International audience1. The spread of antimicrobial resistance is of major concern for human health and leads togrowing economic costs. While it is increasingly hypothesized that wildlife could play animportant role in antimicrobial-resistant bacteria dynamics, empirical data remain scarce.2. The present work builds on a systematic review of the available data in order to highlightthe main information we have and to suggest research pathways that should be followed ifwe aim to fill the gaps in our current knowledge.3. To achieve this goal, we address four questions: (i) Which resistant bacteria are the mostfrequently observed in wildlife? (ii) How are resistant bacteria exchanged between wildlife andthe other hosts involved? (iii) In which habitats are those resistant bacteria found? (iv) Areresistances associated with certain ecological traits of the host?4. Synthesis and applications. We highlight the strong link existing between the impact ofhuman activities on natural habitats and the carriage of antimicrobial-resistant bacteria bywildlife. Furthermore, we underline that omnivorous, anthropophilic and carnivorous speciesare at high risk of being carriers and potentially spreaders of antimicrobial-resistant bacteria.Identifying among those groups key sentinel species may be of particular interest to implementecosystem contamination surveillance. Finally, we discuss possible exchange routes forantimicrobial-resistant bacteria between humans and wildlife. Considering that water is ofmajor importance in those exchanges, a critical way to control antimicrobial resistance spreadmay be to limit aquatic environment contamination by antimicrobial-resistant bacteria andantibiotics

We have identified a clonal complex of Mycobacterium bovis present at high frequency in cattle in population samples from several sub-Saharan west-central African countries. This closely related group of bacteria is defined by a specific chromosomal deletion (RDAf1) and can be identified by the absence of spacer 30 in the standard spoligotype typing scheme. We have named this group of strains the African 1 (Af1) clonal complex and have defined the spoligotype signature of this clonal complex as being the same as the M. bovis BCG vaccine strain but with the deletion of spacer 30. Strains of the Af1 clonal complex were found at high frequency in population samples of M. bovis from cattle in Mali, Cameroon, Nigeria, and Chad, and using a combination of variable-number tandem repeat typing and spoligotyping, we show that the population of M. bovis in each of these countries is distinct, suggesting that the recent mixing of strains between countries is not common in this area of Africa. Strains with the Af1-specific deletion (RDAf1) were not identified in M. bovis isolates from Algeria, Burundi, Ethiopia, Madagascar, Mozambique, South Africa, Tanzania, and Uganda. Furthermore, the spoligotype signature of the Af1 clonal complex has not been identified in population samples of bovine tuberculosis from Europe, Iran, and South America. These observations suggest that the Af1 clonal complex is geographically localized, albeit to several African countries, and we suggest that the dominance of the clonal complex in this region is the result of an original introduction into cows naïve to bovine tuberculosis.

To study the dynamics of bovine tuberculosis (bTB) in France, 4,654 M. bovis strains isolated mainly from livestock and wildlife since 1978 were characterized by spoligotyping and MLVA based on MIRU-VNTR. In our study spoligotyping allowed the discrimination of 176 types although 3 spoligotypes are predominant and account for more than half of the total strain population: SB0120 (26%), SB0134 (11%) and SB0121 (6%). In addition, 11% of the isolates, principally from Southern France, showing close spoligotypes and MIRU-VNTR types have been gathered in a family designated as the “F4-family”. MLVA typing allowed extensive discrimination, particularly for strains with predominant spoligotypes, with a total of 498 genotypes, several of which were highly regionalized. The similarity of the strains’ genetic relationships based on spoligotyping and MIRU-VNTR markers supports the co-existence of different clonal populations within the French M. bovis population. A genetic evolution of the strains was observed both geographically and in time. Indeed, as a result of the reduction of bTB due to the national control campaigns, a large reduction of the strains’ genetic variability took place in the last ten years. However, in the regions were bTB is highly prevalent at present, cases in both livestock and in wildlife are due to the spread of unique local genotype profiles. Our results show that the highly discriminating genotyping tools used in this study for molecular studies of bTB are useful for addressing pending questions, which would lead to a better insight into the epidemiology of the disease, and for finding proper solutions for its sustainable control in France.

BackgroundNothing is known about the epidemiology and resistance mechanisms of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) in Burkina Faso. The objective of this study was to determine ESBL-PE prevalence and to characterize ESBL genes in Burkina Faso.MethodsDuring 2 months (June-July 2014), 1602 clinical samples were sent for bacteriologic investigations to the microbiology laboratories of the tree main hospitals of Burkina Faso. Isolates were identified by mass spectrometry using a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) BioTyper. Antibiotic susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method.ResultsESBL-PE frequency was 58 % (179 strains among the 308 Enterobacteriaceae isolates identified in the collected samples; 45 % in outpatients and 70 % in hospitalized patients). The CTX-M-1 group was dominant (94 %, CTX-M-15 enzyme), followed by the CTX-M-9 group (4 %). ESBL producers were more often found in E. coli (67.5 %) and Klebsiella pneumoniae (26 %) isolates. E. coli isolates (n = 202; 60 % of all Enterobacteriaceae samples) were distributed in eight phylogenetic groups (A = 49, B1 = 15, B2 = 43, C = 22, Clade I = 7, D = 37, F = 13 and 16 unknown); 22 strains belonged to the sequence type ST131. No association between a specific strain and ESBL production was detected.ConclusionsThis report shows the alarming spread of ESBL genes in Burkina Faso. Public health efforts should focus on education (population and healthcare professionals), surveillance and promotion of correct and restricted antibiotic use to limit their dissemination.

