IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2023-09
Date Acceptance
2023-08-16
Citation
Microbial Genomics, 2023, 9 (9), pp.1-11
ISSN
2057-5858
Publisher
Microbiology Society
Start Page
1
End Page
11
Journal / Book Title
Microbial Genomics
Volume
9
Issue
9
Copyright Statement
© 2023 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between
the Microbiology Society and the corresponding author’s institution.
the Microbiology Society and the corresponding author’s institution.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/37672334
Subjects
comparative genomics
Escherichia coli
hybrid genome assembly
insertion sequences
IS1 elements
nitrofurantoin heteroresistance
population analysis profiling
resistance mechanism
structural variation
whole-genome sequencing
Publication Status
Published
Coverage Spatial
England
Article Number
001102
Date Publish Online
2023-09-06