Nested Deletions of the SRL Pathogenicity Island of Shigella flexneri 2a

Abstract

In this study, we determined the boundaries of a 99-kb deletable element of Shigella flexneri 2a strain YSH6000. The element, designated the multiple-antibiotic resistance deletable element (MRDE), had recently been found to contain a 66-kb pathogenicity island (PAI)-like element (designated the SRL PAI) which carries the Shigella resistance locus (SRL), encoding resistance determinants to streptomycin, ampicillin, chloramphenicol, and tetracycline. The YSH6000 MRDE was found to be flanked by two identical IS91 elements present at the S. flexneri homologs of the Escherichia coli genes putA and mdoA on NotI fragment D. Sequence data from two YSH6000-derived MRDE deletants, YSH6000T and S2430, revealed that deletion of the MRDE occurred between the two flanking IS91 elements, resulting in a single IS91 element spanning the two original IS91 loci. Selection for the loss of tetracycline resistance confirmed that the MRDE deletion occurred reproducibly from the same chromosomal site and also showed that the SRL PAI and the SRL itself were capable of independent deletion from the chromosome, thus revealing a unique set of nested deletions. The excision frequency of the SRL PAI was estimated to be 10 ؊5 per cell in the wild type, and mutation of a P4-like integrase gene (int) at the left end of the SRL PAI revealed that int mediates precise deletion of the PAI.

Instability of Pathogenicity Islands in Uropathogenic Escherichia coli 536

“…PAI-negative cells appear in the REPEC strain 84/110-1 and in S. flexneri 2a with frequencies of around 10 Ϫ6 to 10 Ϫ5 , which are comparable to previously obtained data for PAI I 536 and PAI II 536 (43,44). Other PAIs, like the Vibrio cholerae PAI or the Staphylococcus aureus PAI (S. aureus PAI 1), have not only the tendency to be deleted from the chromosome but both are also transmissible to recipient organisms by transducing phages (25,32,39).…”

“…The deletion rates of 10 Ϫ6 to 10 Ϫ5 that were obtained for PAI I 536 to PAI V 536 were similar to the rates previously reported for other PAIs (34,43,44). With the exception of PAI III 536 , where a second deletion mechanism based on homologous recombination between a complete and a truncated IS100 copy was detected, excision and subsequent deletion of PAIs in E. coli 536 is mediated by site-specific recombination between short flanking DR sequences.…”

“…In this context, it has been interesting to find that instability seems to be a characteristic of PAIs in particular pathogens, including UPEC (6,16,33). Furthermore, other PAIs have been identified that share the tendency to be deleted from the bacterial chromosome (2,7,9,34,43,44). In this study, we applied the island-probing approach to analyze for the first time the (in)stability of all so far identified PAIs of one pathogenic strain in detail.…”

“…HPI of Yersinia pestis and Yersinia pseudotuberculosis, the locus of enterocyte effacement (LEE) of rabbit-specific enteropathogenic E. coli (REPEC) strain 84/110-1, and the Shigella resistance locus of S. flexneri (7,9,43,44). PAI-negative cells appear in the REPEC strain 84/110-1 and in S. flexneri 2a with frequencies of around 10 Ϫ6 to 10 Ϫ5 , which are comparable to previously obtained data for PAI I 536 and PAI II 536 (43,44).…”

Genomic Portrait of the Evolution and Epidemic Spread of a Recently Emerged Multidrug-Resistant Shigella flexneri Clone in China

“…Genome sequencing of a representative ST91 strain, 2002017, revealed that it gained 2 unique multidrug resistance (MDR) islands, i.e., the Shigella resistance locus (SRL) and Tn7 (9). The SRL, which was first identified in the Japanese S. flexneri 2a strain YSH6000, carries genes for resistance against streptomycin, ampicillin, chloramphenicol, and tetracycline and also carries an iron acquisition system (9,(15)(16)(17). The SRL in 2002017 carries an additional set of tetracycline resistance genes but does not contain the iron acquisition system present in YSH6000.…”