DNA barcoding post-larvae can improve the knowledge about fish biodiversity: an example from La Reunion, SW Indian Ocean.

The aim of this study was to demonstrate that fish larvae identified using their COI sequences offer a unique opportunity for improving the knowledge of local fish richness. Fish larvae were sampled at the end of their pelagic phase using light-traps set off the West Coast of La Reunion Island, southwestern Indian Ocean, once per month from October 2014 to March 2015. Among the 5174 larvae caught, 214 morphologically different specimens were selected, 196 successfully barcoded, giving a total of 101 different Barcode Index Numbers (BINs). Among these BINs, 55 had never been recorded in La Reunion exclusive economic zone (EEZ), and 13 were new for the BOLD database. Even if the sampling effort for collecting fish post-larvae during this study was relatively low, it allowed adding at least nine new species to an updated checklist of fishes of La Reunion EEZ.

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.

Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.

"Epidemic clones" of Listeria monocytogenes are widespread and ancient clonal groups.

The food-borne pathogen Listeria monocytogenes is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how "epidemic clones" should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define L. monocytogenes clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the "epidemic clone" denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space.

Optimized Multilocus variable-number tandem-repeat analysis assay and its complementarity with pulsed-field gel electrophoresis and multilocus sequence typing for Listeria monocytogenes clone identification and surveillance.

Populations of the food-borne pathogen Listeria monocytogenes are genetically structured into a small number of major clonal groups, some of which have been implicated in multiple outbreaks. The goal of this study was to develop and evaluate an optimized multilocus variable number of tandem repeat (VNTR) analysis (MLVA) subtyping scheme for strain discrimination and clonal group identification. We evaluated 18 VNTR loci and combined the 11 best ones into two multiplexed PCR assays (MLVA-11). A collection of 255 isolates representing the diversity of clonal groups within phylogenetic lineages I and II, including representatives of epidemic clones, were analyzed by MLVA-11, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). MLVA-11 had less discriminatory power than PFGE, except for some clones, and was unable to distinguish some epidemiologically unrelated isolates. Yet it distinguished all major MLST clones and therefore constitutes a rapid method to identify epidemiologically relevant clonal groups. Given its high reproducibility and high throughput, MLVA represents a very attractive first-line screening method to alleviate the PFGE workload in outbreak investigations and listeriosis surveillance.

Listeria monocytogenes-associated joint and bone infections: a study of 43 consecutive cases.

BACKGROUND: Little is known about Listeria monocytogenes-associated bone and joint infections. Only case reports of this infection have been published. METHODS: Retrospective study of culture-proven bone and joint cases reported to the French National Reference Center for Listeria from 1992 to 2010. RESULTS: Forty-three patients were studied: 61% were men, and the median age was 72 (range, 16-89); 24 patients exhibited comorbidities (56%). Thirty-six patients (84%) had orthopedic implant devices: prosthetic joints (n = 34) or internal fixation (n = 2); the median time after insertion was 9 years (0.1-22). Subacute infection was more frequent (median, 4 weeks [range, 2-100], 74%) than acute infection (<7 days, 23%), with nonspecific clinical features; 45% of patients had no fever. Blood cultures were positive in 3 of 19 cases. Isolate polymerase chain reaction genogrouping revealed 4 patterns: IVb (21 of 42, 50%), IIa (17 of 42, 40%), IIb (2 of 42, 5%), and IIc (2 of 42, 5%). Five groups of strains with similar pulsotype patterns were identified without an epidemiological link. Antibiotics, primarily amoxicillin (80%) with aminoglycosides (48%), were prescribed for a median duration of 15 weeks (range, 2-88). Eighteen patients (50%) underwent prosthesis replacement; all were successful after median follow-up of 10 months (range, 1-75). Five of 13 patients for whom material was not removed had protracted infection despite prolonged antibiotherapy; 3 of these patients later underwent prosthesis replacement with sustained recovery. CONCLUSIONS: Osteoarticular listeriosis primarily involves prosthetic joints and occurs in immunocompromised patients. It requires intensive treatment with antibiotherapy and usually requires implant removal or replacement for cure.

Worldwide distribution of major clones of Listeria monocytogenes.

Listeria monocytogenes is worldwide a pathogen, but the geographic distribution of clones remains largely unknown. Genotyping of 300 isolates from the 5 continents and diverse sources showed the existence of few prevalent and globally distributed clones, some of which include previously described epidemic clones. Cosmopolitan distribution indicates the need for genotyping standardization.

Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1.

The World Health Organization Collaborating Centre for Listeria (WHOCCL) has developed in 2004 a multiplex PCR assay that separates the 4 major Listeria monocytogenes serovars (1/2a, 1/2b, 1/2c, and 4b) into distinct PCR serogroups. A new PCR profile has been recently identified, constituted of amplified DNA fragments of prs, ORF2819, ORF2110 and lmo0737. Here we characterize 22 L. monocytogenes isolates of the WHOCCL collection with this PCR IVb variant 1 (IVb-v1) profile. The 22 isolates belong to the clinically predominant serovar 4b, exhibit 6 distinct pulsed-field gel electrophoresis ApaI/AscI combined profiles, and belong to 2 unrelated multilocus sequence types, indicating that the novel profile does not correspond to a recent clonal emergence. We have updated the WHOCCL serogroup-related PCR typing scheme to include this new profile.

Genomic analysis and comparison of Bordetella pertussis isolates circulating in low and high vaccine coverage areas.

The aim of this study was to analyze Bordetella pertussis isolates circulating, between 1991 and 1995, in Niakhar, Senegal area where the pertussis vaccination coverage was low and to compare them with those circulating in France, before and after introduction of generalized pertussis vaccination for toddlers in 1959. We carried out bacteriological analyses, typing, genotyping and DNA microarray analyses. We found that the isolates circulating in Senegal between 1991 and 1995 are part of the same Pulsed Field Gel Electrophoresis Group, express the same antigens and possess the same gene deletions than isolates circulating in France before the introduction of vaccination, but are different from those circulating in 1991-1995. We confirmed the influence of pertussis vaccination on circulating isolates and that isolates vary with the pertussis cycle.