Complete Genome Sequences of Nitrofurantoin-Sensitive and -Resistant Escherichia coli ST540 and ST2747 Strains

Xavier, Basil Britto; Vervoort, J.J.M.; Stewardson, Andrew J.; Adriaenssens, Niels; Coenen, Samuel; Harbarth, Stéphan Juergen; Goossens, Herman; Malhotra-Kumar, Surbhi

doi:10.1128/genomea.00239-14

Cited by 13 publications

(14 citation statements)

References 7 publications

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“…A 559-bp fragment containing the coding sequence of wild-type ribE, including 65-bp upstream and 23-bp downstream regions (GenBank accession no. CP007392; bases 1080502 to 1081060) (13), was prepared by PCR amplification, and the PCR fragment was cloned in a pCR2.1 vector by Topo TA cloning (Invitrogen, Carlsbad, CA), according to the manufacturer's protocol. The resulting recombinant vector, LMZ-pCR2.1, was electrotransformed in ST2747-an, which was made electrocompetent by successive washing steps with an ice-cold 10% glycerol suspension at log phase.…”

Section: Methodsmentioning

confidence: 99%

“…Both ST540-p and ST2747-p, together with their mutants that showed the highest nitrofurantoin MICs aerobically (ST540-a and ST2747-a) and anaerobically (ST540-an and ST2747-an), were subjected to whole-genome sequencing (13). Full genomes were compared to identify mutations in the known resistance determinants nfsA and nfsB, as well as to check for other genomic changes indicative of as-yet-undescribed nitrofurantoin resistance determinants.…”

Section: Nit-r Mutants Generated In Vitromentioning

confidence: 99%

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An In Vitro Deletion in ribE Encoding Lumazine Synthase Contributes to Nitrofurantoin Resistance in Escherichia coli

Vervoort

Xavier

Stewardson

et al. 2014

Antimicrob Agents Chemother

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e Nitrofurantoin has been used for decades for the treatment of urinary tract infections (UTIs), but clinically significant resistance in Escherichia coli is uncommon. Nitrofurantoin concentrations in the gastrointestinal tract tend to be low, which might facilitate selection of nitrofurantoin-resistant (NIT-R) strains in the gut flora. We subjected two nitrofurantoin-susceptible intestinal E. coli strains (ST540-p and ST2747-p) to increasing nitrofurantoin concentrations under aerobic and anaerobic conditions. Whole-genome sequencing was performed for both susceptible isolates and selected mutants that exhibited the highest nitrofurantoin resistance levels aerobically (ST540-a and ST2747-a) and anaerobically (ST540-an and ST2747-an). ST540-a/ST540-an and ST2747-a (aerobic MICs of >64 g/ml) harbored mutations in the known nitrofurantoin resistance determinants nfsA and/or nfsB, which encode oxygen-insensitive nitroreductases. ST2747-an showed reduced nitrofurantoin susceptibility (aerobic MIC of 32 g/ml) and exhibited remarkable growth deficits but did not harbor nfsA/nfsB mutations. We identified a 12-nucleotide deletion in ribE, encoding lumazine synthase, an essential enzyme involved in the biosynthesis of flavin mononucleotide (FMN), which is an important cofactor for NfsA and NfsB. Complementing ST2747-an with a functional wild-type lumazine synthase restored nitrofurantoin susceptibility. Six NIT-R E. coli isolates (NRCI-1 to NRCI-6) from stools of UTI patients treated with nitrofurantoin, cefuroxime, or a fluoroquinolone harbored mutations in nfsA and/or nfsB but not ribE. Sequencing of the ribE gene in six intestinal and three urinary E. coli strains showing reduced nitrofurantoin susceptibility (MICs of 16 to 48 g/ml) also did not identify any relevant mutations. NRCI-1, NRCI-2, and NRCI-5 exhibited up to 4-fold higher anaerobic MICs, compared to the mutants generated in vitro, presumably because of additional mutations in oxygen-sensitive nitroreductases.

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Section: Methodsmentioning

confidence: 99%

Section: Nit-r Mutants Generated In Vitromentioning

confidence: 99%

An In Vitro Deletion in ribE Encoding Lumazine Synthase Contributes to Nitrofurantoin Resistance in Escherichia coli

Vervoort

Xavier

Stewardson

et al. 2014

Antimicrob Agents Chemother

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“…In this study, it was isolated from Jimba Oja and possibly may be a mutant variation of an Escherichia coli strain, further research is suggested on this strain as available information at this period is limited. Escherichia coli strain ST2747 and Escherichia coli strain ST540 complete genome have been proved to be antibiotic resistant (nitrofurantoin resistant) and has necessitated the introduction of older and stronger antibiotics in treating infections caused by it [28]. Escherichia coli strain EADK4 16S ribosomal RNA gene has been found to bear very close similarities with pathogenic E. coli O157:H7 which has cattle as its main reservoir.…”

Section: Resultsmentioning

confidence: 99%

Temporal Appraisal and Molecular Characterization of Escherichia coli from Oyun River, Kwara State, Nigeria

