; 10:1189374. [PMID: 37492434 PMCID: PMC10365272 DOI: 10.3389/fvets.2023.1189374] [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: 03/30/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023] Open
Abstract
Nitrofurantoin, a broad-spectrum nitrofuran class antibiotic, is applied as a first-line antibiotic in treating human urinary tract infections (UTIs) due to its great efficacy and high achievable concentration. The interest in using this antibiotic in companion animals has increased due to the growing demand for effective antibiotics to treat UTIs caused by multidrug-resistant bacteria. Currently, the susceptibility interpretations for nitrofurantoin are based on the breakpoints set for humans, while the canine-specific breakpoints are still unavailable. In this study, we assessed the concentration of nitrofurantoin reaching the dog's urine using the recommended oral dosing regimen. In addition, we examined the efficacy of this breakpoint concentration against the common canine UTI pathogens, Escherichia coli, Staphylococcus pseudintermedius, and Enterococcus faecium. Eight experimental beagle dogs were treated with ~5 mg/kg of nitrofurantoin macrocrystal PO 8qh for 7 days. The urine samples were collected via cystocentesis at 2, 4, and 6 h after administration on day 2 and day 7 and used to quantify nitrofurantoin concentrations by ultra-high performance liquid chromatography. The results showed that 26.13-315.87 μg/mL nitrofurantoin was detected in the dogs' urine with a mean and median concentration of 104.82 and 92.75 μg/mL, respectively. Additionally, individual dogs presented with urinary nitrofurantoin concentrations greater than 64 μg/mL for at least 50% of the dosing intervals. This concentration efficiently killed E. coli, and S. pseudintermedius, but not E. faecium strains carrying an MIC90 value equal to 16, 16, and 128 μg/mL, respectively. Taken together, these results suggest that the value of 64 μg/mL may be set as a breakpoint against UTI pathogens, and nitrofurantoin could be an effective therapeutic drug against E. coli and S. pseudintermedius for canine UTIs.
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Affiliation(s)
- Chien-Che Hung
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Jennifer M. Reinhart
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Carol W. Maddox
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Ryan N. Dilger
- Department of Animal Science, College of Agriculture, Consumer and Environmental Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Lauren Forsythe
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Amy K. Stevenson
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Rebecca J. Franklin-Guild
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Narayan C. Paul
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, United States
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States
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12
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BABINES-OROZCO L, BALBUENA-ALONSO MG, BARRIOS-VILLA E, LOZANO-ZARAIN P, MARTÍNEZ-LAGUNA Y, DEL CARMEN ROCHA-GRACIA R, CORTÉS-CORTÉS G. Antimicrobial resistance in food-associated Escherichia coli in Mexico and Latin America. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:4-12. [PMID: 38188662 PMCID: PMC10767319 DOI: 10.12938/bmfh.2023-022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/11/2023] [Indexed: 01/09/2024]
Abstract
The World Health Organization (WHO) considers antimicrobial resistance to be one of the critical global public health priorities to address. Escherichia coli is a commensal bacterium of the gut microbiota in humans and animals; however, some strains cause infections and are resistant to antibiotics. One of the most common ways of acquiring pathogenic E. coli strains is through food. This review analyzes multidrug-resistant E. coli isolated from food, emphasizing Latin America and Mexico, and the mobile genetic elements (MGEs) responsible for spreading antibiotic resistance determinants among bacteria in different environments and hosts. We conducted a systematic search of the literature published from 2015 to 2022 in open access databases and electronic repositories. The prevalence of 11 E. coli pathotypes was described, with diarrheagenic E. coli pathotypes being the most frequently associated with foodborne illness in different Latin American countries, highlighting the presence of different antibiotic resistance genes mostly carried by IncF-type plasmids or class 1 integrons. Although the global incidence of foodborne illness is high, there have been few studies in Mexico and Latin America, which highlights the need to generate updated epidemiological data from the "One Health" approach, which allows monitoring of the multidrug-resistance phenomenon in E. coli from a common perspective in the interaction of human, veterinary, and environmental health.
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Affiliation(s)
- Lorena BABINES-OROZCO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - María Guadalupe BALBUENA-ALONSO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Edwin BARRIOS-VILLA
- Departamento de Ciencias Químico Biológicas y Agropecuarias,
Unidad Regional Norte, Campus Caborca, Universidad de Sonora, Col. Eleazar Ortiz C.P.
83621 H. Caborca, Sonora, México
| | - Patricia LOZANO-ZARAIN
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Ygnacio MARTÍNEZ-LAGUNA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Rosa DEL CARMEN ROCHA-GRACIA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Gerardo CORTÉS-CORTÉS
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
- Department of Microbiology and Environmental Toxicology,
University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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13
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Bhowmik P, Bharatham N, Murakami S, Ramachandran V, Datta S. Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis. Res Microbiol 2023; 174:104039. [PMID: 36738814 DOI: 10.1016/j.resmic.2023.104039] [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: 11/17/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both, hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.
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Affiliation(s)
- Purnendu Bhowmik
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Nagakumar Bharatham
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, 259 Nagatsuta-cho, 1, Midori Ward, Yokohama, Kanagawa 226-8501, Japan.
| | - Vasanthi Ramachandran
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Bengaluru, Karnataka 560064.
| | - Santanu Datta
- Bugworks Research India Pvt. Ltd, Centre for Cellular and Molecular Platforms, GKVK, Bellary Road, Bengaluru 560065, Karnataka, India.
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14
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Messele YE, Hasoon MF, Trott DJ, Veltman T, McMeniman JP, Kidd SP, Low WY, Petrovski KR. Longitudinal Analysis of Antimicrobial Resistance among Enterococcus Species Isolated from Australian Beef Cattle Faeces at Feedlot Entry and Exit. Animals (Basel) 2022; 12:2690. [PMID: 36230431 PMCID: PMC9559632 DOI: 10.3390/ani12192690] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Enterococcus faecium are commensal bacteria inhabiting the gastrointestinal tract of animals and humans and an important cause of drug-resistant nosocomial infections. This longitudinal study aimed to determine whether changes in the antimicrobial resistance (AMR) phenotype and genotype occurred among Enterococcus spp. isolated from cattle rectal samples obtained at the entry to and exit from an Australian feedlot. The samples obtained at the feedlot induction yielded enterococci (104/150; 69.3%), speciated as E. hirae (90/104; 86.5%), E. faecium (9/104; 8.7%), E. mundtii (3/104; 2.9%), E. durans, and E. casseliflavus (1/104; 1.0% each). AMR was observed to lincomycin (63/104; 60.6%), daptomycin (26/104; 25.0%), nitrofurantoin (9/104; 8.7%), ciprofloxacin (7/104; 6.7%), tetracycline (5/104; 4.8%), tigecycline (4/104; 3.9%), and quinupristin/dalfopristin (3/104; 2.9%). From the rectal swab samples collected at the abattoir from the same animals (i.e., the feedlot exit), the enterococci recovery was significantly higher (144/150; 96.0%), with a marked shift in species distribution dominated by E. faecium (117/144; 81.3%). However, the prevalence of AMR to individual antimicrobials remained largely static between the entry and exit except for the increased resistance to nitrofurantoin (77/144; 53.5%) and quinupristin/dalfopristin (26/144; 18.1%). Overall, 13 AMR genes were observed among the 62 E. faecium isolates. These included aac(6')Ii, aac(6')-Iid, and ant(6)-Ia (aminoglycosides); eatAv, lnu(G), vat(E), msr(C), and erm(B) (macrolides, lincosamides, and streptogramins); efmA (fluoroquinolones); and tet(45), tet(L), tet(M), and tet(S) (tetracyclines). The results confirm the presence of fluoroquinolone- and streptogramin-resistant enterococci in cattle faeces at the feedlot entry in the absence of antimicrobial selection pressure. E. faecium, exhibiting increased nitrofurantoin resistance, became the dominant Enterococcus spp. during the feeding period.
