Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.Fil: Masana, Marcelo Oscar. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimentos; Argentina.Fil: Carbonari, Claudia Carolina. Instituto Nacional de Enfermedades Infecciosas-ANLIS ‘‘Dr. Carlos G. Malbrán’’. Servicio Fisiopatogenia; Argentina.Fil: Fittipaldi, Nahuel. Public Health Ontario. Toronto Laboratories; Canada. University of Toronto. Department of Laboratory Medicine and Pathobiology; Canada.Fil: Teatero, Sarah. Public Health Ontario. Toronto Laboratories; Canada.Fil: Athey, Taryn B. T. Public Health Ontario. Toronto Laboratories; Canada.Fil: Pianciola, Luis. Subsecretaría de Salud de Neuquén. Laboratorio Central; Argentina.Fil: Melano, Roberto G. Public Health Ontario. Toronto Laboratories; Canada. University of Toronto. Department of Laboratory Medicine and Pathobiology; Canada.Fil: Rivas, Marta. Instituto Nacional de Enfermedades Infecciosas-ANLIS ‘‘Dr. Carlos G. Malbrán’’. Servicio Fisiopatogenia; Argentina.Fil: Chinen, Isabel. Instituto Nacional de Enfermedades Infecciosas-ANLIS ‘‘Dr. Carlos G. Malbrán’’. Servicio Fisiopatogenia; Argentina

«Citrobacter rodentium» causes fatal diarrhea through R-spondin 2-mediated activation of Wnt signaling

Acute infectious diarrhea is a serious cause of morbidity and mortality worldwide, in particular among young children in the developing world. Citrobacter rodentium is a mouse-specific pathogen that is widely used as a model for the human-specific diarrheal pathogens enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC). Despite evidence of variability in disease severity and outcome of EPEC and EHEC infection, little is known about the mechanisms that regulate host susceptibility to these organisms. However, the inter-strain differences in susceptibility of mice to C. rodentium can be used to identify genes involved in host response to infection. To this end, we recently identified a major genetic locus within the mouse genome on chromosome 15 that controls mortality during C. rodentium infection. In order to characterize the genetic control of susceptibility to C. rodentium, we first refined the boundaries of the locus of interest using subcongenic mice, which defined a region of 4 Mb containing eight annotated genes. We examined mRNA expression of these genes in colonic tissue in response to infection. Of these genes, R-spondin 2 (Rspo2), an activator of the Wnt/β-catenin signaling pathway, was found to be upregulated by as much as 80-fold in colonic tissue in susceptible mice in response to infection with C. rodentium. We confirmed Rspo2 induction in several other susceptible mouse strains. Rspo2 is an activator of the β-catenin signaling cascade through the canonical Wnt pathway. Thus, we propose that Rspo2 induction in susceptible mice drives a potent Wnt-mediated proliferative response of colonic crypt cells, leading to immature and poorly differentiated colonic epithelium. This work highlights a novel mechanism of susceptibility to bacterium-induced diarrheal disease, and suggests new targets for the treatment of infectious diarrhea.E. coli entero-hémoragique (EHEC) et E. coli entero-pathogenique (EPEC) sont des enterobactéries responsables de gastro-entérites sévères, en particulier chez l'enfant, qui constituent un important problème de santé publique. Néanmoins, les mécanismes physiopathologiques impliqués lors de l'infection par ces pathogènes restent mal connus et aucun traitement spécifique n'est disponible. Citrobacter rodentium est un pathogène naturel des souris, génétiquement proche des EPEC et EHEC, qui possède une même stratégie pathogénique et représente un modèle de choix pour les pathologies humaines. De façon remarquable, dans le modèle murin le fond génétique de l'hôte joue un rôle majeur dans la colite infectieuse: alors que la maladie est généralement non-létale, certaines souches de souris hautement susceptibles meurent de diarrhée aigue. Par une étude génétique de clonage positionnel, notre groupe a récemment identifié sur le chromosome 15 de la souris un locus contrôlant la mortalité suite à l'infection (locus Cri1). Dans ce travail, nous présentons le clonage positionnel du locus Cri1 dans un intervalle de 4 Mb et l'identification du gène Rspo2 comme régulateur de la susceptibilité à l'infection par C. rodentium. Rspo2 est un activateur de la voie de signalisation Wnt qui possède une forte activité mitogénique sur l'épithélium intestinal. Au cours de l'infection, et de façon spécifique aux souches de souris susceptibles, Rspo2 est fortement induit dans la muqueuse du colon, il induit une réponse proliférative exacerbée et la génération d'un épithélium non différentié, caractérisé par des défauts dans l'expression de transporteurs ioniques nécessaire à l'absorption de sel et d'eau. Nos résultats démontrent un nouveau mécanisme critique dans la susceptibilité à l'infection par C. rodentium et suggèrent de nouvelles pistes thérapeutiques contre les bactéries EPEC et EHEC

