Rapid identification of different Escherichia coli ST131 clades [PublishAheadOfPrint]

Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone-resistance and extended-spectrum β-lactamase (ESBL)-producers. The ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C) as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in 2 Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli from extra-intestinal sites [ExPEC] (2014). The assay correctly identified the different clades in all 80 global isolates: clades A (n=12), B (n=12), and C, including subclades C1-M27 (n=16), C1-nM27 (n=20), C2 (n=17) and other C (n=3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A (n=54), B (n=23), and C (n=483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with bla_CTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli and is a promising tool for epidemiological studies of ST131.

http://ift.tt/2sy5BB6