Performances of the rapid polymyxin Acinetobacter and Pseudomonas tests for colistin susceptibility testing

Owing to the emergence of colistin resistance in nonfermenting Gram negative bacteria, reliable and rapid techniques for testing colistin susceptibility are needed. We evaluated the performances of the Rapid Polymyxin Acinetobacter and Pseudomonas tests using a collection of Acinetobacter baumannii and Pseudomonas aeruginosa clinical isolates.Methods: Colistin susceptibility of A. baumannii and P. aeruginosa isolates (colistin susceptible and colistin resistant) was tested with the Rapid Polymyxin Acinetobacter and Pseudomonas tests and compared with the broth microdilution method.Results: The Rapid Polymyxin Acinetobacter and Pseudomonas tests were able to detect all colistin-resistant and all colistin-susceptible A. baumannii and P. aeruginosa isolates within 4 hours.Conclusion: The Rapid Polymyxin Acinetobacter and Pseudomonas tests are reliable techniques for detecting colistin resistance. Overall, both techniques allow an accurate and a rapid screening (<4  hours) of colistin resistance in A. baumannii and P. aeruginosa

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

<p>Abstract</p> <p>Background</p> <p>Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of <it>Escherichia coli</it>. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B₂variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B₁variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.</p> <p>Results</p> <p>We identified the gene encoding esterase B as the acetyl-esterase gene (<it>aes</it>) using gene disruption. The analysis of <it>aes </it>nucleotide sequences in a panel of 78 reference strains, including the <it>E. coli </it>reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from <it>aes </it>sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B₁and B₂by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between <it>aes </it>and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of <it>aes </it>to be associated with virulence.</p> <p>Conclusion</p> <p>Our findings suggest that <it>aes </it>does not play a direct role in the virulence of <it>E. coli </it>extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.</p

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome

Recherche des escherichia coli entérovirulents par PCR multiplex au cours des diarrhées infectieuses

PARIS-BIUP (751062107) / SudocSudocFranceF

Recherche des escherichia coli entérovirulents par PCR multiplex au cours des diarrhées infectieuses

PARIS-BIUP (751062107) / SudocSudocFranceF

Structure des populations naturelles de Escherichia coli (relation avec la virulence et la résistance aux antibiotiques)

L'objectif de ce travail est de préciser à différentes échelles les liens qui existent entre phylogénie, virulence et résistance aux antibiotiques dans l'espèce Escherichia coll. Dans un premier temps, l'étude à porté sur l'estérase B la caractérisant comme un excellent marqueur de phylogénie. L'étude de l'évolution de souches par le séquençage de génomes entiers a ensuite été rélaisé par génomique comparative. Nous avons à cette occasion identifié un module chromosomique de résistance chez une souche responsable d'infections urinaires et multirésistante. La troisième partie du travail a concerné des populations d'isolats naturels provenant d'humains, de leurs animaux domestiques et d'animaux sauvages, caractérisées comme très distinctes. Ces 3 niveaux d'étude de l'évolution de souches nous ont permis de préciser les facteurs qui régissent leur adaptation à différents environnements, les rapports entre leur génome, leurs habitats écologiques et les pressions de sélection subies.The aim of this work was to precise relations between phylogney, virulence and resistance to antibiotics in the species Escherichia coli. At first, we characterized the esterase B, as a perfomant marker of phylogeny. The study of the evolution of strains was then realised using whole genome sequencing. This allowed also us to identify a chromosomic module of resistance in a virulent and multiresistant strain. At least, we characterized 3 distinct populations of strains issued from humans, their domesticated animals and wild animals These 3 levels of study of the evolution of strains allowed to go further into the determination of the factors involved in the adapation of the strains of E. coli to their environments in one side, and their relations between their genome, their habitats and their selective pressure, in the other side.PARIS5-BU Méd.Cochin (751142101) / SudocSudocFranceF

Co-Lateral Effect of Octenidine, Chlorhexidine and Colistin Selective Pressures on Four Enterobacterial Species: A Comparative Genomic Analysis

