Guy Prod'hom

Background Empirical antibacterial therapy in hospitals is usually guided by local epidemiologic features reflected by institutional cumulative antibiograms. We investigated additional information inferred by aggregating cumulative antibiograms by type of unit or according to the place of acquisition (i.e. community vs. hospital) of the bacteria. Materials and methods Antimicrobial susceptibility rates of selected pathogens were collected over a 4-year period in an university-affiliated hospital. Hospital-wide antibiograms were compared with those selected by type of unit and sampling time (48 h after hospital admission). Results Strains isolated >48 h after admission were less susceptible than those presumably arising from the community (48 h after admission. When compared to hospital-wide antibiograms, susceptibility rates were lower in the ICU and surgical units for Escherichia coli to amoxicillin-clavulanate, enterococci to penicillin, and Pseudomonas aeruginosa to anti-pseudomonal beta-lactams, and in medical units for Staphylococcus aureus to oxacillin. In contrast, few differences were observed among strains isolated within 48 h of admission. Conclusions Hospital-wide antibiograms reflect the susceptibility pattern for a specific unit with respect to community-acquired, but not to hospital-acquired strains. Antibiograms adjusted to these parameters may be useful in guiding the choice of empirical antibacterial therapy.

Clin Microbiol Infect 2011; 17: 57–62Clin Microbiol Infect 2011; 17: 57–62AbstractPseudomonas aeruginosa is one of the leading nosocomial pathogens in intensive care units (ICUs). The source of this microorganism can be either endogenous or exogenous. The proportion of cases as a result of transmission is still debated, and its elucidation is important for implementing appropriate control measures. To understand the relative importance of exogenous vs. endogenous sources of P. aeruginosa, molecular typing was performed on all available P. aeruginosa isolated from ICU clinical and environmental specimens in 1998, 2000, 2003, 2004 and 2007. Patient samples were classified according to their P. aeruginosa genotypes into three categories: (A) identical to isolate from faucet; (B) identical to at least one other patient sample and not found in faucet; and (C) unique genotype. Cases in categories A and B were considered as possibly exogenous, and cases in category C as possibly endogenous. A mean of 34 cases per 1000 admissions per year were found to be colonized or infected by P. aeruginosa. Higher levels of faucet contamination were correlated with a higher number of cases in category A. The number of cases in category B varied from 1.9 to 20 cases per 1000 admissions. This number exceeded 10/1000 admissions on three occasions and was correlated with an outbreak on one occasion. The number of cases considered as endogenous (category C) was stable and independent of the number of cases in categories A and B. The present study shows that repeated molecular typing can help identify variations in the epidemiology of P. aeruginosa in ICU patients and guide infection control measures.Pseudomonas aeruginosa is one of the leading nosocomial pathogens in intensive care units (ICUs). The source of this microorganism can be either endogenous or exogenous. The proportion of cases as a result of transmission is still debated, and its elucidation is important for implementing appropriate control measures. To understand the relative importance of exogenous vs. endogenous sources of P. aeruginosa, molecular typing was performed on all available P. aeruginosa isolated from ICU clinical and environmental specimens in 1998, 2000, 2003, 2004 and 2007. Patient samples were classified according to their P. aeruginosa genotypes into three categories: (A) identical to isolate from faucet; (B) identical to at least one other patient sample and not found in faucet; and (C) unique genotype. Cases in categories A and B were considered as possibly exogenous, and cases in category C as possibly endogenous. A mean of 34 cases per 1000 admissions per year were found to be colonized or infected by P. aeruginosa. Higher levels of faucet contamination were correlated with a higher number of cases in category A. The number of cases in category B varied from 1.9 to 20 cases per 1000 admissions. This number exceeded 10/1000 admissions on three occasions and was correlated with an outbreak on one occasion. The number of cases considered as endogenous (category C) was stable and independent of the number of cases in categories A and B. The present study shows that repeated molecular typing can help identify variations in the epidemiology of P. aeruginosa in ICU patients and guide infection control measures.