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Affiliation(s)
- Yohannes E. Messele
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mauida F. Hasoon
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Darren J. Trott
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tania Veltman
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joe P. McMeniman
- Meat & Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
| | - Stephen P. Kidd
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
- Research Centre for Infectious Disease, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Wai Y. Low
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kiro R. Petrovski
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- The Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA 5005, Australia
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15
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- *Correspondence: Shiranee Sriskandan,
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16
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Khamari B, Adak S, Chanakya PP, Lama M, Peketi ASK, Gurung SA, Chettri S, Kumar P, Bulagonda EP. Prediction of nitrofurantoin resistance among Enterobacteriaceae and mutational landscape of in vitro selected resistant E. coli. Res Microbiol 2021; 173:103889. [PMID: 34718096 DOI: 10.1016/j.resmic.2021.103889] [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: 06/03/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022]
Abstract
Nitrofurantoin (NIT) has long been a drug of choice in the treatment of lower urinary tract infections. Recent emergence of NIT resistant Enterobacteriaceae is a global concern. An ordinal logistic regression model based on PCR amplification patterns of five genes associated with NIT resistance (nfsA, nfsB, ribE, oqxA, and oqxB) among 100 clinical Enterobacteriaceae suggested that a combination of oqxB, nfsB, ribE, and oqxA is ideal for NIT resistance prediction. In addition, four Escherichia coli NIT-resistant mutants were in vitro generated by exposing an NIT-susceptible E. coli to varying concentrations of NIT. The in vitro selected NIT resistant mutants (NI2, NI3, NI4 and NI5) were found to have mutations resulting in frameshifts, premature/lost stop codons or failed amplification of nfsA and/or nfsB genes. The in vitro selected NI5 and the transductant colonies with reconstructed NI5 genotype exhibited reduced fitness compared to their parent strain NS30, while growth of a resistant clinical isolate (NR42) was found to be unaffected in the absence of NIT. These results emphasize the importance of strict adherence to prescribed antibiotic treatment regimens and dosage duration. If left unchecked, these resistant bacteria may thrive at sub-therapeutic concentrations of NIT and spread in the community.
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Affiliation(s)
- Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Sudeshna Adak
- OmiX Research and Diagnostic Laboratories Private Limited, Bengaluru, India
| | - Pachi Pulusu Chanakya
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Manmath Lama
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Arun Sai Kumar Peketi
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Saurav Anand Gurung
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Sushil Chettri
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Prakash Kumar
- Department of Microbiology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, India
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17
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Xiong L, Su L, Tan H, Zhao W, Li S, Zhu Y, Lu L, Huang Z, Li B. Molecular Epidemiological Analysis of ST11-K64 Extensively Drug-Resistant Klebsiella pneumoniae Infections Outbreak in Intensive Care and Neurosurgery Units Based on Whole-Genome Sequencing. Front Microbiol 2021; 12:709356. [PMID: 34646245 PMCID: PMC8504482 DOI: 10.3389/fmicb.2021.709356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Klebsiella pneumoniae (Kp) is the primary causative bacteria for nosocomial infections and hospital outbreaks. In particular, extensively drug-resistant K. pneumoniae (XDRKp) causes severe clinical infections in hospitalized patients. Here, we used pulsed-field gel electrophoresis (PFGE), drug susceptibility tests, and the whole-genome sequencing (WGS) technology to examine genetic relatedness and phenotypic traits of the strains isolated during an outbreak period. Based on PFGE, a distinct clones cluster comprised of eight XDRKp was observed. These strains were confirmed as ST11-K64 via multiple-locus sequence typing database of Kp. The strains also had genes related to the regulation of biofilm biosynthesis (type 1 & 3 fimbriae, type IV pili biosynthesis, RcsAB, and type VI secretion system) and multiple drug resistance (β-lactamase and aminoglycoside antibiotic resistance). WGS data based on core-single nucleotide polymorphisms and epidemiological investigation showed that the neurosurgery unit was likely the source of the outbreak, the strain was likely to have been transmitted to the ICU through patients. In addition, the two highly probable transmission routes were in the ICU (exposure through shared hospital beds) and the neurosurgery units (all cases were treated by the same rehabilitation physician and were most likely infected during the physical therapy). Notably, the bed mattress had played a crucial transmission role of this outbreak, served as a pathogen reservoir.
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Affiliation(s)
- Liuxin Xiong
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, China
| | - Lebin Su
- Microbiological Laboratory, Zhaoqing Center for Disease Control and Prevention, Zhaoqing, China
| | - Hanqing Tan
- Microbiological Laboratory, Zhaoqing Center for Disease Control and Prevention, Zhaoqing, China
| | - Wansha Zhao
- Microbiological Laboratory, Zhaoqing Center for Disease Control and Prevention, Zhaoqing, China
| | - Shuying Li
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, China
| | - Yingmei Zhu
- Microbiological Laboratory, Zhaoqing Center for Disease Control and Prevention, Zhaoqing, China
| | - Limiao Lu
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, China
| | - Zhiwei Huang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, China
| | - Baisheng Li
- Institute of Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
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18
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Gautam G, Gogoi S, Saxena S, Kaur R, Dhakad MS. Nitrofurantoin Susceptibility Pattern in Gram-Negative Urinary Isolates: In Need of Increased Vigilance. J Lab Physicians 2021; 13:252-256. [PMID: 34602790 PMCID: PMC8478500 DOI: 10.1055/s-0041-1731106] [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] [Indexed: 11/04/2022] Open
Abstract
Nitrofurantoin is the first-line drug in the treatment of uncomplicated urinary tract infections (UTIs) and its use has increased exponentially in recent years. Objectives
This study aims to determine the susceptibility pattern of nitrofurantoin in gram-negative urinary isolates and to evaluate their bacteriological and epidemiological profile along with co-existing resistance to other important urinary antimicrobials.
Material and Methods
This was a retrospective study conducted in a tertiary care hospital in New Delhi in which 500 gram-negative bacterial urinary isolates were evaluated. Records of antimicrobial susceptibility were reviewed from July to September 2019. Antimicrobial susceptibility was performed using the Kirby–Bauer disk diffusion method on Mueller Hinton agar and interpreted using CLSI 2019. Test for extended spectrum β-lactamase (ESBL) producers was done using double disk approximation test.
Statistical Analysis
Data analysis was performed using the SPSS windows version 25.0 software.
Results
Out of total 500 isolates, 20.17% (94) isolates were resistant (R) to nitrofurantoin and 9.01% (42) were found to be intermediate (I). Highest resistance was seen in
Klebsiella
sp. (44.61%) and
Escherichia coli
(8.12%). About 28.82% of the I/R isolates were of the pediatrics age group and most of the isolates belonged to females (64.69%). High resistance was also seen against ampicillin (92.30%), cefazolin (88.46%), ceftazidime (73.0%), and fluoroquinolones (65.38%). Carbapenemase co-resistance was seen in 57.15% isolates whereas ESBL production was seen in 30.76% of
E. coli
and 12.06% of
Klebsiella
sp.
Conclusion
Increase in multidrug resistance uropathogens along with a near absence of novel oral antibiotics has led to increased consumption of nitrofurantoin since its resistance has increased.
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Affiliation(s)
- Garima Gautam
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Sanjib Gogoi
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Ravinder Kaur
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Megh Singh Dhakad
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
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19
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Bharatham N, Bhowmik P, Aoki M, Okada U, Sharma S, Yamashita E, Shanbhag AP, Rajagopal S, Thomas T, Sarma M, Narjari R, Nagaraj S, Ramachandran V, Katagihallimath N, Datta S, Murakami S. Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. Nat Commun 2021; 12:5400. [PMID: 34518546 PMCID: PMC8437966 DOI: 10.1038/s41467-021-25679-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.
