Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.

OBJECTIVES: To investigate the risk of colonization with ESBL-producing Escherichia coli (ESBL-Ec) in humans in Vietnam associated with non-intensive chicken farming. METHODS: Faecal samples from 204 randomly selected farmers and their chickens, and from 306 age- and sex-matched community-based individuals who did not raise poultry were collected. Antimicrobial usage in chickens and humans was assessed by medicine cabinet surveys. WGS was employed to obtain a high-resolution genomic comparison between ESBL-Ec isolated from humans and chickens. RESULTS: The adjusted prevalence of ESBL-Ec colonization was 20.0% (95% CI 10.8%-29.1%) and 35.2% (95% CI 30.4%-40.1%) in chicken farms and humans in Vietnam, respectively. Colonization with ESBL-Ec in humans was associated with antimicrobial usage (OR = 2.52, 95% CI = 1.08-5.87) but not with involvement in chicken farming. blaCTX-M-55 was the most common ESBL-encoding gene in strains isolated from chickens (74.4%) compared with blaCTX-M-27 in human strains (47.0%). In 3 of 204 (1.5%) of the farms, identical ESBL genes were detected in ESBL-Ec isolated from farmers and their chickens. Genomic similarity indicating recent sharing of ESBL-Ec between chickens and farmers was found in only one of these farms. CONCLUSIONS: The integration of epidemiological and genomic data in this study has demonstrated a limited contribution of non-intensive chicken farming to ESBL-Ec colonization in humans in Vietnam and further emphasizes the importance of reducing antimicrobial usage in both human and animal host reservoirs.

Development of molecular tools for the detection of freshwater diatoms.

This study was undertaken to develop a reliable and reproducible procedure for the detection and quantitative determination of diatoms in environmental samples. A comparative study of seven different DNA extraction kits was carried out to establish conditions for analysis of diatom containing samples. The best performers were identified using both standard and real-time PCR. We show that the yield of diatom DNA is generally quite low when using commercially available extraction kits; in addition, a new protocol was devised to obtain samples suitable for DNA amplification without the need to perform all the steps required for DNA extraction. This method was tested on environmental samples spiked, in a wide range of total cell mass, with the rarely occurring diatom Neidium affine together with a highly species-specific oligonucleotide designed on the small subunit (SSU) rRNA gene. Thus, we propose a fast and effective procedure that, combined with the use of species-specific oligonucleotide probes can detect minute amounts of a spiked diatom within a complex diatom community. This study provides experimental conditions for a fast and accurate detection of diatoms, and demonstrates the feasibility of the use of molecular tools in the evaluation of water quality.

Diatom quantification and their distribution with salinity brines in coastal sediments of Terra Nova Bay (Antarctica).

Benthic diatoms represent an important element of global nutritional productivity; to raise attention on their role, which is often neglected due to analytical difficulties, surface (1 cm top layer) coastal sediments from Gerlache inlet to Penguin Bay at Terra Nova Bay were collected and stored at -20 °C. DNA amplification by real-time PCR, based on diatom-specific oligonucleotide primers designed on small-subunit rRNA (SSU rRNA), was performed in addition to diatom conventional cell counting and spectrophotometric determination of photo-pigments. Moreover, cations and anions were determined in sediments with the aim to identify factors involved in the control of diatom abundance. Diatom distribution was found quite heterogeneous displaying significant differences from site to site. The salinity in sediments ranged from 45.1 at Gerlache inlet to 76.2 at Penguin Bay and it was correlated with cell abundance, biodiversity, amount of pigments and amplified DNA. The dominant species, Fragilariopsis curta, was associated to sediment salinity brines.