J.P. Pirnay

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.

Analysis of epidemic Pseudomonas aeruginosa isolated by isoelectric focusing of pyoverdine and RAPD-PCR: modern tools for an integrated anti-nosocomial infection strategy in burn wound centres

The Gram-negative bacterium Pseudomonas aeruginosa is an important life-threatening nosocomial pathogen in burn units. In this study we analysed epidemic P. aeruginosa isolates from patients and their hospital environment using two new molecular techniques in order to establish strain relatedness for epidemiological purposes. One technique was pyoverdine typing by isoelectric focusing (PVD-IEF) and the other was a genomic PCR-based fingerprinting technique called random amplification of polymorphic DNA actually referred to as RAPD-PCR. The described short epidemic (6 weeks) included 37 consecutive isolates from 9 different patients as well as two environmental isolates recovered, at the same time, from one of the hydrotherapy facilities. Only two of the three known pyoverdine types of P. aeruginosa could be found. Type I was absent while type II represented 49 per cent and type III, 51 per cent of the isolates. The two consecutive isolates from the environment were both of type III. The RAPD-PCR fingerprinting discriminated four patterns. Profile 1 represented 60 per cent; profile 2, 34 per cent; and profiles 3 and 4 only 3 per cent of the isolates respectively. The environmental isolates also had a RAPD-PCR 1 profile, arguing for the hydrotherapy facility as a possible contamination source. Prompt measures could prevent an outbreak. The study demonstrates the applicability of the techniques in a routine microbiology lab as well as their usefulness, in combination with other techniques, in the fight against nosocomial infections, which are so critical in burn units. Both techniques showed undoubtable evidence of the occurrence of polymicrobial infection of individual patients by P. aeruginosa species. Meanwhile pyoverdine typing by IEF seems suited to studying more profoundly the role of pyoverdines in burns.

Developing an international Pseudomonas aeruginosa reference panel

Pseudomonas aeruginosa is a major opportunistic pathogen in cystic fibrosis (CF) patients and causes a wide range of infections among other susceptible populations. Its inherent resistance to many antimicrobials also makes it difficult to treat infections with this pathogen. Recent evidence has highlighted the diversity of this species, yet despite this, the majority of studies on virulence and pathogenesis focus on a small number of strains. There is a pressing need for a P. aeruginosa reference panel to harmonize and coordinate the collective efforts of the P. aeruginosa research community. We have collated a panel of 43 P. aeruginosa strains that reflects the organisms diversity. In addition to the commonly studied clones, this panel includes transmissible strains, sequential CF isolates, strains with specific virulence characteristics, and strains that represent serotype, genotype or geographic diversity. This focussed panel of P. aeruginosa isolates will help accelerate and consolidate the discovery of virulence determinants, improve our understanding of the pathogenesis of infections caused by this pathogen, and provide the community with a valuable resource for the testing of novel therapeutic agents.

HIV transmission by transplantation of allograft skin: a review of the literature.

The fear of human immunodeficiency virus (HIV) transmission by means of allograft skin has led to a cautious approach to allograft donor selection. However, no irrefutable diagnostic test exists to determine the possible presence of HIV at the time of donation. In order to find ways of improving HIV donor screening practices for skin banks, we review the presence of HIV in human skin, explore the possible transmission of HIV by transplantation of human allograft skin, and discuss the reliability of existing HIV tests. The use of the polymerase chain reaction (PCR) as a sensitive detection system for HIV infection of skin biopsies, in combination with conventional routine HIV blood screening tests; could lower the risk of transmitting HIV to severely burned patients.

Methicillin Resistant Staphylococcus aureus (MRSA) detection at admission and during hospitalisation at the Brussels Burn Centre

Background: Worldwide MRSA infections pose lifethreatening problems among critically ill and elderly. In Belgium the proportion of MRSA/MSSA is 23%, increasing to 35% on Intensive Care Units (ICU). Seen the consequences on morbidity, mortality and cost anti-nosocomial infection strategies are implemented. Collecting and analyzing those data is essential for evaluating and monitoring the situation. Methods: At admission all patients are systematically screened by nasal and peri-anal/or groin region. The swabs are cultured on Chapman medium and consecutively put on Vitek for antibiotic-susceptibility testing. During hospitalization a screening is done two times weekly. Results: From January 2002 till December 2007, 703 patients were admitted at our ICU and 1494 at our Medium Care Unit (MCU). Nasal swabs showed to be the best screening sampling procedure. The mean MRSA positive carriage at ICU admission is 1.5%. An increased trend was observed since 2004 (1 to 4%). At the MCU however a remarkably lower mean admission incidence of 0.5% was observed, with also the same trend for increase since 2004 (0.1 to 0.5). The nosocomially acquired MRSA infection rate is 5% on the ICU and 4% on the MCU. The higher incidence at the ICU admission is probably due to the fact that this patient population includes patients who are referred from another ICU, beside two other risk factors in this population, the age and often a marginal origin from a social-economic lower class. Conclusion: We observe a trend for increase the last 3 years which reflects the presence of MRSA in the community. This increase however is in contrast with the recently reported decrease of MRSA nosocomial infections in the global Belgian hospitalization population. Our nosocomial infection rate stayed at the same level and warrants an improved infection control in the future Reference: European Antibiotic Resistance Surveillance System (EARSS), 2004.