Introduction / objectivesThe incidence of vancomycin-resistant enterococci (VRE) remains sporadic in Switzerland. We report an unprecedented VRE (E.faecium van B) outbreak in a 900-bed tertiary care hospital and describe its molecular epidemiology.MethodsVRE was detected in clinical specimens by standard procedures. Carriage screening was performed by rectal swab. Swabs were inoculated into an enrichment broth and grown on chromogenic VRE agar. Isolates were typed by PFGE.ResultsIn November 2010, a first case of VRE was detected in a urine culture. The investigation identified 3 secondary cases in roommates (asymptomatic carriage). A second clinical case was detected in January 2011. Four secondary cases were identified. Both index cases were previously hospitalized in the same regional hospital. All patients transferred from the regional hospital were screened for VRE. In addition, weekly screening was initiated in patients hospitalized in the epidemic ward.In total, from November 201 ...

Clin Microbiol Infect 2010; 16: 1289–1296Clin Microbiol Infect 2010; 16: 1289–1296AbstractMethicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections worldwide. To differentiate reliably among S. aureus isolates, we recently developed double locus sequence typing (DLST) based on the analysis of partial sequences of clfB and spa genes. In the present study, we evaluated the usefulness of DLST for epidemiological investigations of MRSA by routinely typing 1242 strains isolated in Western Switzerland. Additionally, particular local and international collections were typed by pulsed field gel electrophoresis (PFGE) and DLST to check the compatibility of DLST with the results obtained by PFGE, and for international comparisons. Using DLST, we identified the major MRSA clones of Western Switzerland, and demonstrated the close relationship between local and international clones. The congruence of 88% between the major PFGE and DLST clones indicated that our results obtained by DLST were compatible with earlier results obtained by PFGE. DLST could thus easily be incorporated in a routine surveillance procedure. In addition, the unambiguous definition of DLST types makes this method more suitable than PFGE for long-term epidemiological surveillance. Finally, the comparison of the results obtained by DLST, multilocus sequence typing, PFGE, Staphylococcal cassette chromosome mec typing and the detection of Panton-Valentine leukocidin genes indicated that no typing scheme should be used on its own. It is only the combination of data from different methods that gives the best chance of describing precisely the epidemiology and phylogeny of MRSA.Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infections worldwide. To differentiate reliably among S. aureus isolates, we recently developed double locus sequence typing (DLST) based on the analysis of partial sequences of clfB and spa genes. In the present study, we evaluated the usefulness of DLST for epidemiological investigations of MRSA by routinely typing 1242 strains isolated in Western Switzerland. Additionally, particular local and international collections were typed by pulsed field gel electrophoresis (PFGE) and DLST to check the compatibility of DLST with the results obtained by PFGE, and for international comparisons. Using DLST, we identified the major MRSA clones of Western Switzerland, and demonstrated the close relationship between local and international clones. The congruence of 88% between the major PFGE and DLST clones indicated that our results obtained by DLST were compatible with earlier results obtained by PFGE. DLST could thus easily be incorporated in a routine surveillance procedure. In addition, the unambiguous definition of DLST types makes this method more suitable than PFGE for long-term epidemiological surveillance. Finally, the comparison of the results obtained by DLST, multilocus sequence typing, PFGE, Staphylococcal cassette chromosome mec typing and the detection of Panton-Valentine leukocidin genes indicated that no typing scheme should be used on its own. It is only the combination of data from different methods that gives the best chance of describing precisely the epidemiology and phylogeny of MRSA.

During a 6-year period, we isolated three Abiotrophia defectiva, six Granulicatella adiacens and two G. ‘para-adiacens’ strains from clinical specimens. All A. defectiva strains were isolated from immunocompetent patients with endovascular infections, whereas the Granulicatella spp. strains were isolated from immunosuppressed patients with primary bacteremia. As the capacity of bacteria to adhere to the host extracellular matrix (ECM) has been implicated in the pathogenesis of endovascular infection, we investigated the ability of A. defectiva and Granulicatella spp. isolates to bind different ECM components immobilized in microtiter plates. Adherence tests showed a strong attachment of A. defectiva strains to fibronectin, whereas Granulicatella spp. strains were not adherent. The poor adherence of Granulicatella spp. strains to the ECM could be correlated with a lower propensity to induce endocarditis.