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Affiliation(s)
- Nagakumar Bharatham
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Purnendu Bhowmik
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Maho Aoki
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ui Okada
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Sreevalli Sharma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Eiki Yamashita
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Anirudh P. Shanbhag
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Sreenath Rajagopal
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Teby Thomas
- grid.418280.70000 0004 1794 3160St. John’s Research Institute, Bengaluru, Karnataka India
| | - Maitrayee Sarma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Riya Narjari
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | | | - Vasanthi Ramachandran
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Nainesh Katagihallimath
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Santanu Datta
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Satoshi Murakami
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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20
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Fosfomycin and nitrofurantoin: classic antibiotics and perspectives. J Antibiot (Tokyo) 2021; 74:547-558. [PMID: 34244614 DOI: 10.1038/s41429-021-00444-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
Antibiotics are essential molecules for the treatment and prophylaxis of many infectious diseases. However, drugs that combat microbial infections can become a human health threat due to their high and often indiscriminate consumption, considered one of the factors of antimicrobial resistance (AMR) emergence. The AMR crisis, the decrease in new drug development by the pharmaceutical industry, and reduced economic incentives for research have all reduced the options for treating infections, and new strategies are necessary, including the return of some traditional but "forgotten" antibiotics. However, prescriptions for these older drugs including nitrofurantoin and oral fosfomycin, have been based on the results of pioneer studies, and the limited knowledge generated 50-70 years ago may not be enough. To avoid harming patients and further increasing multidrug resistance, systematic evaluation is required, mainly for the drugs prescribed for community-acquired infections, such as urinary tract infections (UTI). Therefore, this review has the objective of reporting the use of two classic drugs from the nitrofuran and phosphonic acid classes for UTI control nowadays. Furthermore, we also explore new approaches used for these antibiotics, including new combination regimes for spectral amplification, and the prospects for reducing bacterial resistance in the fight against bacteria responsible for UTI.
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21
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The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN. Biochem J 2021; 478:2601-2617. [PMID: 34142705 PMCID: PMC8286842 DOI: 10.1042/bcj20210160] [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] [Received: 03/11/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 01/23/2023]
Abstract
NfsA is a dimeric flavoprotein that catalyses the reduction in nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free Escherichia coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan ring, rather than the nitro group that is reduced, near the N5 of the FMN. Molecular dynamics simulations show that this orientation is only favourable in the oxidised enzyme, while potentiometry suggests that little semiquinone is formed in the free protein. This suggests that the reduction occurs by direct hydride transfer from FMNH− to nitrofurantoin bound in the reverse orientation to that in the crystal structure. We present a model of nitrofurantoin bound to reduced NfsA in a viable hydride transfer orientation. The substrate 1,4-benzoquinone and the product hydroquinone are positioned close to the FMN N5 in the respective crystal structures with NfsA, suitable for reaction, but are mobile within the active site. The structure with a second FMN, bound as a ligand, shows that a mobile loop in the free protein forms a phosphate-binding pocket. NfsA is specific for NADPH and a similar conformational change, forming a phosphate-binding pocket, is likely to also occur with the natural cofactor.
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22
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Khamari B, Kumar P, Pradeep BE. Resistance to nitrofurantoin is an indicator of extensive drug-resistant (XDR) Enterobacteriaceae. J Med Microbiol 2021; 70. [PMID: 33830906 DOI: 10.1099/jmm.0.001347] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Nitrofurantoin is one of the preferred antibiotics in the treatment of uropathogenic multidrug-resistant (MDR) infections. However, resistance to nitrofurantoin in extensively drug-resistant (XDR) bacteria has severely limited the treatment options.Gap statement. Information related to co-resistance or collateral sensitivity (CS) with reference to nitrofurantoin resistant bacteria is limited.Aim. To study the potential of nitrofurantoin resistance as an indicator of the XDR phenotype in Enterobacteriaceae.Methods. One hundred (45 nitrofurantoin-resistant, 21 intermediately resistant and 34 nitrofurantoin-susceptible) Enterobacteriaceae were analysed in this study. Antibiotic susceptibility testing (AST) against nitrofurantoin and 17 other antimicrobial agents across eight different classes was performed by using the Vitek 2.0 system. The isolates were screened for the prevalence of acquired antimicrobial resistance (AMR) and efflux pump genes by PCR.Results. In total, 51 % of nitrofurantoin-resistant and 28 % of intermediately nitrofurantoin resistant isolates exhibited XDR characteristics, while only 3 % of nitrofurantoin-sensitive isolates were XDR (P=0.0001). Significant co-resistance was observed between nitrofurantoin and other tested antibiotics (β-lactam, cephalosporin, carbapenem, aminoglycoside and tetracycline). Further, the prevalence of AMR and efflux pump genes was higher in the nitrofurantoin-resistant strains compared to the susceptible isolates. A strong association was observed between nitrofurantoin resistance and the presence of bla PER-1, bla NDM-1, bla OXA-48, ant(2) and oqxA-oqxB genes. Tigecycline (84 %) and colistin (95 %) were the only antibiotics to which the majority of the isolates were susceptible.Conclusion. Nitrofurantoin resistance could be an indicator of the XDR phenotype among Enterobacteriaceae, harbouring multiple AMR and efflux pump genes. Tigecycline and colistin are the only antibiotics that could be used in the treatment of such XDR infections. A deeper understanding of the co-resistance mechanisms in XDR pathogens and prescription of AST-based appropriate combination therapy may help mitigate this problem.
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Affiliation(s)
- Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, India
| | - Prakash Kumar
- Department of Microbiology, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, India
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23
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Abbott IJ, Roberts JA, Meletiadis J, Peleg AY. Antimicrobial pharmacokinetics and preclinical in vitro models to support optimized treatment approaches for uncomplicated lower urinary tract infections. Expert Rev Anti Infect Ther 2020; 19:271-295. [PMID: 32820686 DOI: 10.1080/14787210.2020.1813567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Urinary tract infections (UTIs) are extremely common. Millions of people, particularly healthy women, are affected worldwide every year. One-in-two women will have a recurrence within 12-months of an initial UTI. Inadequate treatment risks worsening infection leading to acute pyelonephritis, bacteremia and sepsis. In an era of increasing antimicrobial resistance, it is critical to provide optimized antimicrobial treatment. AREAS COVERED Literature was searched using PubMed and Google Scholar (up to 06/2020), examining the etiology, diagnosis and oral antimicrobial therapy for uncomplicated UTIs, with emphasis on urinary antimicrobial pharmacokinetics (PK) and the application of dynamic in vitro models for the pharmacodynamic (PD) profiling of pathogen response. EXPERT OPINION The majority of antimicrobial agents included in international guidelines were developed decades ago without well-described dose-response relationships. Microbiology laboratories still apply standard diagnostic methodology that has essentially remained unchanged for decades. Furthermore, it is uncertain how relevant standard in vitro susceptibility is for predicting antimicrobial efficacy in urine. In order to optimize UTI treatments, clinicians must exploit the urine-specific PK of antimicrobial agents. Dynamic in vitro models are valuable tools to examine the PK/PD and urodynamic variables associated with UTIs, while informing uropathogen susceptibility reporting, optimized dosing schedules, clinical trials and treatment guidelines.
