Vincent Cattoir

OBJECTIVES: WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. METHODS: The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. RESULTS: Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. CONCLUSIONS: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

BACKGROUND: Three anatomical sites are commonly used to insert central venous catheters, but insertion at each site has the potential for major complications. METHODS: In this multicenter trial, we randomly assigned nontunneled central venous catheterization in patients in the adult intensive care unit (ICU) to the subclavian, jugular, or femoral vein (in a 1:1:1 ratio if all three insertion sites were suitable [three-choice scheme] and in a 1:1 ratio if two sites were suitable [two-choice scheme]). The primary outcome measure was a composite of catheter-related bloodstream infection and symptomatic deep-vein thrombosis. RESULTS: A total of 3471 catheters were inserted in 3027 patients. In the three-choice comparison, there were 8, 20, and 22 primary outcome events in the subclavian, jugular, and femoral groups, respectively (1.5, 3.6, and 4.6 per 1000 catheter-days; P=0.02). In pairwise comparisons, the risk of the primary outcome was significantly higher in the femoral group than in the subclavian group (hazard ratio, 3.5; 95% confidence interval [CI], 1.5 to 7.8; P=0.003) and in the jugular group than in the subclavian group (hazard ratio, 2.1; 95% CI, 1.0 to 4.3; P=0.04), whereas the risk in the femoral group was similar to that in the jugular group (hazard ratio, 1.3; 95% CI, 0.8 to 2.1; P=0.30). In the three-choice comparison, pneumothorax requiring chest-tube insertion occurred in association with 13 (1.5%) of the subclavian-vein insertions and 4 (0.5%) of the jugular-vein insertions. CONCLUSIONS: In this trial, subclavian-vein catheterization was associated with a lower risk of bloodstream infection and symptomatic thrombosis and a higher risk of pneumothorax than jugular-vein or femoral-vein catheterization. (Funded by the Hospital Program for Clinical Research, French Ministry of Health; ClinicalTrials.gov number, NCT01479153.).

OBJECTIVES: To develop a rapid and reliable single-tube-based PCR technique for detecting simultaneously the plasmid-mediated quinolone resistance qnrA, qnrB and qnrS genes. METHODS: After multiple alignments, primers were designed to detect known qnr variants (six for qnrA-, six for qnrB- and two for qnrS-like genes). They were used for screening a collection of 64 expanded-spectrum beta-lactamase (ESBL)-producing enterobacterial isolates from Kuwait, collected from 2002 to 2004, as ESBL genes have been often associated with qnr genes. Sequencing was performed to identify qnr and associated ESBL genes. RESULTS: In optimized conditions, all positive controls (used separately or mixed) confirmed the specificity of the PCR primers. Out of 64 isolates, only 3 isolates were positive for a qnrB-like gene (4.7%), whereas no qnrA-like and qnrS-like gene was detected. A qnrB2 gene was detected in an Enterobacter cloacae K34 (SHV-12+) isolate, whereas qnrB1-like (termed qnrB7) and qnrB6-like (termed qnrB8) genes were identified from E. cloacae K37 (SHV-12+) and Citrobacter freundii K70 (VEB-1b+) isolates, respectively. CONCLUSIONS: We report here a fast and reliable technique for rapid screening of qnr-positive strains to be used for epidemiological surveys. A low prevalence of Qnr determinants among ESBL-producing Enterobacteriaceae was identified in the study with Kuwaiti isolates.

Phages and cancer immunity Gut bacteria are involved in the education of T cell immune responses, and the intestinal ecosystem influences anticancer immunity. Fluckiger et al. report microbial antigens that might cross-react with antigens associated with tumor cells. They found that a type of intestinal bacteria called enterococci harbor a bacteriophage that modulates immune responses. In mouse models, administration of enterococci containing the bacteriophage boosted T cell responses after treatment with chemotherapy or programmed cell death protein 1 (PD-1) blockade. In humans, the presence of the bacteriophage was associated with improved survival after PD-1 immunotherapy. A fraction of human T cells specific for naturally processed melanoma epitopes appeared to be able to recognize microbial peptides. This “molecular mimicry” may represent cross-reactivity between tumors and microbial antigens. Science , this issue p. 936