The genus Serratia revisited by genomics.

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus.

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5).

Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov.

Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ≥2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous.

Community-wide outbreak of Escherichia coli O157:H7 associated with consumption of frozen beef burgers.

On 24-25 October 2005 a cluster of five haemolytic uraemic syndrome (HUS) cases was reported in southwest France. An investigation was undertaken to identify the outbreak source and implement control measures. Cases were defined as individuals with HUS or diarrhoea with isolation of Escherichia coli O157:H7 in stools or a positive antibody response to E.

Surveillance of hemolytic uremic syndrome in children less than 15 years of age, a system to monitor O157 and non-O157 Shiga toxin-producing Escherichia coli infections in France, 1996-2006.

Background: Since the 1980s, Shiga toxin-producing Escherichia coli (STEC), especially E. coli O157:H7, has been an important cause of food borne disease in industrial countries. In France, as there was no routine screening for STEC in clinical laboratories, enhanced surveillance of hemolytic uremic syndrome (HUS) in children less than 15 years of age was established in 1996 to monitor trends in the incidence of STEC infections.

Identification of a group of shigella-like isolates as Shigella boydii 20.

Infections by Shigella species are an important cause of diarrhoeal disease worldwide. Of 4198 Shigella isolates received by the French National Reference Centre for Escherichia coli and Shigella, 180 from patients with diarrhoea and dysentery in 2000-2004 did not react with any available polyclonal rabbit antisera used to identify the established Shigella serogroups. This study describes the molecular and phenotypic characteristics of these isolates in seroagglutination tests, molecular serotyping (rfb-RFLP and fliC-RFLP), ribotyping, detection of invasivity and enterotoxins genes, and antibiotic sensitivity.

O148 Shiga toxin-producing Escherichia coli outbreak: microbiological investigation as a useful complement to epidemiological investigation.

An outbreak of Shiga toxin-producing Escherichia coli (STEC) O148 infection occurred among wedding attendees in France in June 2002. A retrospective cohort study was performed and ten cases were identified, including two adults with haemolytic uraemic syndrome (HUS). The analytical study revealed that > 80% of affected individuals had eaten lightly roasted mutton and poultry pâté, but only the consumption of pâté tended to be associated with illness (relative risk 3.

Clonal relationship among Vibrio cholerae O1 El Tor strains causing the largest cholera epidemic in Kenya in the late 1990s.

Eighty Vibrio cholerae O1 strains selected to represent the 1998-to-1999 history of the largest cholera epidemic in Kenya were characterized by ribotyping, antimicrobial susceptibility, and random amplified polymorphic DNA patterns. Except for 19 strains from 4 local outbreaks in North Eastern Province along the Somalia border, the other 61 strains from 25 outbreaks occurring in districts scattered around the country were all ribotype B27 and resistant to chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim. The 61 strains showed similar and specific amplified DNA patterns.

Molecular epidemiology of C. diphtheriae strains during different phases of the diphtheria epidemic in Belarus.

Background: The reemergence of epidemic diphtheria in Belarus in 1990s has provided us with important information on the biology of the disease and the diversity of the causative agent Corynebacterium diphtheriae. Molecular investigations were conducted with the aim to analyze the genetic variability of C diphtheriae during the post-epidemic period.

Methods: The biotype and toxigenicity status of 3513 C.

Molecular epidemiology of multidrug-resistant Shigella dysenteriae type 1 causing dysentery outbreaks in Central African Republic, 2003-2004.

Shigella dysenteriae type 1 (Sd1) represents a particular threat in developing countries because of the severity of the infection and its epidemic potential. Antimicrobial susceptibility testing and molecular subtyping by pulsed-field gel electrophoresis (PFGE) and plasmid profiling (PP) of Sd1 isolates collected during two dysentery outbreaks (2013 and 445 cases of bloody diarrhoea) in Central African Republic (CAR) during the period 2003-2004 were reported. Eleven Sd1 comparison strains (CS) acquired by travellers or residents of Africa (n=10) or Asia (n=1) between 1993 and 2003 were also analysed.

Interstitial pulmonary inflammation due to Microbacterium sp. after heart transplantation.

A coryneform bacterium was isolated from the bronchoalveolar aspirate of a patient with interstitial pulmonary inflammation. Commercial systems identified the isolate as Corynebacterium sp. or Aureobacterium sp.

Escherichia coli O157 outbreak associated with fresh unpasteurized goats' cheese.

A family cluster of three cases of Escherichia coli O157 infection was identified in France. Two cases developed haemolytic-uraemic syndrome. The source was fresh unpasteurized goats' cheese, produced by an independent producer.

Value of morphotyping for the characterization of Candida albicans clinical isolates.

