Abstract
BackgroundThe mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic E. coli (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the mutS gene and the o454-nlpD genomic region among 510 E. coli strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of E. coli, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the o454-nlpD region.MethodsSize variation in the o454-nlpD region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between mutS gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between o454-nlpD patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of o454-nlpD patterns was investigated by means of Random Forest algorithm.ResultsFour main structures (patterns I-IV) of the o454-nlpD region among ExPEC and commensal E. coli strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (csgA, malX, chuA, sit, and vat) to be suitable to predict pattern III strains.ConclusionThe significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir. Furthermore, top-ranked VAGs for classification and prediction of pattern III were identified. These data are most valuable for defining ExPEC pathotype in future in vivo assays.
Highlights
The mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns
E. coli is broadly classified into commensals, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC), the latter group being further divided into uropathogenic E. coli (UPEC), septicaemiaassociated E. coli (SEPEC), neonatal meningitis E. coli (NMEC), and avian pathogenic E. coli (APEC)
Size variation and DNA polymorphism in the fhlA-nlpD region with respect to the phylogenetic background of E. coli strains PCR amplification of the o454-nlpD region among 510 E. coli strains revealed a mosaic structure of the o454-nlpD genomic region
Summary
The mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. Collectively termed ExPEC, to reflect their shared ability to express functionally similar virulence factors and to denote considerable overlaps concerning serotypes and phylogenetic background [3,4], this group of strains exhibits large genome diversity. This has been mainly attributed to the frequent location of virulence associated genes (VAGs) on plasmids, pathogenicity islands, or phages, allowing the VAGs to be highly interchangeable among strains through horizontal gene transfer (HGT) [5,6]. The distribution (presence/ absence) of virulence factors thought to be involved in the ability of a strain to cause diverse diseases varies among strains of these phylogenetic groups, indicating a role of the genetic background in the expression of virulence [11,12,13]
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