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Affiliation(s)
- Iain J Abbott
- Department of Infectious Diseases, the Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Jason A Roberts
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.,School of Pharmacy, Centre for Translational Anti-infective Pharmacodynamics, The University of Queensland, Brisbane, Australia.,Department of Intensive Care Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Haidari, Greece
| | - Anton Y Peleg
- Department of Infectious Diseases, the Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia.,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
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24
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Sorlozano-Puerto A, Lopez-Machado I, Albertuz-Crespo M, Martinez-Gonzalez LJ, Gutierrez-Fernandez J. Characterization of Fosfomycin and Nitrofurantoin Resistance Mechanisms in Escherichia coli Isolated in Clinical Urine Samples. Antibiotics (Basel) 2020; 9:antibiotics9090534. [PMID: 32847131 PMCID: PMC7558542 DOI: 10.3390/antibiotics9090534] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 01/29/2023] Open
Abstract
Fosfomycin and nitrofurantoin are antibiotics of choice to orally treat non-complicated urinary tract infections (UTIs) of community origin because they remain active against bacteria resistant to other antibiotics. However, epidemiologic surveillance studies have detected a reduced susceptibility to these drugs. The objective of this study was to determine possible mechanisms of resistance to these antibiotics in clinical isolates of fosfomycin- and/or nitrofurantoin-resistant UTI-producing Escherichia coli. We amplified and sequenced murA, glpT, uhpT, uhpA, ptsI, cyaA, nfsA, nfsB, and ribE genes, and screened plasmid-borne fosfomycin-resistance genes fosA3, fosA4, fosA5, fosA6, and fosC2 and nitrofurantoin-resistance genes oqxA and oqxB by polymerase chain reaction. Among 29 isolates studied, 22 were resistant to fosfomycin due to deletion of uhpT and/or uhpA genes, and 2 also possessed the fosA3 gene. Some modifications detected in sequences of NfsA (His11Tyr, Ser33Arg, Gln67Leu, Cys80Arg, Gly126Arg, Gly154Glu, Arg203Cys), NfsB (Gln44His, Phe84Ser, Arg107Cys, Gly192Ser, Arg207His), and RibE (Pro55His), and the production of truncated NfsA (Gln67 and Gln147) and NfsB (Glu54), were associated with nitrofurantoin resistance in 15/29 isolates; however, the presence of oqxAB plasmid genes was not detected in any isolate. Resistance to fosfomycin was associated with the absence of transporter UhpT expression and/or the presence of antibiotic-modifying enzymes encoded by fosA3 plasmid-mediated gene. Resistance to nitrofurantoin was associated with modifications of NfsA, NfsB, and RibE proteins. The emergence and spread of these resistance mechanisms, including transferable resistance, could compromise the future usefulness of fosfomycin and nitrofurantoin against UTIs. Furthermore, knowledge of the genetic mechanisms underlying resistance may lead to rapid DNA-based testing for resistance.
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Affiliation(s)
- Antonio Sorlozano-Puerto
- Department of Microbiology, School of Medicine and PhD Program in Clinical Medicine and Public Health, University of Granada-ibs, 18016 Granada, Spain; (A.S.-P.); (I.L.-M.); (M.A.-C.)
| | - Isaac Lopez-Machado
- Department of Microbiology, School of Medicine and PhD Program in Clinical Medicine and Public Health, University of Granada-ibs, 18016 Granada, Spain; (A.S.-P.); (I.L.-M.); (M.A.-C.)
| | - Maria Albertuz-Crespo
- Department of Microbiology, School of Medicine and PhD Program in Clinical Medicine and Public Health, University of Granada-ibs, 18016 Granada, Spain; (A.S.-P.); (I.L.-M.); (M.A.-C.)
| | - Luis Javier Martinez-Gonzalez
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), 18016 Granada, Spain;
| | - Jose Gutierrez-Fernandez
- Department of Microbiology, School of Medicine and PhD Program in Clinical Medicine and Public Health, University of Granada-ibs, 18016 Granada, Spain; (A.S.-P.); (I.L.-M.); (M.A.-C.)
- Laboratory of Microbiology, Virgen de las Nieves University Hospital-ibs, 18014 Granada, Spain
- Correspondence:
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25
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Zhu Y, Zhang W, Schwarz S, Wang C, Liu W, Chen F, Luan T, Liu S. Characterization of a blaIMP-4-carrying plasmid from Enterobacter cloacae of swine origin. J Antimicrob Chemother 2020; 74:1799-1806. [PMID: 30879063 DOI: 10.1093/jac/dkz107] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To characterize an MDR blaIMP-4-harbouring plasmid from Enterobacter cloacae EC62 of swine origin in China. METHODS Plasmid pIMP-4-EC62 from E. cloacae EC62 was transferred by conjugation via filter mating into Escherichia coli J53. Plasmid DNA was extracted from an E. coli J53 transconjugant and sequenced using single-molecule real-time (SMRT) technology. MIC values for both the isolate EC62 and the transconjugant were determined using the broth microdilution and agar dilution methods. Plasmid stability in both the isolate EC62 and the transconjugant was assessed through a series of passages on antibiotic-free media. RESULTS Plasmid pIMP-4-EC62 is 314351 bp in length, encodes 369 predicted proteins and harbours a novel class 1 integron carrying blaIMP-4 and a group II intron. The blaIMP-4-bearing plasmid belongs to the IncHI2/ST1 incompatibility group. Sequence analysis showed that pIMP-4-EC62 carries four MDR regions and several gene clusters encoding heavy metal resistance. Plasmid pIMP-4-EC62 was stably maintained in both the E. cloacae EC62 isolate and the transconjugant E. coli J53-pIMP-4-EC62 in the absence of selective pressure. Analysis of the evolutionary relatedness of selected IncHI2 plasmids indicates that ST1-type plasmids are key carriers of carbapenemase genes among IncHI2 plasmids. CONCLUSIONS pIMP-4-EC62 represents the first fully sequenced IncHI2-type blaIMP-4-harbouring plasmid from E. cloacae in China. Co-location of blaIMP-4 with other resistance genes on an MDR plasmid is likely to further accelerate the dissemination of blaIMP-4 by co-selection among bacteria from humans, animals and the environment under the selective pressure of other antimicrobial agents, heavy metals and disinfectants.
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Affiliation(s)
- Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Changzhen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenyu Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fuguang Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tian Luan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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26
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Salam LB. Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil. 3 Biotech 2020; 10:238. [PMID: 32405442 PMCID: PMC7205953 DOI: 10.1007/s13205-020-02219-z] [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: 02/27/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.
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Affiliation(s)
- Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Summit University, Offa, Kwara Nigeria
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Amladi AU, Abirami B, Devi SM, Sudarsanam TD, Kandasamy S, Kekre N, Veeraraghavan B, Sahni RD. Susceptibility profile, resistance mechanisms & efficacy ratios of fosfomycin, nitrofurantoin & colistin for carbapenem-resistant Enterobacteriaceae causing urinary tract infections. Indian J Med Res 2019; 149:185-191. [PMID: 31219082 PMCID: PMC6563748 DOI: 10.4103/ijmr.ijmr_2086_17] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background & objectives The escalation in carbapenem resistance among Enterobacteriaceae has resulted in a lack of effective therapeutic alternatives. Older antimicrobials, fosfomycin, nitrofurantoin and colistin for urinary tract infections (UTIs) caused by carbapenem-resistant Enterobacteriaceae (CRE) may be effective treatment options. The objectives of this study were to evaluate the utility of fosfomycin, nitrofurantoin and colistin in treating UTI caused by CRE and molecular characterization of the plasmid-mediated carbapenem resistance mechanisms. Methods Consecutive, non-duplicate isolates of CR Escherichia coli and Klebsiella spp. from urine cultures were included (n=150). Minimum inhibitory concentrations (MIC) were determined by E-test (fosfomycin and nitrofurantoin) and broth microdilution (colistin). Efficacy ratios were derived by dividing susceptibility breakpoints by observed MIC values of the drugs for the isolates. Isolates were screened for genes coding for carbapenemases using multiplex PCR. Fosfomycin, nitrofurantoin and colistin-resistant isolates were screened for plasmid-borne resistance genes fos A3, oqx AB and mcr-1, respectively using PCR. Results Among E. coli, 98.9, 56 and 95 per cent isolates were susceptible to fosfomycin, nitrofurantoin and colistin, respectively, while 94 and 85 per cent of Klebsiella spp. were susceptible to fosfomycin and colistin, respectively. The efficacy ratios indicated fosfomycin as the drug of choice for UTI caused by CR E. coli and Klebsiella spp., followed by colistin. The blaNDM gene was most common, followed by blaOXA48-like. Plasmid-borne genes encoding resistance to fosfomycin, nitrofurantoin and colistin were absent. Interpretation & conclusions With increasing resistance against the current treatment options, older drugs may emerge as effective options. Molecular screening of resistant isolates is essential to prevent the spread of plasmid-borne resistance against these drugs.
