Nitrofurantoin-resistant Escherichia coli in the UK: genetic determinants, diversity, and undetected occurrences

Background

Antimicrobial resistance in enteric or urinary E. coli might predispose invasive E. coli infection and bacteraemia. Nitrofurantoin resistance occurs in <6% of UK urinary E. coli isolates, however, 2018 national recommendations to prescribe nitrofurantoin for uncomplicated urinary tract infection (UTI) raised concerns for increased prevalence of nitrofurantoin-resistant E. coliin the future. Therefore, we investigated mechanisms of nitrofurantoin resistance in UK E. coli isolates and assessed their occurrences in a large dataset of E. coli genomes.

Methods

To elucidate chromosomal and acquired genetic determinants of nitrofurantoin resistance in E. coli, we analysed whole-genome sequences of nine randomly selected nitrofurantoin-resistant UTI E. coli isolates from West London. We then performed targeted analysis of 12,412 E. coli genomes collected from across the UK and predicted nitrofurantoin susceptibility from identified genotypes.

Results

Using comparative genomics, we found known and novel point mutations or insertion sequences (ISs) in chromosomal genes encoding oxygen-insensitive nitroreductases NfsA and NfsB in the nine isolates. Most of these genetic alterations resulted in gene inactivation. We also identified the same kinds of mutations in NfsA, NfsB, and their associated enzyme RibE in a number of 12,412 E. coli genomes. We also observed homoplasic mutations in all these proteins. By contrast, multidrug efflux pump OqxAB, which confers resistance when horizontally transferred, was only encoded by one genome.

Conclusions

Chromosomal de novo mutations and ISs are main causes of nitrofurantoin resistance in UK E. coli. Prevalence of nitrofurantoin resistance should be monitored among urine, blood, and enteric isolates as nitrofurantoin exposure increases.

Frequency of transmission, asymptomatic shedding, and airborne spread of Streptococcus pyogenes in schoolchildren exposed to scarlet fever: a prospective, longitudinal, multicohort, molecular epidemiological, contact-tracing study in England, UK

BACKGROUND

Despite recommendations regarding prompt treatment of cases and enhanced hygiene measures, scarlet fever outbreaks increased in England between 2014 and 2018. We aimed to assess the effects of standard interventions on transmission of Streptococcus pyogenes to classroom contacts, households, and classroom environments to inform future guidance.

METHODS

We did a prospective, longitudinal, multicohort, molecular epidemiological, contact-tracing study in six settings across five schools in Greater London, UK. Schools and nurseries were eligible to participate if they had reported two cases of scarlet fever within 10 days of each other among children aged 2-8 years from the same class, with the most recent case arising in the preceding 48 h. We cultured throat swabs from children with scarlet fever, classroom contacts, and household contacts at four timepoints. We also cultured hand swabs and cough plates from all cases in years 1 and 2 of the study, and from classroom contacts in year 2. Surface swabs from toys and other fomites in classrooms were cultured in year 1, and settle plates from classrooms were collected in year 2. Any sample with S pyogenes detected was recorded as positive and underwent emm genotyping and genome sequencing to compare with the outbreak strain.

FINDINGS

Six classes, comprising 12 cases of scarlet fever, 17 household contacts, and 278 classroom contacts were recruited between March 1 and May 31, 2018 (year 1), and between March 1 and May 31, 2019 (year 2). Asymptomatic throat carriage of the outbreak strains increased from 11 (10%) of 115 swabbed children in week 1, to 34 (27%) of 126 in week 2, to 26 (24%) of 108 in week 3, and then five (14%) of 35 in week 4. Compared with carriage of outbreak S pyogenes strains, colonisation with non-outbreak and non-genotyped S pyogenes strains occurred in two (2%) of 115 swabbed children in week 1, five (4%) of 126 in week 2, six (6%) of 108 in week 3, and in none of the 35 children in week 4 (median carriage for entire study 2·8% [IQR 0·0-6·6]). Genome sequencing showed clonality of outbreak isolates within each of six classes, confirming that recent transmission accounted for high carriage. When transmissibility was tested, one (9%) of 11 asymptomatic carriers of emm4 and five (36%) of 14 asymptomatic carriers of emm3.93 had a positive cough plate. The outbreak strain was identified in only one (2%) of 60 surface swabs taken from three classrooms; however, in the two classrooms with settle plates placed in elevated locations, two (17%) of 12 and six (50%) of 12 settle plates yielded the outbreak strain.

INTERPRETATION

Transmission of S pyogenes in schools is intense and might occur before or despite reported treatment of cases, underlining a need for rapid case management. Despite guideline adherence, heavy shedding of S pyogenes by few classroom contacts might perpetuate outbreaks, and airborne transmission has a plausible role in its spread. These findings highlight the need for research to improve understanding and to assess effectiveness of interventions to reduce airborne transmission of S pyogenes.

FUNDING

Action Medical Research, UK Research Innovation, and National Institute for Health Research.