Implementation of Fourier transform infrared spectroscopy for the rapid typing of uropathogenic Escherichia coli.

In this paper, we demonstrate that Fourier transform infrared (FT-IR) spectroscopy is able to discriminate rapidly between uropathogenic Escherichia coli (UPEC) of key lineages with only relatively simple sample preparation. A total of 95 bacteria from six different epidemiologically important multilocus sequence types (ST10, ST69, ST95, ST73, ST127 and ST131) were used in this project and principal component-discriminant function analysis (PC-DFA) of these samples produced clear separate clustering of isolates, based on the ST. Analysis of data using partial least squares-discriminant analysis (PLS-DA), incorporating cross-validation, indicated a high prediction accuracy of 91.19% for ST131. These results suggest that FT-IR spectroscopy could be a useful method for the rapid identification of members of important UPEC STs.

Prevalence and distribution of plasmid-mediated quinolone resistance genes in clinical isolates of Escherichia coli lacking extended-spectrum beta-lactamases.

OBJECTIVES: The aac(6')-Ib-cr gene has been described in plasmids from CTX-M-15-producing Escherichia coli in the worldwide ST131 lineage, but has not been systematically sought in other quinolone-resistant strains in the UK. A rise in quinolone resistance in bacteraemia isolates in the UK preceded the increased prevalence of CTX-M-producing strains. This study aimed to describe the presence of plasmid-encoded quinolone resistance genes in historical and current strains of E. coli not producing extended-spectrum beta-lactamases (ESBLs). METHODS: Ciprofloxacin-resistant, non-ESBL-producing E. coli isolates included nationally distributed isolates from the BSAC UK bacteraemia surveillance programme between 2001 and 2005, urinary isolates from a regional project in 2000 and local strains in 2006. The aac(6')-Ib-cr gene was detected using PCR followed by restriction fragment length polymorphism analysis. Multiplex PCR was used to detect qnr genes. Isolates with aac(6')-Ib-cr were assessed for aminoglycoside susceptibilities and were serotyped. RESULTS: The prevalence of the aac(6')-Ib-cr gene was 3% and 9% in current local urinary and historic national bacteraemia quinolone-resistant non-ESBL-producing E. coli, respectively. Of 521 regional urinary E. coli isolates from 2000, 14 were norfloxacin-resistant, none of which carried the aac(6')-Ib-cr gene. National positive bacteraemia isolates from 2001/2 were type O102-ST405 and, in 2004/5, types O1-ST645 and O25-ST131. Positive local urinary isolates from 2006 included serotypes O1 and O25. CONCLUSIONS: In the UK, aac(6')-Ib-cr occurs in E. coli in the absence of CTX-M-15, but with a restricted serotype distribution. Its presence in widespread bacteraemia isolates of a single type from 2001 to 2002, prior to the spread of CTX-M-15 in Britain, might suggest a lineage from which plasmid recombination occurred in man or other species.