Region-specific genomic signatures of multidrug-resistant Helicobacter pylori isolated from East and South India.

Helicobacter pylori is a ubiquitous bacterium and contributes significantly to the burden of chronic gastritis, peptic ulcers, and gastric cancer across the world. Adaptive phenotypes and virulence factors in H. pylori are heterogeneous and dynamic. However, limited information is available about the molecular nature of antimicrobial resistance phenotypes and virulence factors of H. pylori strains circulating in India. In the present study, we analyzed the whole genome sequences of 143 H. pylori strains, of which 32 are isolated from two different regions (eastern and southern) of India. Genomic repertoires of individual strains show distinct region-specific signatures. We observed lower resistance phenotypes and genotypes in the East Indian (Kolkata) H. pylori isolates against amoxicillin and furazolidone antibiotics, whereas higher resistance phenotypes to metronidazole and clarithromycin. Also, at molecular level, a greater number of AMR genes were observed in the east Indian H. pylori isolates as compared to the southern Indian isolates. From our findings, we suggest that metronidazole and clarithromycin antibiotics should be used judicially in the eastern India. However, no horizontally acquired antimicrobial resistance gene was observed in the current H. pylori strains. The comparative genome analysis shows that the number of genes involved in virulence, disease and resistance of H. pylori isolated from two different regions of India is significantly different. Single-nucleotide polymorphisms (SNPs) based phylogenetic analysis distinguished H. pylori strains into different clades according to their geographical locations. Conditionally beneficial functions including antibiotic resistance phenotypes that are linked with faster evolution rates in the Indian isolates.

Identification of novel adenovirus genotype 90 in children from Bangladesh.

Novel adenovirus genotypes are associated with outbreaks of disease, such as acute gastroenteritis, renal disease, upper respiratory tract infection and keratoconjunctivitis. Here, we identify novel and variant adenovirus genotypes in children coinfected with enterotoxigenic Escherichia coli, in Bangladesh. Metagenomic sequencing of stool was performed and whole adenovirus genomes were extracted. A novel species D virus, designated genotype 90 (P33H27F67) was identified, and the partial genome of a putative recombinant species B virus was recovered. Furthermore, the enteric types HAdV-A61 and HAdV-A40 were found in stool specimens. Knowledge of the diversity of adenovirus genomes circulating worldwide, especially in low-income countries where the burden of disease is high, will be required to ensure that future vaccination strategies cover the diversity of adenovirus strains associated with disease.

Lechevalieria atacamensis sp. nov., Lechevalieria deserti sp. nov. and Lechevalieria roselyniae sp. nov., isolated from hyperarid soils.

The taxonomic positions of three Lechevalieria-like strains isolated from hyperarid soils of the Atacama Desert, Chile, were established by using a polyphasic approach. The organisms had chemical and morphological properties consistent with their classification in the genus Lechevalieria. They formed a distinct subclade in the Lechevalieria 16S rRNA gene clade and were most closely related to the type strain of Lechevalieria xinjiangensis. DNA-DNA relatedness data showed that each of the isolates and Lechevalieria xinjiangensis DSM 45081(T) belong to distinct genomic species. The new isolates and the type strains of recognized Lechevalieria species were readily distinguished based on a number of phenotypic properties. A combination of the genotypic and phenotypic data showed that the three isolates represent three novel species of the genus Lechevalieria. The names proposed for these taxa are Lechevalieria atacamensis sp. nov. (type strain C61(T) =CGMCC 4.5536(T) =NRRL B-24706(T)), Lechevalieria deserti sp. nov. (type strain C68(T) =CGMCC 4.5535(T) =NRRL B-24707(T)) and Lechevalieria roselyniae sp. nov. (type strain C81(T) =CGMCC 4.5537(T) =NRRL B-24708(T)).