Kolawole

Adeyemi

2020

JAMB

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Introduction: Escherichia coli, an indicator of feacal contamination has been proven to be the cause of several disease outbreaks in countries and continents around the world. Aim: To determine the genotypic variants of Escherichia coli present in Oyun River and provide information regarding the high-risk variants of E. coli in Oyun River. Study Design: The study cuts across the two seasons of Nigeria’s tropical climate weather, being the peak of the Harmattan season and the onset of the Rainy season. Three sampling sites (Jimba Oja; Unilorin Dam and Oyun in Ilorin, Kwara State) along the River course were examined for three months (February – April). Methodology: Heterotrophic counts, coli form counts and molecular characterization via PCR using 16 sRNA primers, of water samples were done using standard microbiological and molecular methods. Results: Bacteriological results showed monthly mean values of microbial counts, ranged from 23.5 x 106 – 45.17 x 106 cfu/mL and total coli form count ranged from 53 cfu/100 mL to 256 cfu/100 mLs, both of which exceed the WHO standards of 100 cfu/mL for total microbial count and <1 cfu/100 mLs for total coliforms. A total of forty-eight coliforms were isolated, thirty two of which were Escherichia coli. Sequencing and BLAST analysis of eleven of the isolates using NCBI’s online database revealed five different strains. They include: Escherichia coli FAP1 genome (9.1%); Escherichia coli strain ST2747 (54.5%); Escherichia coli strain EADK4 (9.1%); Escherichia coli strain ST540 (18.2%) and Escherichia coli strain NCM3722 (9.1%). Correlation of results with previous studies showed that most of the strains identified were pathogenic. The E. coli strains isolated, coupled with the bacterial load, coliform count and some physicochemical parameters of Oyun River makes it unsafe for public consumption if not treated. Efforts therefore should be made to treat the water before use, while making frantic efforts to prevent further contamination of Oyun River.

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“…Chromosomal mutations known to be associated with resistance to fluoroquinolones in E. coli were extracted from the genome-wide SNP calls obtained previously based on mapping the reads to the E. coli strain 12009 O103:H2 reference genome 6 . These included specific mutations in the QRDR of gyrA, gyrB, parC and parE 57 , and non-synonymous substitutions in nfsA (residues [11][12][13][14][15] which confer resistance to nitrofurantoin 58,59 .…”

Section: Detection Of Snps Conferring Resistance To Fluoroquinolones mentioning

confidence: 99%

Drivers of antimicrobial resistance amongst intestinalEscherichia coliisolated from children in South Asia and sub-Saharan Africa

Ingle

Levine

Kotloff

et al. 2017

Preprint

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Antimicrobial resistance (AMR) dynamics are poorly understood in developing countries, where data on the prevalence of AMR in enteric bacteria are sparse, particularly among children and in the community setting. Here we use a combination of phenotyping, genomics and antimicrobial usage data to investigate patterns of AMR amongst atypical enteropathogenic E. coli (aEPEC) strains isolated from children <5 years old in seven countries (four in sub-Saharan Africa and three in South Asia) over a three-year period. We detected very high rates of AMR, with 65% of isolates displaying resistance to ≥3 drug classes; the rates of AMR were the same amongst strains associated with diarrhea and strains that were carried asymptomatically. Whole genome sequencing identified a diversity of genetic mechanisms for AMR, which could explain >95% of observed phenotypic resistance. Analysis of AMR gene co-occurrence revealed clusters of acquired AMR genes that were frequently co-located on small plasmids and transposons, providing opportunities for acquisition of multidrug resistance in a single step. We used discriminant analysis to investigate potential drivers of AMR within the bacterial population, and found that genetic determinants of AMR were associated with geographical location of isolation but not with phylogenetic lineage of the E. coli strain or disease status of the human host. Comparison with antimicrobial usage data showed that the prevalence of resistance to newer drugs (fluoroquinolones and third-generation cephalosporins) was correlated with usage, which was generally higher in South Asia than Africa. In particular, fluoroquinolone resistance-associated mutations in gyrA were significantly associated with use of these drugs for treatment of diarrheic children. Notably resistance to older drugs such as trimethoprim, chloramphenicol and ampicillin, which are conferred by acquired AMR genes that were frequently clustered together in mobile genetic elements, were common in all locations despite differences in usage; this suggests that reversion to sensitivity is unlikely to occur even if these drugs are removed from circulation. This study provides much-needed insights into the frequencies of AMR in intestinal E. coli in community-based children in developing countries and to antimicrobial usage for diarrhea where the burden of infections is greatest.

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Complete Genome Sequences of Nitrofurantoin-Sensitive and -Resistant Escherichia coli ST540 and ST2747 Strains

Cited by 13 publications

References 7 publications

An In Vitro Deletion in ribE Encoding Lumazine Synthase Contributes to Nitrofurantoin Resistance in Escherichia coli

An In Vitro Deletion in ribE Encoding Lumazine Synthase Contributes to Nitrofurantoin Resistance in Escherichia coli

Temporal Appraisal and Molecular Characterization of Escherichia coli from Oyun River, Kwara State, Nigeria

Drivers of antimicrobial resistance amongst intestinalEscherichia coliisolated from children in South Asia and sub-Saharan Africa

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