Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.

INTRODUCTION: There is compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Antibiotics cause profound changes in the microbiome. However, the effect of intrapartum and early-life antibiotics on the maternal intestinal and breast milk microbiome, and the infant oral and intestinal microbiome, and whether effects are only short term or persist long term remain uncertain. METHODS AND ANALYSES: In this prospective cohort study, we will use metagenomic sequencing to determine: (1) the effect of intrapartum antibiotics on the composition of the breast milk, and the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (2) the effect of antibiotic exposure in the first year of life on the composition of the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (3) the effect of disruption of the infant oral and intestinal microbiome on health outcomes and (4) the compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. ETHICS AND DISSEMINATION: The ABERRANT study has been approved by the commission cantonale d'éthique de la recherche sur l'être humain (CER-VD) du Canton de Vaud (#2019-01567). Outcomes will be disseminated through publication and will be presented at scientific conferences. TRIAL REGISTRATION NUMBER: NCT04091282.

Prevalence and quantification of contamination of knitted cotton outer gloves during hip and knee arthroplasty surgery.

INTRODUCTION: Knitted cotton outer gloves offer protection against surgical glove perforation and provide improved grip on instruments. These gloves absorb blood and other fluids during surgery, and may therefore also accumulate contaminating bacteria. To date, there is no published data on microbial contamination of such gloves during surgery. METHODS: Knitted cotton outer gloves used in primary and revision hip and knee arthroplasty from two Swiss hospitals were analysed by quantitative bacteriology. Samples were subjected to sonication and vortexing, followed by membrane filtration of the sonicate. Membranes were incubated under aerobic and anaerobic culture conditions, respectively, for 21 days. Total microbial load for each pair of gloves was determined by colony-forming units (CFU) count. Strain identification was performed with MALDI-TOF. RESULTS: A total of 43 pairs of gloves were collected from continuous series of surgeries. Under aerobic culture conditions, total CFU counts ranged 0-1103, 25 (58%) samples remaining sterile, and 4 (9%) yielding > 100 CFU. Under anaerobic culture conditions, total CFU counts ranged 0-3579, 22 (51%) samples remaining sterile, 6 (14%) yielding > 100 CFU. The only covariate significantly associated with the level of contamination was the provider hospital (p < 0.0001 for aerobic and p = 0.007 for anaerobic cultures). Strain identification revealed only skin commensals, mainly coagulase-negative staphylococci and Propionibacterium spp. CONCLUSION: While contamination of surgical latex gloves is a well-known issue, no study has examined so far contamination of knitted cotton outer gloves. No or very low microbial contamination could be identified in the majority of the knitted cotton outer gloves assayed. However, a relevant proportion showed contamination far higher than estimated minimal thresholds for implant-associated infection. Clinical relevance of these findings remains to be established.

[Vancomycine-resistant enterocci (VRE) : a new reality in our hospitals]. / Entérocoque résistant à la vancomycine (ERV) : une nouvelle réalité dans nos hôpitaux.

Limiting the emergence and spread of multi-resistant bacteria is a global concern and the management of colonized patient represents a real challenge, especially in the hospital setting, where risks of acquisition and transmission are increased. Switzerland is not protected from undesirable trends : for instance, recent outbreaks of vancomycin-resistant enterococci (VRE) have been reported in several hospitals in western Switzerland. Since 2011, more than 250 patients have been tested positive during these outbreak episodes and the molecular analysis of the documented strains shows an unexpected diversity, including both sporadic and epidemic strains. This emerging threat requires strict monitoring, prevention and infection control strategies in our healthcare facilities.

Limiter l'émergence et la diffusion des bactéries multirésistantes (BMR) est une urgence mondiale et la gestion des patients porteurs représente un véritable défi, notamment en milieu hospitalier, où les risques d'acquisition et de transmission de ces germes sont multipliés. La Suisse n'est pas épargnée par ce phénomène. En témoignent les épidémies récentes à entérocoques résistant à la vancomycine (ERV) dans plusieurs hôpitaux de Suisse romande. Depuis 2011, plus de 250 patients ont été dépistés positifs durant ces épisodes et l'analyse moléculaire par séquençage complet de génome montre une diversité inattendue des souches, qu'elles soient sporadiques ou à potentiel épidémique. Cette menace émergente, bien réelle, implique une stratégie de surveillance, prévention et contrôle de l'infection stricte dans nos établissements de soins.

Diagnostic Molecular Mycobacteriology in Regions With Low Tuberculosis Endemicity: Combining Real-time PCR Assays for Detection of Multiple Mycobacterial Pathogens With Line Probe Assays for Identification of Resistance Mutations.

Molecular assays have not yet been able to replace time-consuming culture-based methods in clinical mycobacteriology. Using 6875 clinical samples and a study period of 35months we evaluated the use of PCR-based assays to establish a diagnostic workflow with a fast time-to-result of 1-2days, for 1. detection of Mycobacterium tuberculosis complex (MTB), 2. detection and identification of nontuberculous mycobacteria (NTM), and 3. identification of drug susceptible MTB. MTB molecular-based detection and culture gave concordant results for 97.7% of the specimens. NTM PCR-based detection and culture gave concordant results for 97.0% of the specimens. Defining specimens on the basis of combined laboratory data as true positives or negatives with discrepant results resolved by clinical chart reviews, we calculated sensitivity, specificity, PPV and NPV for PCR-based MTB detection as 84.7%, 100%, 100%, and 98.7%; the corresponding values for culture-based MTB detection were 86.3%, 100%, 100%, and 98.8%. PCR-based detection of NTM had a sensitivity of 84.7% compared to 78.0% of that of culture-based NTM detection. Molecular drug susceptibility testing (DST) by line-probe assay was found to predict phenotypic DST results in MTB with excellent accuracy. Our findings suggest a diagnostic algorithm to largely replace lengthy culture-based techniques by rapid molecular-based methods.