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Affiliation(s)
| | - Baby Abirami
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - S Manjula Devi
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | | | - Nitin Kekre
- Department of Urology, Christian Medical College, Vellore, India
| | | | - Rani Diana Sahni
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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Das A, Banerjee T, Anupurba S. Susceptibility of Nitrofurantoin and Fosfomycin Against Outpatient Urinary Isolates of Multidrug-Resistant Enterococci over a Period of 10 Years from India. Microb Drug Resist 2019; 26:1509-1515. [PMID: 31794690 DOI: 10.1089/mdr.2019.0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With the increasing emergence of drug resistance in enterococci, there have been very limited data on the efficacy of orally available nitrofurantoin and fosfomycin on enterococci causing urinary tract infections (UTIs), particularly for multidrug-resistant (MDR) strains. This study aimed to determine the in vitro effectiveness of these two drugs against the MDR enterococci. A total of 514 phenotypically and genotypically confirmed isolates of enterococci (239, 46.5% Enterococcus faecalis and 275, 53.5% Enterococcus faecium) showed E. faecalis as significantly more resistant (p < 0.05) to ciprofloxacin and high strength gentamicin. Vancomycin resistance was seen in 37 (7.2%) isolates. Of these, 114 (22.18%) isolates (51, 44.73% E. faecalis and 63, 55.26% E. faecium) were MDR. Nitrofurantoin minimum inhibitory concentrations (MICs) for the MDR enterococci varied from 1 to 128 μg/mL (MIC50 8 μg/mL, MIC90 64 μg/mL for E. faecalis), while fosfomycin MICs for the MDR E. faecalis, including vancomycin resistant enterococci (VRE) were in susceptible range (≤64 μg/mL, MIC50 8 μg/mL, MIC90 16 μg/mL). An efficacy ratio of ≥8 for nitrofurantoin was observed in the 39 (76.5%) MDR E. faecalis and 44 (69.8%) MDR E. faecium isolates as against the 50 (98%) E. faecalis isolates for fosfomycin. Although nitrofurantoin has been widely prescribed for the treatment of UTIs for the past several years, it was still found to be active in vitro against the urinary isolates of MDR enterococci, including VRE. As for fosfomycin, it holds robust potential to be used against the urinary MDR enterococci and VRE (E. faecalis).
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Affiliation(s)
- Arghya Das
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Tuhina Banerjee
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Mottaghizadeh F, Mohajjel Shoja H, Haeili M, Darban-Sarokhalil D. Molecular epidemiology and nitrofurantoin resistance determinants of nitrofurantoin-non-susceptible Escherichia coli isolated from urinary tract infections. J Glob Antimicrob Resist 2019; 21:335-339. [PMID: 31627025 DOI: 10.1016/j.jgar.2019.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES The worldwide emergence of multidrug-resistant uropathogens has resulted in the revival of old antibiotics such as nitrofurantoin (NIT) for the treatment of uncomplicated urinary tract infections (UTIs). This study aimed to identify determinants of NIT resistance and to investigate the genetic diversity of NIT-resistant (NIT-R) Escherichia coli isolates. METHODS Six NIT-R and three NIT-susceptible clinical E. coli isolates from patients with UTI were studied. The susceptibility of the isolates to various classes of antibiotics was evaluated by disk diffusion. The presence of plasmid-encoded efflux pump genes (oqxA and oqxB) was investigated by PCR. Nucleotide sequences of the nfsA, nfsB and ribE genes were determined. The genetic relatedness of the NIT-R isolates was evaluated by multilocus sequence typing (MLST). RESULTS All six NIT-R isolates were characterised with high-level NIT resistance (MIC ≥ 512 mg/L) and they belonged to five distinct STs including ST131 (n = 2), ST73, ST405, ST10 and ST354 (n = 1 each). Amikacin, carbapenems, minocycline, tigecycline and fosfomycin were the most active agents against the studied uropathogens. The oqxA and oqxB genes were not detected in any isolate. All NIT-R isolates harboured inactivating genetic alterations in nfsA and nfsB [NfsA H11Y, S33N, S38Y, W212R substitutions, Δg638 (frameshift), Δa64-g73 (frameshift) and NfsB F84S, P45S, W94Stop, E197Stop substitutions, ΔnfsB locus]. The ribE gene of most isolates was unaffected, except for one isolate co-harbouring a deleterious RibE G85C substitution and NfsA/B alterations. CONCLUSION NIT resistance in the studied E. coli isolates was mainly mediated by nfsA and nfsB alterations.
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Affiliation(s)
- Fatemeh Mottaghizadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Hanieh Mohajjel Shoja
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Mehri Haeili
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Kobylka J, Kuth MS, Müller RT, Geertsma ER, Pos KM. AcrB: a mean, keen, drug efflux machine. Ann N Y Acad Sci 2019; 1459:38-68. [PMID: 31588569 DOI: 10.1111/nyas.14239] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.
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Affiliation(s)
- Jessica Kobylka
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Miriam S Kuth
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
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Use of other antimicrobial drugs is associated with trimethoprim resistance in patients with urinary tract infections caused by E. coli. Eur J Clin Microbiol Infect Dis 2019; 38:2283-2290. [PMID: 31494829 PMCID: PMC6858404 DOI: 10.1007/s10096-019-03672-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/06/2019] [Indexed: 01/08/2023]
Abstract
In recent years, high frequencies of trimethoprim resistance in urinary tract infections (UTIs) caused by E. coli are have been reported. Co-resistance to other antimicrobial drugs may play a role in this increase. Therefore, we investigated whether previous use of other antimicrobial drugs was associated with trimethoprim resistance. We conducted a nested case-control study with urinary cultures with E. coli from participants of the Rotterdam Study sent in by general practitioners to the regional laboratory between 1 January 2000 and 1 April 2016. Multivariable logistic regression analysis was performed to study the association between prior prescriptions of several antimicrobial drug groups and trimethoprim resistance using individual participant data. Urinary cultures of 1264 individuals with a UTI caused by E. coli were included. When adjusted for previous other antimicrobial drug use, a history of > 3 prescriptions of extended-spectrum penicillins (OR 1.68; 95% CI 1.10-2.55) was significantly associated with trimethoprim resistance of E. coli as was the use of > 3 prescriptions of sulfonamides and trimethoprim (OR 2.22; 95% CI 1.51-3.26). The use of > 3 prescriptions of nitrofuran derivatives was associated with a lower frequency of trimethoprim resistance (OR 0.60; 95% CI 0.39-0.92), after adjustment for other antimicrobial drug prescriptions. We found that previous use of extended-spectrum penicillins is associated with trimethoprim resistance. On the contrary, previous nitrofurantoin use was associated with a lower frequency of trimethoprim resistance. Especially in individuals with recurrent UTI, co-resistance should be taken into account and susceptibility testing before starting trimethoprim should be considered.
