No abstract

Knowledge of archaeal population structure, function and interactions is of great interest for a deeper understanding of the anaerobic digestion step in wastewater treatment process, that represents a bottle neck in the optimization of digesters performance. Although culture-independent techniques have enabled the exploration of archaeal population in such systems, their population dynamics and interactions still require further investigation. In the present study, 2646 almost full archaeal 16S rRNA gene sequences retrieved from 22 anaerobic digesters located worldwide were analyzed and classified into 83 Operational Taxonomic Units (OTUs) for Euryarchaeotes and 2 OTUs for Crenarchaeotes. Among the Euryarchaeotes, Methanosarcinales represent the predominant archaeal population (47.5% of total sequences), followed by the ARC I (WSA2) lineage (25.3%), Methanomicrobiales (19.9%) and Methanobacteriales (1.9%). Theses lineages are predominant in nine, five, two and one digesters respectively. However, the remaining 5 digesters show no predominance of any methanogenic group. According to the predominance of theses lineages, 5 digester profiles were distinguished. This study revealed a clear interaction between the 4 methanogenic lineages. A core of 12 OTUs represented by five, four, two and one OTU for Methanosarcinales, Methanomicrobiales, ARC I and Methanobacteriales respectively were quantitatively abundant in at least 50% of the analyzed digesters. 16S rRNA targeted hybridization oligonucleotide probes targeting the predominant OTUs are being developed to follow their population dynamics under various parameters.

Non-typhoidal Salmonella (NTS) strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibilities of a collection of  Salmonella isolates (n=54) recovered from poultry and bivalve molluscs were performed. The study also investigated the virulence and resistance genes profiling as well as the phylogenetic relationships through PFGE and ERIC/PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella  isolates. siiA ,  sopB ,  cat2 ,  safC ,  sefB and sopE2 genes were present in most (83.32%-100%) of the isolates, while the remaining tested genes ( spvC , spvB, and sopE ) were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%) and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin/clavulanic acid (14.8%), trimethoprim/sulfamethoxazole (9.3%) and ciprofloxacin (5.5%). The results of the present study indicate that S.  Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confers a selective advantage for the evolution of the bacteria which represents an alarming problem for global public health. The genetic study via Pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus PCR (ERIC/PCR) showed the high diversity of the clonal origins of the bacteria and the sources of contamination,and revealed the great capacity of the pathogen to diversify within food-producing animals.