Prevalence, distribution and evolutionary significance of the IS629 insertion element in the stepwise emergence of Escherichia coli O157:H7

<p>Abstract</p> <p>Background</p> <p>Insertion elements (IS) are known to play an important role in the evolution and genomic diversification of <it>Escherichia coli </it>O157:H7 lineages. In particular, IS<it>629 </it>has been found in multiple copies in the <it>E. coli </it>O157:H7 genome and is one of the most prevalent IS in this serotype. It was recently shown that the lack of O157 antigen expression in two O rough <it>E. coli </it>O157:H7 strains was due to IS<it>629 </it>insertions at 2 different locations in the <it>gne </it>gene that is essential for the O antigen biosynthesis.</p> <p>Results</p> <p>The comparison of 4 <it>E. coli </it>O157:H7 genome and plasmid sequences showed numerous IS<it>629 </it>insertion sites, although not uniformly distributed among strains. Comparison of IS<it>629</it>s found in O157:H7 and O55:H7 showed the presence of at least three different IS<it>629 </it>sub-types. O157:H7 strains carry IS<it>629 </it>elements sub-type I and III whereby the ancestral O55:H7 carries sub-type II. Analysis of strains selected from various clonal groups defined on the <it>E. coli </it>O157:H7 stepwise evolution model showed that IS<it>629 </it>was not observed in sorbitol fermenting O157 (SFO157) clones that are on a divergent pathway in the emergence of O157:H7. This suggests that the absence of IS<it>629 </it>in SFO157 strains probably occurred during the divergence of this lineage, albeit it remains uncertain if it contributed, in part, to their divergence from other closely related strains.</p> <p>Conclusions</p> <p>The highly variable genomic locations of IS<it>629 </it>in O157:H7 strains of the A6 clonal complex indicates that this insertion element probably played an important role in genome plasticity and in the divergence of O157:H7 lineages.</p

Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing

Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems.info:eu-repo/semantics/publishedVersio

Haloargentinum marplatensis gen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)

A facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii⊺, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the genera Lentibacillus and Virgibacillus (94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii⊺ were C16:0 (42.1%) and anteiso-C15:0 (31.2%) and also presented iso-C16:0 (11.0%), anteiso-C17:0 (10.4%) and C18:0 (5.2%). Based on data presented here, strain 11aii⊺ is considered to represent a novel genus and species, for which the name Haloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii⊺ as type strain.Fil: Perez, Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Gomila, Margarita. Universitat de les Illes Balears; EspañaFil: Murialdo, Silvia Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Ingeniería Bioquímica; ArgentinaFil: Ameztoy, Irene Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Gonzalez Escalona, Narjol. Center For Food Safety And Applied Nutrition; Estados UnidosFil: Ramirez, Elida Elvia. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; ArgentinaFil: Yeannes, Maria Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Departamento de Ingeniería Química. Grupo de Investigación en Preservación y Calidad de Alimentos; Argentin

Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago

This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016–2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.The University of the West Indies, St. Augustine Campus Research and Publication Funds Committee.https://www.journals.elsevier.com/poultry-sciencehj2023Production Animal Studie

mcr-Colistin resistance genes mobilized by IncX4, IncHI2, and IncI2 plasmids in Escherichia coli of pigs and white stork in Spain