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Evaluating the level of nitroreductase activity in clinical Klebsiella pneumoniae isolates to support strategies for nitro drug and prodrug development. Int J Antimicrob Agents 2019; 54:538-546. [PMID: 31398484 DOI: 10.1016/j.ijantimicag.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 11/22/2022]
Abstract
To understand the potential utility of novel nitroreductase (NR)-activated prodrugs, NR enzyme activity was assessed in clinical Klebsiella pneumoniae isolates using a NR-activated fluorescent probe. NR activity was constant throughout the bacterial growth cycle, but individual K. pneumoniae isolates exhibited a wide range of NR activity levels. The genes of major NR enzymes (nfsA and nfnB) showed a number of sequence variants. Aside from a C-terminal extension of NfnB, which may be responsible for lower NR activity in specific isolates, the genetic differences did not explain the variation in activity. Analysis of important clinical strains (ST11, ST258, ST14 and ST101) showed significant variation in NR activity between isolates within the same sequence type despite conservation of nfsA/nfnB sequences. Addition of methyl viologen (MV), a known activator of soxRS, caused a significant increase in NR activity for all strains, with proportionally larger increases in activity seen for strains with low uninduced NR levels. Real-time PCR on selected strains following exposure to MV showed upregulation of soxS (15-32-fold) and nfsA (5-22-fold) in all strains tested. Expression of nfnB was upregulated 2-5-fold in 4/6 strains tested. High levels of NR activity in the absence of MV activation correlated with nitrofurantoin susceptibility. These data provide evidence that NR gene mutations and regulatory pathways influence NR activity in K. pneumoniae isolates and this is likely to impact treatment efficacy with novel nitro-containing drugs or prodrugs.
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Xu Q, Jiang J, Zhu Z, Xu T, Sheng ZK, Ye M, Xu X, Wang M. Efflux pumps AcrAB and OqxAB contribute to nitrofurantoin resistance in an uropathogenic Klebsiella pneumoniae isolate. Int J Antimicrob Agents 2019; 54:223-227. [PMID: 31200021 DOI: 10.1016/j.ijantimicag.2019.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/01/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
Abstract
Klebsiella pneumoniae is a common cause of urinary tract infections (UTIs). Nitrofurantoin (NIT), with high therapeutic concentrations in urine, is recommended as the first-line drug for both empiric treatment and chemoprophylaxis of UTIs. Although NIT resistance in K. pneumoniae is relatively high, the resistance mechanism is not well understood. This study collected a NIT-resistant K. pneumoniae [NRKP, minimum inhibitory concentration (MIC)=128 mg/L] and investigated the resistance mechanism. Addition of efflux pump inhibitors increased the susceptibility of NRKP to NIT (MIC decreased from 128 to 32 mg/L), implying the important role of efflux pumps in NIT resistance. Quantitative reverse transcriptase polymerase chain reaction analysis showed that NRKP had >100-fold increased expression of ramA, which was demonstrated to be caused by ramR mutation. Deletion of ramA led to a four-fold decrease in the MIC of NIT, and the expression levels of efflux pumps acrB and oqxB were downregulated by four- to seven-fold. Complementation of ramA restored both the MIC value and the expression level of acrB and oqxB in the ramA mutant strain. In order to confirm the role of acrB and oqxB in NIT resistance, gene knockout strains were constructed. Deletion of acrB or oqxB alone led to a four-fold decrease in the MIC of NIT, and deletion of acrB and oqxB simultaneously led to a 16-fold decrease in the MIC of NIT. These results demonstrate that AcrAB and OqxAB contribute to NIT resistance in K. pneumoniae.
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Affiliation(s)
- Qingqing Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianping Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhenhan Zhu
- Clinical Pharmacy, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Jiangsu, China
| | - Teng Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Zi-Ke Sheng
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiping Ye
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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35
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Hawkey PM, Warren RE, Livermore DM, McNulty CAM, Enoch DA, Otter JA, Wilson APR. Treatment of infections caused by multidrug-resistant Gram-negative bacteria: report of the British Society for Antimicrobial Chemotherapy/Healthcare Infection Society/British Infection Association Joint Working Party. J Antimicrob Chemother 2019. [PMID: 29514274 DOI: 10.1093/jac/dky027] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Working Party makes more than 100 tabulated recommendations in antimicrobial prescribing for the treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria (GNB) and suggest further research, and algorithms for hospital and community antimicrobial usage in urinary infection. The international definition of MDR is complex, unsatisfactory and hinders the setting and monitoring of improvement programmes. We give a new definition of multiresistance. The background information on the mechanisms, global spread and UK prevalence of antibiotic prescribing and resistance has been systematically reviewed. The treatment options available in hospitals using intravenous antibiotics and in primary care using oral agents have been reviewed, ending with a consideration of antibiotic stewardship and recommendations. The guidance has been derived from current peer-reviewed publications and expert opinion with open consultation. Methods for systematic review were NICE compliant and in accordance with the SIGN 50 Handbook; critical appraisal was applied using AGREE II. Published guidelines were used as part of the evidence base and to support expert consensus. The guidance includes recommendations for stakeholders (including prescribers) and antibiotic-specific recommendations. The clinical efficacy of different agents is critically reviewed. We found there are very few good-quality comparative randomized clinical trials to support treatment regimens, particularly for licensed older agents. Susceptibility testing of MDR GNB causing infection to guide treatment needs critical enhancements. Meropenem- or imipenem-resistant Enterobacteriaceae should have their carbapenem MICs tested urgently, and any carbapenemase class should be identified: mandatory reporting of these isolates from all anatomical sites and specimens would improve risk assessments. Broth microdilution methods should be adopted for colistin susceptibility testing. Antimicrobial stewardship programmes should be instituted in all care settings, based on resistance rates and audit of compliance with guidelines, but should be augmented by improved surveillance of outcome in Gram-negative bacteraemia, and feedback to prescribers. Local and national surveillance of antibiotic use, resistance and outcomes should be supported and antibiotic prescribing guidelines should be informed by these data. The diagnosis and treatment of both presumptive and confirmed cases of infection by GNB should be improved. This guidance, with infection control to arrest increases in MDR, should be used to improve the outcome of infections with such strains. Anticipated users include medical, scientific, nursing, antimicrobial pharmacy and paramedical staff where they can be adapted for local use.
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Affiliation(s)
- Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | | | - Cliodna A M McNulty
- Microbiology Department, Gloucestershire Royal Hospital, Great Western Road, Gloucester GL1 3NN, UK
| | - David A Enoch
- Public Health England, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - A Peter R Wilson
- Department of Microbiology and Virology, University College London Hospitals, London, UK
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Wijma RA, Fransen F, Muller AE, Mouton JW. Optimizing dosing of nitrofurantoin from a PK/PD point of view: What do we need to know? Drug Resist Updat 2019; 43:1-9. [PMID: 30947111 DOI: 10.1016/j.drup.2019.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/15/2019] [Accepted: 03/06/2019] [Indexed: 12/21/2022]
Abstract
Nitrofurantoin is an old antibiotic and an important first-line oral antibiotic for the treatment of uncomplicated urinary tract infections. However despite its long term use for over 60 years, little information is available with respect to its dose justification and this may be the reason of highly variable recommended doses and dosing schedules. Furthermore, nitrofurantoin is not a uniform product -crystal sizes of nitrofurantoin, and therefore pharmacokinetic properties, differ significantly by product. Moreover, pharmacokinetic profiling of some products is even lacking, or difficult to interpret because of its unstable chemical properties. Pharmacokinetic and pharmacodynamic data is now slowly becoming available. This review provides an overview of nitrofurantoins antibacterial, pharmacokinetic and pharmacodynamic properties. This shows that a clear rationale of current dosing regimens is scanty.
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Affiliation(s)
- Rixt A Wijma
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Fiona Fransen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anouk E Muller
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Medical Microbiology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Johan W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands.