A simple and efficient ligation-mediated PCR (LMPCR) is described for amplifying DNA adjacent to known sequences. The method uses one primer specific for the known sequence and a second specific for a synthetic linker ligated to restricted genomic DNA. Perkin-Elmer AmpliTaq Gold polymerase is used to minimize non-specific primer annealing and amplification. This LMPCR method was successfully applied to isolate DNA sequences flanking mobile elements present in mycobacterial mutants generated by transposon mutagenesis.

Detection of responsible bacteria and determination of their susceptibility to antibiotics are important diagnostic steps for severe infections in intensive care units. This paper reviews for the major types of bacterial infections the indications for molecular tests in comparison to conventional diagnostic approaches. Despite the recent availability of automatic devices and their speed, molecular tests are still of limited use

We investigated tuberculosis transmission during a nine-year period (1988–1996) in an countrywide community-based cohort of HIV-infected persons in Switzerland (the Swiss HIV Cohort Study [SHCS]). We estimated the proportion of tuberculosis cases due to reinfection and relapse, and assessed factors which may increase the risk of tuberculosis transmission. HIV-infected persons were followed prospectively and molecular fingerprinting with insertion sequence (IS) 6110, 36-bp direct repeat, and IS6110-PCR was used to determine M. tuberculosis case clustering. Out of 7999 SHCS participants, 267 persons developed tuberculosis. 158 M. tuberculosis isolates from 138 patients were available for study. Molecular analysis identified 33 (24%) episodes of tuberculosis associated with 12 clusters including 2 to 8 patients. Two patients experienced reinfection, and nine had a relapse. Detailed contact investigation identified definite or possible epidemiological links between 21 of 33 cluster patients (64%). Multivariate logistic regression analysis did not identify any risk marker significantly associated with clustering. During a nine-year period, one fourth of tuberculosis case were grouped in clusters within a selection of 138 HIV-infected patients. This may represent the lowest estimation of recently acquired tuberculosis infection. There were no large institutional on community outbreaks among HIV-infected participants of the Swiss HIV Cohort Study.

Methods: In this prospective study, all blood cultures submitted for mycobacteria detection, taken mainly from HIV-infected patients, were incubated for 12 weeks. The clinical impact of a late positive blood culture result was assessed retrospectively.Methods: In this prospective study, all blood cultures submitted for mycobacteria detection, taken mainly from HIV-infected patients, were incubated for 12 weeks. The clinical impact of a late positive blood culture result was assessed retrospectively.Results: From a total of 750 blood cultures, 68 had a growth index (GI) >10 due to the presence of mycobacteria. Of 545 negative blood cultures with a GI <10 within 12 weeks examined by Ziehl—Neelsen, one bottle revealed acid-fast bacilli further identified as Mycobacterium genavense by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. For six of 39 patients with positive blood cultures, the delay to positivity was > 6 weeks (one M. tuberculosis, three M. genavense, two M. avium intracellulare complex). The prolonged incubation and the systematic terminal Ziehl—Neelsen increased the recovery of M. genavense from 5% to 14.5%. However, for only three patients did the late microbiological result lead to the introduction of antimycobacterial therapy.From a total of 750 blood cultures, 68 had a growth index (GI) >10 due to the presence of mycobacteria. Of 545 negative blood cultures with a GI <10 within 12 weeks examined by Ziehl—Neelsen, one bottle revealed acid-fast bacilli further identified as Mycobacterium genavense by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. For six of 39 patients with positive blood cultures, the delay to positivity was > 6 weeks (one M. tuberculosis, three M. genavense, two M. avium intracellulare complex). The prolonged incubation and the systematic terminal Ziehl—Neelsen increased the recovery of M. genavense from 5% to 14.5%. However, for only three patients did the late microbiological result lead to the introduction of antimycobacterial therapy.Conclusions: Neither a prolonged incubation longer than 6 weeks nor a terminal Ziehl—Neelsen-stained smear of the negative blood cultures at 12 weeks seem to be clinically justified.Neither a prolonged incubation longer than 6 weeks nor a terminal Ziehl—Neelsen-stained smear of the negative blood cultures at 12 weeks seem to be clinically justified.