Colistin has become the last-line antimicrobial for the treatment of multidrug resistant (MDR) Enterobacterales in human medicine. To date, several colistin resistance genes have been described. Of them mcr-1 is disseminated worldwide in Escherichia coli of human and animal origin. The aim of this study was to characterize mcr-mediated resistance plasmids from E. coli of animal origin in Spain. From our strain collection, 70 E. coli of pig origin collected between 2005 and 2014 (10 per year, except for years 2009-2010-2013) were randomly selected and screened for the presence of mcr-genes. Additionally, 20 E. coli isolated in 2011 from white storks (Ciconia ciconia) from the same urban household waste landfill associated colony were also included. Whole genome sequencing of mcr-positive isolates was carried out on a MiSeq (Illumina). Hybrid whole genome sequencing strategy combining nanopore and Illumina technologies were performed in a selection of isolates to close the genomes and plasmids and identify the presence of antimicrobial resistance genes. Minimum inhibitory concentration (MIC) was used to assess the susceptibility to colistin. Mating experiments were carried out to evaluate transferability of the mcr-genes. A total of 19 mcr-1 and one mcr-4 positive isolates were detected, 15 from pigs distributed during the study period, and five from storks collected in 2011. No other mcr-variants were found. The MICs for colistin ranged between 4 and >4 mg/L. High diversity of STs were detected among the mcr-1 positive E. coli isolates, with only ST-10 shared between pigs and white storks. Except for one isolate, all were genotypic and phenotypically MDR, and five of them also harbored cephalosporin resistance genes (bla CTX-M- 14, bla SHV- 12, and three bla CMY- 2). mcr-1 genes were mobilizable by conjugation, associated with IncX4, IncHI2, and IncI2 plasmids. In our study, mcr-1 genes have been circulating in pig farms since 2005 harbored by a variety of E. coli clones. Its persistence may be driven by co-selection since plasmids containing mcr-1 also exhibit resistance to multiple drugs used in veterinary medicine. Furthermore, this is the first report of the presence of mcr-1 gene in isolates from white storks in Spain. This finding highlights the potential importance of wildlife that forage at urban household waste landfills in the transmission and spread of colistin resistance genes.info:eu-repo/semantics/publishedVersio

mcr -Colistin Resistance Genes Mobilized by IncX4, IncHI2, and IncI2 Plasmids in Escherichia coli of Pigs and White Stork in Spain

Colistin has become the last-line antimicrobial for the treatment of multidrug resistant (MDR) Enterobacterales in human medicine. To date, several colistin resistance genes have been described. Of them mcr -1 is disseminated worldwide in Escherichia coli of human and animal origin. The aim of this study was to characterize mcr -mediated resistance plasmids from E. coli of animal origin in Spain. From our strain collection, 70 E. coli of pig origin collected between 2005 and 2014 (10 per year, except for years 2009-2010-2013) were randomly selected and screened for the presence of mcr -genes. Additionally, 20 E. coli isolated in 2011 from white storks (Ciconia ciconia) from the same urban household waste landfill associated colony were also included. Whole genome sequencing of mcr -positive isolates was carried out on a MiSeq (Illumina). Hybrid whole genome sequencing strategy combining nanopore and Illumina technologies were performed in a selection of isolates to close the genomes and plasmids and identify the presence of antimicrobial resistance genes. Minimum inhibitory concentration (MIC) was used to assess the susceptibility to colistin. Mating experiments were carried out to evaluate transferability of the mcr -genes. A total of 19 mcr -1 and one mcr -4 positive isolates were detected, 15 from pigs distributed during the study period, and five from storks collected in 2011. No other mcr -variants were found. The MICs for colistin ranged between 4 and >4 mg/L. High diversity of STs were detected among the mcr-1 positive E. coli isolates, with only ST-10 shared between pigs and white storks. Except for one isolate, all were genotypic and phenotypically MDR, and five of them also harbored cephalosporin resistance genes (bla , bla , and three bla ). mcr -1 genes were mobilizable by conjugation, associated with IncX4, IncHI2, and IncI2 plasmids. In our study, mcr -1 genes have been circulating in pig farms since 2005 harbored by a variety of E. coli clones. Its persistence may be driven by co-selection since plasmids containing mcr -1 also exhibit resistance to multiple drugs used in veterinary medicine. Furthermore, this is the first report of the presence of mcr -1 gene in isolates from white storks in Spain. This finding highlights the potential importance of wildlife that forage at urban household waste landfills in the transmission and spread of colistin resistance genes