Until recently, morphotyping, a method evaluating fringe and surface characteristics of streak colonies grown on malt agar, has been recommended as a simple and unexpensive typing method for Candida albicans isolates. The discriminatory power and reproducibility of Hunter's modified scheme of Phongpaichit's morphotyping has been evaluated on 28 C. albicans isolates recovered from the oral cavity of asymptomatic human immunodeficiency virus-positive subjects, and compared to two molecular typing methods: randomly amplified polymorphic DNA (RAPD) fingerprinting, and contour clamped homogeneous electric field (CHEF) electrophoretic karyotyping.

Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates.

Phylogenetic relationships within the genus Pseudomonas were examined by comparing partial (about 1000 nucleotides) rpoB gene sequences. A total of 186 strains belonging to 75 species of Pseudomonas sensu stricto and related species were studied. The phylogenetic resolution of the rpoB tree was approximately three times higher than that of the rrs tree.

Molecular evolution of the lysine decarboxylase-defective phenotype in Shigella sonnei.

Shigella, the etiological agent of the bacillary dysentery, belongs to the extremely diverse species of Escherichia coli. In the evolutionary route of Shigella from commensal E. coli ancestors towards a pathogenic lifestyle, the critical events have been the acquisition of the pINV plasmid, through horizontal transfer and the inactivation of pre-existing genes.

Investigation of the clonal dissemination of Klebsiella pneumoniae isolates producing extended-spectrum beta-lactamases in a neonatal ward, Sousse, Tunisia.

This study was designed to investigate the spread of extended-spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-Kp) strains in Sousse hospital, during 7-month period by using phenotypic and genotypic markers. A total of 57 clinical isolates of ESBL-Kp, 22 strains recovered from seriously infected neonates and 35 strains recovered from colonized neonates and hospitalized in the neonatal ward of Sousse hospital, Tunisia, was subjected to 99 carbon source utilization tests, ribotyping and pulse-field gel electrophoresis (PFGE) profiles of total genomic DNA. Biotyping, ribotyping and PFGE typing showed that four different clones circulated in the neonatal ward between January and July 1997 and suggested that the epidemic strain belonged to the same biotype, ribotype and PFGE pattern, and was represented by 18 isolates from infected neonates and 28 isolates from colonized neonates.

Characterization of Escherichia coli O157 : H7 isolates causing haemolytic uraemic syndrome in France.

Forty-seven non-epidemic Escherichia coli O157 : H7 isolates causing haemolytic uraemic syndrome in France were characterized. The isolates clustered into 36 clones using PFGE typing. All the isolates harboured eae and one or more copies of stx2 and belonged to phylogenetic group D.

Molecular typing of Agrobacterium species isolates from catheter-related bloodstream infections.

Agrobacterium isolates from intravenous catheters of three hospitalized patients were initially identified as A. tumefaciens, but inability to produce 3-ketolactose revealed that two of them were A. vitis.

Case management of a multidrug-resistant Shigella dysenteriae serotype 1 outbreak in a crisis context in Sierra Leone, 1999-2000.

From December 1999 to the end of February 2000, 4218 cases of dysentery were reported in Kenema district, southeastern Sierra Leone, by a Médecins Sans Frontières team operating in this region. Shigella dysenteriae serotype 1 was isolated from the early cases. The overall attack rate was 7.

Endemic, epidemic clone of Salmonella enterica serovar typhi harboring a single multidrug-resistant plasmid in Vietnam between 1995 and 2002.

Salmonella enterica serovar Typhi strains resistant to ampicillin, chloramphenicol, tetracyclines, streptomycin, and cotrimoxazole, isolated from sporadic cases and minor outbreaks in Vietnam between 1995 and 2002, were typed and compared. Plasmid fingerprinting, Vi bacteriophage typing, XbaI pulsed-field gel electrophoresis, and PstI ribotyping showed that endemic, epidemic multidrug-resistant typhoid fever was due, for at least 74.1% of the isolates, to one or two clones of serovar Typhi harboring a single resistance plasmid.

New group D streptococcal species.

Background & Objectives: The heterogeneity of group D streptococci led to the identification of various biotypes of Streptococcus equinus and Streptococcus bovis and to the description of new species. The objective of the present study was to improve the phenotypic delineation between species and to clarify their respective phylogenetic position.

Methods: Physiological and genomic analyses were carried out in 84 representative strains of the group D streptococci.

Outbreak of Pseudomonas putida bacteraemia in a neonatal intensive care unit.

During the period of 9-27 March 2001, Pseudomonas putida strains were recovered from 10 neonates hospitalized in the neonatal intensive care unit of Farhat Hached Hospital, Sousse (Tunisia). Seven neonates developed bacteraemia, and three had an umbilical catheter-related infection (without bacteraemia). A total of 18 isolates were cultured from blood (N = 11) and catheters (N = 7).