Serotype IV Sequence Type 468 Group B Streptococcus Neonatal Invasive Disease, Minnesota, USA

To further understand the emergence of serotype IV group B Streptococcus (GBS) invasive disease, we used whole-genome sequencing to characterize 3 sequence type 468 strains isolated from neonates in Minnesota, USA. We found that strains of tetracycline-resistant sequence type 468 GBS have acquired virulence genes from a putative clonal complex 17 GBS donor by recombination

Fluoroquinolone Resistance among Clonal Complex 1 Group B Streptococcus Strains

Fluoroquinolone resistance in group B Streptococcus is increasingly being reported worldwide. Here, we correlated fluoroquinolone resistance with mutations in gyrA, gyrB, parC, and parE genes, identified by mining whole-genome sequencing (WGS) data of 190 clonal complex 1 group B Streptococcus strains recovered from patients with invasive diseases in North America. We report a high prevalence of fluoroquinolone resistance (12%) among GBS strains in our collection. Our approach is the first step towards accurate prediction of fluoroquinolone resistance from WGS data in this opportunistic pathogen.Peer Reviewe

Capsular Switching and Other Large-Scale Recombination Events in Invasive Sequence Type 1 Group B Streptococcus

We report several cases of recombination events leading to capsular switching among sequence type (ST) 1 group B Streptococcus strains. These strains otherwise shared a common genome backbone with serotype V ST1 strains. However, the genomes of ST1 serotype V strains and those of serotypes VI, VII, and VIII strains differed substantially

Genetic Diversity and Antimicrobial Drug Resistance of Serotype VI Group B Streptococcus, Canada

Two genetically dissimilar sequence type 1 clades dominate the serotype VI group B Streptococcus population of strains causing invasive disease in Canada. Isolates of this rare serotype, recovered mainly from adult patients, were all susceptible to penicillin and vancomycin. However, we observed resistance to erythromycin and clindamycin

Determining Streptococcus suis serotype from short-read whole-genome sequencing data

Abstract Background Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to determine S. suis serotypes, but they cannot differentiate between serotypes 1 and 14, and between serotypes 2 and 1/2. Here, we developed a pipeline permitting in silico serotype determination from whole-genome sequencing (WGS) short-read data that can readily identify all 29 S. suis serotypes. Results We sequenced the genomes of 121 strains representing all 29 known S. suis serotypes. We next combined available software into an automated pipeline permitting in silico serotyping of strains by differential alignment of short-read sequencing data to a custom S. suis cps loci database. Strains of serotype pairs 1 and 14, and 2 and 1/2 could be differentiated by a missense mutation in the cpsK gene. We report a 99 % match between coagglutination- and pipeline-determined serotypes for strains in our collection. We used 375 additional S. suis genomes downloaded from the NCBI’s Sequence Read Archive (SRA) to validate the pipeline. Validation with SRA WGS data resulted in a 92 % match. Included pipeline subroutines permitted us to assess strain virulence marker content and obtain multilocus sequence typing directly from WGS data. Conclusions Our pipeline permits rapid and accurate determination of S. suis serotype, and other lineage information, directly from WGS data. By discriminating between serotypes 1 and 14, and between serotypes 2 and 1/2, our approach solves a three-decade longstanding S. suis typing issue

Human Case of Streptococcus suis Disease, Ontario, Canada

We report a case of Streptococcus suis human disease in Ontario, Canada, caused by a serotype 2 strain genotypically similar to those commonly isolated from pigs in North America. Initially, the isolate was misidentified as a viridans group Streptococcus. Human S. suis infections may be underdiagnosed in North America