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Five Listeria monocytogenes isolates (CLIP 21369, CLIP 73298, CLIP 74811, CLIP 75679, and CLIP 79372) were found to be resistant to fluoroquinolones during the screening for antibiotic resistance of 488 L. monocytogenes isolates from human cases of listeriosis in France. On the basis of a fourfold or greater decrease in the ciprofloxacin MIC in the presence of reserpine, fluoroquinolone resistance was attributed to active efflux of the drugs. The lde gene (Listeria drug efflux; formerly lmo2741) encodes a 12-transmembrane-segment putative efflux pump belonging to the major facilitator superfamily of secondary transporters that displayed 44% identity with PmrA from Streptococcus pneumoniae. Insertional inactivation of the lde gene in CLIP 21369 indicated that the corresponding protein was responsible for fluoroquinolone resistance and was involved in the level of susceptibility to dyes such as ethidium bromide and acridine orange.Listeria monocytogenes is widely distributed in the environment and can cause serious human infections, such as bacteremia and central nervous system infections, primarily in neonates and immunocompromised adults, and abortions (22). Food-borne transmission is recognized as the main route of acquisition of the infection during epidemic and sporadic listerioses (3, 18). Listeriosis differs from most food-borne diseases by its high fatality rate (20 to 30% of cases), despite the administration of appropriate antibiotics (3, 9). L. monocytogenes is generally susceptible to a wide range of antibiotics but is not susceptible to cephalosporins and fosfomycin (8). However, during the last few years, increasing numbers of strains resistant to one or more antibiotics have been reported (1,2,8,11,19,20).Although indications for the use of fluoroquinolones do not include listeriosis, they can, due to their increasing use for other pathologies such as respiratory tract infections, select resistant Listeria. In gram-positive bacteria, resistance usually results from mutational alterations in the so-called quinolone resistance-determining regions (QRDRs) of the intracellular targets of fluoroquinolones, the type II DNA topoisomerases gyrase and topoisomerase IV, or active export of the drugs via efflux pumps (12). We have detected ciprofloxacin-resistant L. monocytogenes clinical isolates and characterized the efflux pump involved in resistance.(An initial report of this work was presented at the 41st Interscience Conference on Antimicrobial Agents and Chemotherapy [S. Godreuil, M. Galimand, G. Gerbaud, and P. Courvalin, Abstr. 41st Intersci. Conf. Antimicrob. Agents Chemother., abstr. UL-11, 2001].) MATERIALS AND METHODSStrains, plasmids, and growth conditions. Screening of 488 L. monocytogenes isolates responsible for human listeriosis in France for resistance to fluoroquinolones was carried out on brain heart infusion agar (Difco Laboratories, Detroit, Mich.) containing 4 g of ciprofloxacin per ml. Strains that were found to be resistant and susceptible L. monocytogenes EGD were studied ( Table 1)....

The ANRS (Agence Nationale de Recherche sur le Sida) 12229 PAANTHER (Pediatric Asian African Network for Tuberculosis and HIV Research) 01 study is registered at ClinicalTrials.gov (NCT01331811).

Rearrangements of the anaplastic lymphoma kinase (ALK) gene in non-small cell lung cancer (NSCLC) represent a novel molecular target in a small subset of tumors. Although ALK rearrangements are usually assessed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), molecular approaches have recently emerged as relevant alternatives in routine laboratories. Here, we evaluated the use of two different amplicon-based next-generation sequencing (NGS) methods (AmpliSeq and Archer®FusionPlex®) to detect ALK rearrangements, and compared these with IHC and FISH. A total of 1128 NSCLC specimens were screened using conventional analyses, and a subset of 37 (15 ALK-positive, and 22 ALK-negative) samples were selected for NGS assays. Although AmpliSeq correctly detected 25/37 (67.6%) samples, 1/37 (2.7%) and 11/37 (29.7%) specimens were discordant and uncertain, respectively, requiring further validation. In contrast, Archer®FusionPlex® accurately classified all samples and allowed the correct identification of one rare DCTN1-ALK fusion, one novel CLIP1-ALK fusion, and one novel GCC2-ALK transcript. Of particular interest, two out of three patients harboring these singular rearrangements were treated with and sensitive to crizotinib. These data show that Archer®FusionPlex® may provide an effective and accurate alternative to FISH testing for the detection of known and novel ALK rearrangements in clinical diagnostic settings.