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Phylogenetic relationships, biofilm formation, motility, antibiotic resistance and extended virulence genotypes among Escherichia coli strains from women with community-onset primitive acute pyelonephritis.

ABSTRACT: The present work set out to search for a virulence repertoire distinctive for Escherichia coli causing primitive acute pyelonephritis (APN). To this end, the virulence potential of 18 E. coli APN strains was genotypically and phenotypically assessed, comparatively with 19 strains causing recurrent cystitis (RC), and 16 clinically not significant (control, CO) strains. Most of the strains belong to phylogenetic group B1 (69.8%; p<0.01), and APN strains showed unique features, which are the presence of phylogroup A, and the absence of phylogroup B2 and non-typeable strains. Overall, the most dominant virulence factor genes (VFGs) were ecpA and fyuA (92.4 and 86.7%, respectively; p<0.05), and the mean number of VFGs was significantly higher in uropathogenic strains. Particularly, papAH and malX were exclusive for uropathogenic strains. APN and RC strains showed a significantly higher prevalence of fyuA, usp, and malX than of CO strains. Compared to RC strains, APN ones showed a higher prevalence of iha, but a lower prevalence of iroN, cnf1, and kpsMT-II. Hierarchical cluster analysis showed a higher proportion of two gene clusters (malX and usp, and fyuA and ecpA) were detected in the APN and RC groups than in CO, whereas iutA and iha clusters were detected more frequently in APN strains. The motility level did not differ among the study-groups and phylogroups considered, although a higher proportion of swarming strains was observed in APN strains. Antibiotic-resistance rates were generally low except for ampicillin (37.7%), and were not associated with specific study- or phylogenetic groups. APN and RC strains produced more biofilm than CO strains. In APN strains, iha was associated with higher biofilm biomass formation, whereas iroN and KpSMT-K1 were associated with a lower amount of biofilm biomass. Further work is needed to grasp the virulence and fitness mechanisms adopted by E. coli causing APN, and hence develop new therapeutic and prophylactic approaches.

SUBMITTER: Pompilio A

PROVIDER: S-EPMC5951556 | biostudies-other | 2018

REPOSITORIES: biostudies-other

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Phylogenetic relationships, biofilm formation, motility, antibiotic resistance and extended virulence genotypes among Escherichia coli strains from women with community-onset primitive acute pyelonephritis.

Pompilio Arianna A Crocetta Valentina V Savini Vincenzo V Petrelli Dezemona D Di Nicola Marta M Bucco Silvia S Amoroso Luigi L Bonomini Mario M Di Bonaventura Giovanni G

PloS one 20180514 5

The present work set out to search for a virulence repertoire distinctive for Escherichia coli causing primitive acute pyelonephritis (APN). To this end, the virulence potential of 18 E. coli APN strains was genotypically and phenotypically assessed, comparatively with 19 strains causing recurrent cystitis (RC), and 16 clinically not significant (control, CO) strains. Most of the strains belong to phylogenetic group B1 (69.8%; p<0.01), and APN strains showed unique features, which are the presen ...[more]

PMID: 29758033

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Project description:BackgroundPseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants.ResultsWe examined the genetic basis for biofilm production on polystyrene at room (22 °C) and body temperature (37 °C) within 280 P. aeruginosa. 193 isolates (69 %) produced more biofilm at 22 °C than at 37 °C. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with greater biofilm production at 22 °C. Many of these are present on a 165 kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium), transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation.ConclusionsUsing genetic association approaches we discovered a number of accessory genes and core-genome SNPs that were associated with enhanced early biofilm formation at 22 °C compared to 37 °C. These included a 165 kb genomic island containing multiple heavy metal resistance genes, transcriptional regulators and methyltransferases. We hypothesize that this genomic island may be associated with overall genotypes that are environmentally adapted to survive at lower temperatures. Further work to examine their importance in, for example gene-knockout studies, are required to confirm their relevance. GWAS and pan-GWAS approaches have great potential as a first step in examining the genetic basis of novel bacterial phenotypes.

Project description:The genus Polymixia is the only survivor of a Late Cretaceous marine fish radiation and is often said to be the most primitive living acanthomorph (i.e., Polymixia possesses the greatest number of primitive character states for Acanthomorpha). Recent studies, including this one, place Polymixia as the sister to all other Paracanthopterygii. Despite its importance, most species of Polymixia are extremely difficult to discriminate on the basis of morphology. As a result, the number of valid species is uncertain. Moreover, there has never been a phylogenetic analysis of the genus. Thus, a molecular phylogenetic study was needed to clarify species boundaries and to resolve relationships within the genus. Tissue or DNA samples backed by museum vouchers were obtained for most species, with additional samples from new geographic areas representing specimens with distinctively different meristics and uncertain identifications. Seven loci (five nuclear and two mitochondrial) were sequenced, from which Bayesian and maximum-likelihood trees were generated. Results reveal nine species-level clades, of which five represent previously known species (Polymixia berndti, P. japonica, P. longispina, P. lowei, and P. nobilis). Surprisingly, results also reveal four previously unknown species-level clades, one close to P. lowei, one close to P. nobilis, and two new species clades related to P. japonica. The species clades are distinguished by their phylogenetic histories, sequence differences, geographic distributions, and morphologies. The clade containing P. berndti is recovered as the sister to all other species of Polymixia. Its genetic variability suggests that it might contain two or more species and it is referred to here as a "species complex". Polymixia nobilis, the type species, was previously thought to be restricted to the Atlantic, but is now shown to be widespread in the Pacific and possibly in the Indian Ocean. Specimens from waters off Australia identified as P. busakhini actually belong to P. nobilis. In contrast, P. japonica is confirmed only in the area near Japan and the East China Sea; other more distant records are misidentifications. Wide (antipodal) geographic distributions are seen in several clades, including P. nobilis, the P. berndti species complex, and the P. japonica species group. The new phylogeny helps explain the evolution of some morphological characters previously used to distinguish groups of species, particularly dorsal-fin soft-ray count, shape of rows of scale ctenii, and number of pyloric caeca.

Dataset Information

Phylogenetic relationships, biofilm formation, motility, antibiotic resistance and extended virulence genotypes among Escherichia coli strains from women with community-onset primitive acute pyelonephritis.

Publications

Phylogenetic relationships, biofilm formation, motility, antibiotic resistance and extended virulence genotypes among Escherichia coli strains from women with community-onset primitive acute pyelonephritis.

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