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Li J, Zhang H, Ning J, Sajid A, Cheng G, Yuan Z, Hao H. The nature and epidemiology of OqxAB, a multidrug efflux pump. Antimicrob Resist Infect Control 2019; 8:44. [PMID: 30834112 PMCID: PMC6387526 DOI: 10.1186/s13756-019-0489-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 02/03/2019] [Indexed: 01/03/2023] Open
Abstract
Background OqxAB efflux pump has been found to mediate multidrug resistance (MDR) in various bacteria over the past decades. The updates on the nature and epidemiology of OqxAB efflux pump need to be fully reviewed to broaden our understanding of this MDR determinant. Methods A literature search using the keyword of "oqxAB" was conducted in the online databases of Pubmed and ISI Web of Science with no restriction on the date of publication. The 87 publications were included into this review as references due to their close relevance to the nature and/or epidemiology of OqxAB efflux pump. Results The oqxAB gene generally locates on chromosome and/or plasmids flanked by IS26-like elements in clinical isolates of Enterobacteriaceae and Klebsiella pneumoniae, conferring low to intermediated resistance to quinoxalines, quinolones tigecycline, nitrofurantoin, several detergents and disinfectants (benzalkonium chloride, triclosan and SDS). It could co-spread with other antimicrobial resistance genes (bla CTX-M, rmtB and aac(6')-Ib etc.), virulence genes and heavy metal resistance genes (pco and sil operons). Both RarA (activator) and OqxR (repressor) play important roles on regulation of the expression of OqxAB. Conclusions The dissemination of oqxAB gene may pose a great risk on food safety and public health. Further investigation and understanding of the natural functions, horizontal transfer, and regulation mechanism of the OqxAB efflux pump will aid in future strategies of antimicrobial usage.
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Affiliation(s)
- Jun Li
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,2Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Heying Zhang
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China
| | - Jianan Ning
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China
| | - Abdul Sajid
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,4College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University Mardan, Mardan, KP Pakistan
| | - Guyue Cheng
- 3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
| | - Zonghui Yuan
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
| | - Haihong Hao
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
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Lee DS, Lee SJ, Choe HS. Community-Acquired Urinary Tract Infection by Escherichia coli in the Era of Antibiotic Resistance. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7656752. [PMID: 30356438 PMCID: PMC6178185 DOI: 10.1155/2018/7656752] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/19/2018] [Accepted: 09/09/2018] [Indexed: 01/27/2023]
Abstract
Urinary tract infections (UTIs) caused by Escherichia coli (E. coli) are the most common types of infections in women. The antibiotic resistance of E. coli is increasing rapidly, causing physicians to hesitate when selecting oral antibiotics. In this review, our objective is to ensure that clinicians understand the current seriousness of antibiotic-resistant E. coli, the mechanisms by which resistance is selected for, and methods that can be used to prevent antibiotic resistance.
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Affiliation(s)
- Dong Sup Lee
- Department of Urology, St. Vincent's Hospital, The Catholic University of Korea, College of Medicine, Republic of Korea
| | - Seung-Ju Lee
- Department of Urology, St. Vincent's Hospital, The Catholic University of Korea, College of Medicine, Republic of Korea
| | - Hyun-Sop Choe
- Department of Urology, St. Vincent's Hospital, The Catholic University of Korea, College of Medicine, Republic of Korea
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Zhang X, Zhang Y, Wang F, Wang C, Chen L, Liu H, Lu H, Wen H, Zhou T. Unravelling mechanisms of nitrofurantoin resistance and epidemiological characteristics among Escherichia coli clinical isolates. Int J Antimicrob Agents 2018; 52:226-232. [PMID: 29753133 DOI: 10.1016/j.ijantimicag.2018.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/19/2018] [Accepted: 04/29/2018] [Indexed: 11/15/2022]
Abstract
The aim of this study was to investigate mechanisms of nitrofurantoin resistance and epidemiological characteristics in Escherichia coli clinical isolates. From a total of 1444 E. coli clinical isolates collected from our hospital in 2015, 18 (1.2%) nitrofurantoin-resistant E. coli isolates were identified with nitrofurantoin minimum inhibitory concentrations (MICs) ranging from 128 µg/mL to ≥512 µg/mL. The prevalence of the nfsA gene in nitrofurantoin-resistant, -intermediate and -susceptible isolates was 88.9%, 88.9% and 100%, respectively, and the prevalence of the nfsB gene was 66.7%, 61.1% and 100%, respectively. Eight nitrofurantoin-resistant isolates and two nitrofurantoin-intermediate isolates possessed oqxAB genes. In nitrofurantoin-resistant isolates, mutations in NfsA (the majority of mutated sites were I117T and G187D, accounting for 38.9%) and/or NfsB were detected, whereas only NfsA mutations were found in intermediate isolates and no sequence changes were detected in susceptible isolates. A ≥4-fold decrease in MIC was observed in eight nitrofurantoin-resistant isolates following addition of the efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone (CCCP). The mean expression level of oqxB in nitrofurantoin-resistant isolates increased ca. 7-fold compared with intermediate isolates. Multilocus sequence typing (MLST) categorised the 18 nitrofurantoin-resistant isolates into 11 different sequence types. Pulsed-field gel electrophoresis (PFGE) analysis revealed that homology among the nitrofurantoin-resistant isolates was low and sporadic. In conclusion, mutations in nfsA and nfsB were the main mechanisms leading to nitrofurantoin resistance, and overexpression of the oqxAB gene might help to further increase the MIC of nitrofurantoin.
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Affiliation(s)
- Xiaoxiao Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yizhi Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Fang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Department of Clinical Laboratory, The Traditional Chinese Medical Hospital of Ningbo, Ningbo, Zhejiang Province, China
| | - Chong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Haiyang Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hong Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Hong Wen
- Nosocomial Infection Management Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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Genomic insights into nitrofurantoin resistance mechanisms and epidemiology in clinical Enterobacteriaceae. Future Sci OA 2018; 4:FSO293. [PMID: 29796297 PMCID: PMC5961450 DOI: 10.4155/fsoa-2017-0156] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/23/2018] [Indexed: 11/18/2022] Open
Abstract
Aim: Multidrug-resistant enterobacteria are highly associated with invasive devices and intensive care units. Increasing resistance to carbapenems is leading to the use of older and neglected antibiotics such as nitrofurantoin (NFT). The genomics of NFT resistance was investigated. Results & conclusion: High-level resistance to NFT (minimum inhibitory concentration ≥128–512 mg/l) was recorded in 31/36 isolates (89.6%), many of which were from intensive care units (n = 20), urine (n = 17) or invasive procedures (n = 10). Efflux pump inhibitors had little effect on NFT's minimum inhibitory concentrations albeit oqxAB was prevalent in most isolates (n = 32). Various species- and clone-specific mutations mediating high-level NFT resistance were detected in nfsA, nfsB and ribE proteins through comparative genomics. Global phylogenomics showed local and independent emergence of NFT resistance in Enterobacteriaceae. NFT stewardship is advised. Nitrofurantoin (NFT) is an important antibiotic indicated for uncomplicated urinary tract infections. Resistance to NFT is slow and uncommon, making it an important drug for treating urinary tract infections resistant to common and last-resort antibiotics such as cephalosporins, fluoroquinolones, aminoglycosides and carbapenems. Increasing resistance to most antibiotics among uropathogens makes NFT a key choice for clinicians. Thus, the high-level NFT resistance in extradrug- and pandrug-resistant uropathogens found in this study is exceptionally worrying as treatment options will be extremely limited. Mutations in nfsA, nfsB and ribE genes in the same and different strains emerged locally and independently to confer NFT resistance.
