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Background  Enteropathogenic Escherichia coli (EPEC) are classified into typical and atypical strains based on the presence of the E. coli adherence factor (EAF) plasmid. The EAF plasmid contains the bfp (bundle-forming pilus) operon and the perABC (plasmid encoded regulator) gene cluster. A 1-kb cryptic region of EAF plasmid has been widely used as a genetic probe for EPEC detection. However, some EPEC strains may harbor an EAF plasmid lacking the EAF probe sequence, which makes the differentiation between typical and atypical a complex task. In this study, we report the genetic analysis of the EAF plasmid-encoded genes in a collection of EPEC clinical isolates.    Methods  A total of 222 EPEC clinical isolates, which were previously classified as typical (n = 70) or atypical (n = 152) by EAF probe reactivity, were screened for the presence of different EAF sequences by PCR and DNA hybridization.    Results  All typical strains possessed intact  bfpA  and  perA  genes, and most of them were positive in the PCR for EAF probe sequence. However, a subset of 30 typical strains, 22 of which belonged to O119 serogroup, presented a 1652 pb deletion in the region between 1093-bp downstream  perC  and 616-bp of the EAF fragment. The  bfpA, bfpG , and  per  genes were found in all typical strains. In addition, 32 (21 %) atypical strains presented the  perA  gene, and 20 (13.2 %) also presented the  bfpA  gene. Among the 32 strains, 16 belonged to the O119:H2, O119:HND, and ONT:HND serotypes. All 32 atypical strains contained  perA  mutation frameshifts and possessed an IS 1294  element upstream of the  per  operon as detected by PCR followed by restriction fragment length polymorphism (RFLP) typing and multiplex PCR. Among the 20  bfpA  probe-positive strains, eight O119 strains possessed deletion in the  bfp  operon at the 3′end of  bfpA  due to an IS 66  element.    Conclusion  Our data show that typical O119 strains may contain a deletion within the EAF probe sequence not previously reported. This new finding suggests that care should be taken when using the previously described EAF PCR assay in epidemiological studies for the detection of typical O119 strains. In addition, we were able to confirm that some atypical strains carry vestiges of the EAF plasmid.

bmc microbiology

Genetic analysis of enteropathogenic Escherichia coli (EPEC) adherence factor (EAF) plasmid reveals a new deletion within the EAF probe sequence among O119 typical EPEC strains