Bacterial adaptation to antiseptic selective pressure might be associated with decreased susceptibility to antibiotics. In Gram-negative bacteria, some correlations between reduced susceptibility to chlorhexidine (CHX) and polymyxins have been recently evidenced in Klebsiella pneumoniae. In the present study, four isolates belonging to distinct enterobacterial species, namely K. pneumoniae, Escherichia coli, Klebsiella oxytoca and Enterobacter cloacae, were submitted to in-vitro selective adaptation to two antiseptics, namely CHX and octenidine (OCT), and to the antibiotic colistin (COL). Using COL as selective agent, mutants showing high MICs for that molecule were recovered for E. cloacae, K. pneumoniae and K. oxytoca, exhibiting a moderate decreased susceptibility to CHX, whereas OCT susceptibility remained unchanged. Using CHX as selective agent, mutants with high MICs for that molecule were recovered for all four species, with a cross-resistance observed for COL, while OCT susceptibility remained unaffected. Finally, selection of mutants using OCT as selective molecule allowed recovery of K. pneumoniae, K. oxytoca and E. cloacae strains showing only slightly increased MICs for that molecule, without any cross-elevated MICs for the two other molecules tested. No E. coli mutant with reduced susceptibility to OCT could be obtained. It was therefore demonstrated that in-vitro mutants with decreased susceptibility to CHX and COL may be selected in E. coli, K. pneumoniae, K. oxytoca and E. cloacae, showing cross-decreased susceptibility to COL and CHX, but no significant impact on OCT efficacy. On the other hand, mutants were difficult to obtain with OCT, being obtained for K. pneumoniae and E. cloacae only, showing only very limited decreased susceptibility in those cases, and with no cross effect on other molecules. Whole genome sequencing enabled deciphering of the molecular basis of adaptation of these isolates under the respective selective pressures, with efflux pumps or lipopolysaccharide biosynthesis being the main mechanisms of adaptation.</jats:p

Co-Lateral Effect of Octenidine, Chlorhexidine and Colistin Selective Pressures on Four Enterobacterial Species: A Comparative Genomic Analysis

Bacterial adaptation to antiseptic selective pressure might be associated with decreased susceptibility to antibiotics. In Gram-negative bacteria, some correlations between reduced susceptibility to chlorhexidine (CHX) and polymyxins have been recently evidenced in Klebsiella pneumoniae. In the present study, four isolates belonging to distinct enterobacterial species, namely K. pneumoniae, Escherichia coli, Klebsiella oxytoca and Enterobacter cloacae, were submitted to in-vitro selective adaptation to two antiseptics, namely CHX and octenidine (OCT), and to the antibiotic colistin (COL). Using COL as selective agent, mutants showing high MICs for that molecule were recovered for E. cloacae, K. pneumoniae and K. oxytoca, exhibiting a moderate decreased susceptibility to CHX, whereas OCT susceptibility remained unchanged. Using CHX as selective agent, mutants with high MICs for that molecule were recovered for all four species, with a cross-resistance observed for COL, while OCT susceptibility remained unaffected. Finally, selection of mutants using OCT as selective molecule allowed recovery of K. pneumoniae, K. oxytoca and E. cloacae strains showing only slightly increased MICs for that molecule, without any cross-elevated MICs for the two other molecules tested. No E. coli mutant with reduced susceptibility to OCT could be obtained. It was therefore demonstrated that in-vitro mutants with decreased susceptibility to CHX and COL may be selected in E. coli, K. pneumoniae, K. oxytoca and E. cloacae, showing cross-decreased susceptibility to COL and CHX, but no significant impact on OCT efficacy. On the other hand, mutants were difficult to obtain with OCT, being obtained for K. pneumoniae and E. cloacae only, showing only very limited decreased susceptibility in those cases, and with no cross effect on other molecules. Whole genome sequencing enabled deciphering of the molecular basis of adaptation of these isolates under the respective selective pressures, with efflux pumps or lipopolysaccharide biosynthesis being the main mechanisms of adaptation

Feedback From Medical and Biology Students on Distance Learning: Focus on a Useful Interactive Software, Wooclap^®

The coronavirus disease 2019 epidemic has prompted all universities to completely change their teaching in a very rapid way around the world. In France, most of the university courses for the year 2020 had to be delivered at distance. This can be an opportunity for some to rethink the place and the form of distance learning (DL). We present here the feedback of students about DL, who answered a questionnaire about classes they followed between October and December 2020. In addition, we evaluated the use and utility of an audience response system promoting interaction. Our results showed that overall the organization and internet connections allowed DL to run smoothly. Interestingly, all students were in favor of the development of a mixed solution, with distant lectures and face-to-face practical lessons. Finally, the use of interactive software such as Wooclap® has proven to be easy to use and to develop for all lessons. </jats:p