Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers.

The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.

Serratia marcescens outbreak in a neonatal intensive care unit: crucial role of implementing hand hygiene among external consultants.

BACKGROUND: Serratia marcescens represents an important pathogen involved in hospital acquired infections. Outbreaks are frequently reported and are difficult to eradicate. The aim of this study is to describe an outbreak of Serratia marcescens occurred from May to November 2012 in a neonatal intensive care unit, to discuss the control measures adopted, addressing the role of molecular biology in routine investigations during the outbreak. METHODS: After an outbreak of Serratia marcescens involving 14 neonates, all admitted patients were screened for rectal and ocular carriage every two weeks. Extensive environmental sampling procedure and hand sampling of the staff were performed. Antimicrobial susceptibility pattern and molecular analysis of isolates were carried out. Effective hand hygiene measures involving all the external consultants has been implemented. Colonized and infected babies were cohorted. Dedicated staff was established to care for the colonized or infected babies. RESULTS: During the surveillance, 65 newborns were sampled obtaining 297 ocular and rectal swabs in five times. Thirty-four Serratia marcescens isolates were collected: 11 out of 34 strains were isolated from eyes, being the remaining 23 isolated from rectal swabs. Two patients presented symptomatic conjunctivitis. Environmental and hand sampling resulted negative. During the fifth sampling procedure no colonized or infected patients have been identified. Two different clones have been identified. CONCLUSIONS: Ocular and rectal colonization played an important role in spread of infections. Implementation of infection control measures, involving also external specialists, allowed to control a serious Serratia marcescens outbreak in a neonatal intensive care unit.

Severe infections caused by Panton-Valentine leukocidin-positive Staphylococcus aureus in infants: report of three cases and review of literature.

UNLABELLED: We report three cases of severe infections in infants caused by Panton-Valentine leukocidin positive Staphylococcus aureus and evolved with a positive outcome. The literature of Panton-Valentine leukocidin positive Staphylococcus aureus infections in infants is reviewed. CONCLUSION: Our findings suggest that a prompt identification of Panton-Valentine leukocidin positive Staphylococcus aureus and an appropriate therapy can reduce mortality and long-term sequelae. Further research is needed to specify features of Panton-Valentine leukocidin positive Staphylococcus aureus infections in infants.

Nosocomial Rotavirus Gastroenteritis in pediatric patients: a multi-center prospective cohort study.

BACKGROUND: Few data are available on the incidence of nosocomial Rotavirus infections (NRVI) in pediatric hospitals and on their economic impact. The goals of this study were: to evaluate the incidence of NRVI in various Italian pediatric wards during the course of two peak RV seasons; to investigate possible risk factors for NRVI; to estimate the costs caused by NRVI. METHODS: prospective cohort study. POPULATION: All the children under 30 months of age who were admitted without any symptom or diagnosis of gastroenteritis in the pediatric hospitals of Florence, Naples, Brescia and Ancona, Italy, during the winter-spring periods 2006-2007 and 2007-2008. Serial RV rapid tests and clinical monitoring were carried out on the cohort. Telephone interviews were performed from 3 to 5 days after discharge. RESULTS: 520 out of 608 children completed the study (85.6%). The overall incidence of NRVI was 5.3% (CI95% 3.6-7.5), (7.9 per 1,000 days of hospital stay, CI 95% 5.3-11.3). The average duration of hospital stay was significantly longer for children who had NRVI (8.1 days, SD 5.4) than for non-infected children (6.4 days, SD 5.8, difference 1.7 days, p = 0.004). The risk of contracting NRVI increased significantly if the child stayed in hospital more than 5 days, RR = 2.8 (CI95% 1.3-6), p = 0.006. In Italy the costs caused by NRVI can be estimated at 8,019,155.44 Euro per year. 2.7% of the children hospitalized with no gastroenteritis symptoms tested positive for RV. CONCLUSIONS: Our study showed a relevant incidence of NRVI, which can increase the length of the children's stay in hospital. Limiting the number of nosocomial RV infections is important to improve patients' safety as well as to avoid additional health costs.

Use of the gyrB gene to discriminate among species of the Burkholderia cepacia complex.

Bacteria of the Burkholderia cepacia complex (Bcc) are opportunistic pathogens that can cause serious infections in lungs of cystic fibrosis patients. The Bcc comprises at least nine species that have been discriminated by a polyphasic taxonomic approach. In this study, we focused on the gyrB gene, universally distributed among bacteria, as a new target gene to discriminate among the Bcc species. New PCR primers were designed to amplify a gyrB DNA fragment of about 1900 bp from 76 strains representative of all Bcc species. Nucleotide sequences of PCR products were determined and showed more than 400 polymorphic sites with high sequence similarity values from most isolates of the same species. Phylogenetic tree analysis revealed that most of the 76 gyrB sequences grouped, forming clusters, each corresponding to a given Bcc species.

Patient risk of contact with respiratory pathogens from inanimate surfaces in a cystic fibrosis outpatient clinic. A prospective study over a four-year period.

Acquisition of respiratory pathogens such as Pseudomonas aeruginosa (PA) is associated with increased morbidity and mortality in cystic fibrosis (CF). Research on the prevalence of these pathogens on environmental surfaces of a CF Center is scanty, and so far no study has determined what risk CF patients have of coming in contact with them during their visits to the CF Center. This study is aimed at assessing the prevalence of some respiratory pathogens in samples taken systematically during a 4-year period from inanimate surfaces and sinks in a CF Outpatient Clinic, and to estimate the risk that a non-PA colonized CF patient has of contact with PA when visiting the CF Center. Microbiological samples were taken and cultured from the inanimate surfaces and sinks of the Outpatient clinic of a CF Center once a month from 2001 to 2005. Four hundred and sixty environmental specimens were collected: 36.3% were positive for respiratory pathogens (23% of rooms' inert surfaces, 49.5% of sinks). Achromobacter xylosoxidans was found in 0.8% of surface samples. PA was isolated in 22.8% samples. The estimated risk for each non-colonized patient of coming in contact with PA on the surfaces in the Clinic at each visit was 5.4 per thousand (CI95% 0.9-30.1). Genotyping of a sample of environmental PA strains revealed a genetic relation between environmental and clinical isolates in most cases. Micro-organisms relevant for CF patients can be found on inanimate surfaces of a CF Center, although the risk for patients of coming in contact with PA during their visits to the CF center seems low.