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Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces. Sci Rep 2018; 8:814. [PMID: 29339831 PMCID: PMC5770469 DOI: 10.1038/s41598-017-18506-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/13/2017] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health issue. In an effort to minimize this threat to astronauts, who may be immunocompromised and thus at a greater risk of infection from antimicrobial resistant pathogens, a comprehensive study of the ISS “resistome’ was conducted. Using whole genome sequencing (WGS) and disc diffusion antibiotic resistance assays, 9 biosafety level 2 organisms isolated from the ISS were assessed for their antibiotic resistance. Molecular analysis of AMR genes from 24 surface samples collected from the ISS during 3 different sampling events over a span of a year were analyzed with Ion AmpliSeq™ and metagenomics. Disc diffusion assays showed that Enterobacter bugandensis strains were resistant to all 9 antibiotics tested and Staphylococcus haemolyticus being resistant to none. Ion AmpliSeq™ revealed that 123 AMR genes were found, with those responsible for beta-lactam and trimethoprim resistance being the most abundant and widespread. Using a variety of methods, the genes involved in antimicrobial resistance have been examined for the first time from the ISS. This information could lead to mitigation strategies to maintain astronaut health during long duration space missions when return to Earth for treatment is not possible.
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Biošić M, Škorić I, Beganović J, Babić S. Nitrofurantoin hydrolytic degradation in the environment. CHEMOSPHERE 2017; 186:660-668. [PMID: 28818593 DOI: 10.1016/j.chemosphere.2017.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/29/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Occurrence of pharmaceuticals, especially antibiotics in the environment increased attention to their environmental fate. Hydrolysis is one of two abiotic processes by which compounds are degraded in the environment. According to authors knowledge this is the first study investigating hydrolytic degradation of nitrofurantoin at pH-values normally found in the environment. Nitrofurantoin hydrolytic degradation appeared to be much slower at acidic (pH 4) solution compared to neutral (pH 7) and alkaline (pH 9) solutions at all three investigated temperatures (20 °C, 40 °C and 60 °C). In all cases nitrofurantoin hydrolysis followed the first-order kinetics with half-lives ranged from 0.5 days at pH 9 and 60 °C to 3.9 years at pH 4 and 20 °C. Temperature dependence of the hydrolysis rate constant was quantified by Arrhenius equation; obtained Ea values were as follows: 100.7 kJ mol-1 at pH 4, 111.2 kJ mol-1 at pH 7 and 102.3 kJ mol-1 at pH 9. Increase in hydrolysis rate constants for each 10 °C increase in temperature were 3.4, 3.9 and 3.5 at pH 4, pH 7 and pH 9, respectively. The structures of hydrolytic degradation products were determined and degradation pathways were suggested. Three main processes occurred depending on pH-values: protonation of the nitrofurantoin followed by cleavage of the NN single bond, heterocyclic non-aromatic ring cleavage, and reduction of the non-aromatic heterocyclic ring.
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Affiliation(s)
- Martina Biošić
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia.
| | - Irena Škorić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
| | - Jasmina Beganović
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
| | - Sandra Babić
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
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Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates. mBio 2017; 8:mBio.01341-17. [PMID: 29089428 PMCID: PMC5666156 DOI: 10.1128/mbio.01341-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The spread of antibiotic resistance is driving interest in new approaches to control bacterial pathogens. This includes applying multiple antibiotics strategically, using bacteriophages against antibiotic-resistant bacteria, and combining both types of antibacterial agents. All these approaches rely on or are impacted by associations among resistance phenotypes (where bacteria resistant to one antibacterial agent are also relatively susceptible or resistant to others). Experiments with laboratory strains have shown strong associations between some resistance phenotypes, but we lack a quantitative understanding of associations among antibiotic and phage resistance phenotypes in natural and clinical populations. To address this, we measured resistance to various antibiotics and bacteriophages for 94 natural and clinical Escherichia coli isolates. We found several positive associations between resistance phenotypes across isolates. Associations were on average stronger for antibacterial agents of the same type (antibiotic-antibiotic or phage-phage) than different types (antibiotic-phage). Plasmid profiles and genetic knockouts suggested that such associations can result from both colocalization of resistance genes and pleiotropic effects of individual resistance mechanisms, including one case of antibiotic-phage cross-resistance. Antibiotic resistance was predicted by core genome phylogeny and plasmid profile, but phage resistance was predicted only by core genome phylogeny. Finally, we used observed associations to predict genes involved in a previously uncharacterized phage resistance mechanism, which we verified using experimental evolution. Our data suggest that susceptibility to phages and antibiotics are evolving largely independently, and unlike in experiments with lab strains, negative associations between antibiotic resistance phenotypes in nature are rare. This is relevant for treatment scenarios where bacteria encounter multiple antibacterial agents.IMPORTANCE Rising antibiotic resistance is making it harder to treat bacterial infections. Whether resistance to a given antibiotic spreads or declines is influenced by whether it is associated with altered susceptibility to other antibiotics or other stressors that bacteria encounter in nature, such as bacteriophages (viruses that infect bacteria). We used natural and clinical isolates of Escherichia coli, an abundant species and key pathogen, to characterize associations among resistance phenotypes to various antibiotics and bacteriophages. We found associations between some resistance phenotypes, and in contrast to past work with laboratory strains, they were exclusively positive. Analysis of bacterial genome sequences and horizontally transferred genetic elements (plasmids) helped to explain this, as well as our finding that there was no overall association between antibiotic resistance and bacteriophage resistance profiles across isolates. This improves our understanding of resistance evolution in nature, potentially informing new rational therapies that combine different antibacterials, including bacteriophages.
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Wong MH, Xie M, Xie L, Lin D, Li R, Zhou Y, Chan EW, Chen S. Complete Sequence of a F33:A-:B- Conjugative Plasmid Carrying the oqxAB, fosA3, and blaCTX-M-55 Elements from a Foodborne Escherichia coli Strain. Front Microbiol 2016; 7:1729. [PMID: 27833607 PMCID: PMC5081371 DOI: 10.3389/fmicb.2016.01729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
This study reports the complete sequence of pE80, a conjugative IncFII plasmid recovered from an Escherichia coli strain isolated from chicken meat. This plasmid harbors multiple resistance determinants including oqxAB, fosA3, blaCTX-M-55, and blaTEM-1, and is a close variant of the recently reported p42-2 element, which was recovered from E. coli of veterinary source. Recovery of pE80 constitutes evidence that evolution or genetic re-arrangement of IncFII type plasmids residing in animal-borne organisms is an active event, which involves acquisition and integration of foreign resistance elements into the plasmid backbone. Dissemination of these plasmids may further compromise the effectiveness of current antimicrobial strategies.
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Affiliation(s)
- Marcus H Wong
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
| | - Miaomiao Xie
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic University Shenzhen, China
| | - Liqi Xie
- Division of Food Inspection and Supervision, Shenzhen Entry-Exit Inspection and Quarantine Bureau Shenzhen, China
| | - Dachuan Lin
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
| | - Ruichao Li
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
| | - Yuanjie Zhou
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
| | - Edward W Chan
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, Shenzhen Research Institute, The Hong Kong Polytechnic UniversityShenzhen, China; State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic UniversityKowloon, Hong Kong
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Hooper DC, Jacoby GA. Topoisomerase Inhibitors: Fluoroquinolone Mechanisms of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025320. [PMID: 27449972 DOI: 10.1101/cshperspect.a025320] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quinolone antimicrobials are widely used in clinical medicine and are the only current class of agents that directly inhibit bacterial DNA synthesis. Quinolones dually target DNA gyrase and topoisomerase IV binding to specific domains and conformations so as to block DNA strand passage catalysis and stabilize DNA-enzyme complexes that block the DNA replication apparatus and generate double breaks in DNA that underlie their bactericidal activity. Resistance has emerged with clinical use of these agents and is common in some bacterial pathogens. Mechanisms of resistance include mutational alterations in drug target affinity and efflux pump expression and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes are commonly in a localized domain of the GyrA and ParC subunits of gyrase and topoisomerase IV, respectively, and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include other antimicrobials as well as quinolones. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is because of Qnr proteins that protect the target enzymes from quinolone action, a mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones.
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Affiliation(s)
- David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts 01805
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