Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus

Background: E.coli ST131 is a globally disseminated clone of multi-drug resistant E. coli responsible for that vast majority of global extra-intestinal E. coli infections. Recent global genomic epidemiological studies have highlighted the highly clonal nature of this group of bacteria, however there appears to be inconsistency in some phenotypes associated with the clone, in particular capsule types as determined by K-antigen testing both biochemically and by PCR. Results: We performed improved quality assemblies on ten ST131 genomes previously sequenced by our group and compared them to a new reference genome sequence JJ1886 to identify the capsule loci across the drug-resistant clone H30Rx. Our data shows considerable genetic diversity within the capsule locus of H30Rx clone strains which is mirrored by classical K antigen testing. The varying capsule locus types appear to be randomly distributed across the H30Rx phylogeny suggesting multiple recombination events at this locus, but that this capsule heterogeneity has little to no effect on virulence associated phenotypes in vitro. Conclusions: Our data provides a framework for determining the capsular genetics of E. coli ST131 and further beyond to ExPEC strains, and highlights how capsular mosaicism may be an important strategy in becoming a successful globally disseminated human pathogen

Oral Health Status Of Handicapped Primary School Pupils In Dar Es Salaam, Tanzania

Background: There is hardly any information regarding oral health status of handicapped primary school pupils in Tanzania. Determination of their oral health status could help in planning sustainable intervention programmes for this disadvantaged group. Objectives: To determine caries and periodontal status and treatment needs of handicapped primary school pupils in Dar es Salaam, Tanzania. Design: A descriptive cross-sectional study. Setting: Uhuru Mchanganyiko and Buguruni special schools, Dar es Salaam. Results: The sample consisted of 179 (55.8%) males and 142 (44.2%) females aged between 7 and 22 years. Majority (71%) were deaf followed by blind (17.8%) and mentally retarded (8.7%). Six (1.9%) pupils were both deaf and blind, while one (0.3%) pupil was blind and mentally retarded. Forty one (12.8%) pupils had at least one decayed deciduous tooth, with the mean (dmfs) ranging from 0.25 to 3.24. The deaf had the highest mean decayed surfaces, followed by the mentally retarded and the blind. There was only one (0.3%) pupil who had a filled deciduous tooth. Thirty three (10.3%) pupils had decayed permanent teeth and 31 (9.7%) had missing permanent teeth. None of the decayed permanent teeth were restored. The blind had the lowest mean deciduous surfaces (DS) scores of between 0 and 1.0. In the mentally retarded group the mean DS ranged from 0.25 to 1.75. About 73.5% of the studied group had bleeding of the gums, with the blind having the highest mean bleeding index scores (p < 0.001) and about 82.8% of the pupils had calculus, with highest mean scores mainly among the blind (p= 0.008). Conclusion: The caries prevalence among handicapped primary school pupils was quite low. However, there was relatively high level of gingival bleeding and calculus. Regarding treatment needs, 23% required dental fillings mainly of one and two surface restorations and 82% required scaling and polishing. Despite these treatment needs these pupils had not received any dental attention. East African Medical Journal Vol. 85 (3) 2008: pp. 113-11

Biotypes of oral Candida albicans isolates in a Tanzanian child population

published_or_final_versio

Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens

A new pathogenicity island carrying an allelic variant of the Subtilase cytotoxin is common among Shiga toxin producing Escherichia coli of human and ovine origin

AbstractSubtilase (SubAB) is a cytotoxin elaborated by some Shiga Toxin (Stx)-producing Escherichia coli (STEC) strains usually lacking the locus of enterocyte effacement (LEE). Two variants of SubAB coding genes have been described: subAB1, located on the plasmid of the STEC O113 98NK2 strain, and subAB2, located on a pathogenicity island (PAI) together with the tia gene, encoding an invasion determinant described in enterotoxigenic E. coli. In the present study, we determined the entire nucleotide sequence of the PAI containing the subAB2 operon, termed Subtilase-Encoding PAI (SE-PAI), and identified its integration site in the pheV tRNA locus. In addition, a PCR strategy for discriminating the two subAB allelic variants was developed and used to investigate their presence in E. coli strains belonging to different pathotypes and in a large collection of LEE-negative STEC of human and ovine origin. The results confirmed that subAB genes are carried predominantly by STEC and showed their presence in 72% and 86% of the LEE-negative strains from human cases of diarrhoea and from healthy sheep respectively. Most of the subAB-positive strains (98%) identified possessed the subAB2 allelic variant and were also positive for tia, suggesting the presence of SE-PAI. Altogether, our observations indicate that subAB2 is the prevalent SubAB-coding operon in LEE-negative STEC circulating in European countries, and that sheep may represent an important reservoir for human infections with these strains. Further studies are needed to assess the role of tia and/or other genes carried by SE-PAI in the colonization of the host intestinal mucosa

Characteristics of the enteroaggregative Shiga toxin/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June 2011

n/

Complete Genome Sequences of Escherichia coli Strains 1303 and ECC-1470 Isolated from Bovine Mastitis

Escherichia coli is the leading causative agent of acute bovine mastitis. Here, we report the complete genome sequence of E. coli O70:H32 strain 1303, isolated from an acute case of bovine mastitis, and E. coli Ont:Hnt strain ECC-1470, isolated from a persistent infection

Open-source genomic analysis of Shiga-toxin–producing E. coli O104:H4

An outbreak caused by Shiga-toxin–producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, these studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance