Genome analysis of clinical genotype Vibrio vulnificus isolated from seafood in Mangaluru Coast, India provides insights into its pathogenicity.

Vibrio vulnificus an opportunistic human pathogen native to marine/estuarine environment, is one of the leading causes of death due to seafood consumption and exposure of wounds to seawater worldwide. The present study involves the whole genome sequence analysis of an environmental strain of V. vulnificus (clinical genotype) isolated from seafood along the Mangaluru coast of India. The sequenced genome data was subjected to in-silico analysis of phylogeny, virulence genes, antimicrobial resistance determinants, and secretary proteins using suitable bioinformatics tools. The sequenced isolate had an overall genome length of 4.8 Mb and GC content of 46% with 4400 coding DNA sequences. The sequenced strain belongs to a new sequence type (Multilocus sequence typing) and was also found to branch with a phylogenetic lineage that groups the most infectious strains of V. vulnificus. The seafood isolate had complete genes involved in conferring serum resistance yet showed limited serum resistance. The study identified several genes against the antibiotics that are commonly used in their treatment, highlighting the need for alternative treatments. Also, the secretory protein analysis revealed genes associated with major pathways like ABC transporters, two-component systems, quorum sensing, biofilm formation, cationic antimicrobial peptide (CAMP) resistance, and others that play a critical role in the pathogenesis of the V. vulnificus. To the best of our knowledge, this is the first report of a detailed analysis of the genomic information of a V. vulnificus isolated from the Indian subcontinent and provides evidence that raises public health concerns about the safety of seafood.

Non-clinical isolates of Vibrio parahaemolyticus harbouring traits of potential pathogenicity and fitness: A molecular analysis.

Here we investigated the distribution of virulence and fitness attributes V. parahaemolyticus isolated from marine environment (n = 105). We discovered ∼1% of isolates positive for tdh, 8.57% for trh, and 4.76% had tdh and trh genes. More than 50% of the isolates had pathogenicity islands specific to pandemic clones and secretion systems which are detected partially or entirely. VPaI-1 found in 59.04%; VPaI-4 in 60%; VPaI-5 in 34.28%; VPaI-2 in 99.04%; VPaI-3 in 91.42% and VPaI-6 in 99.04% isolates. Also, 34.28% of the isolates harboured T3SS2 encoding VPaI 7; T3SS1 in 98.09%; T6SS2 in 99.04% isolates and T6SS1 in 60.95% isolates. The cytotoxicity analysis showed a significant effect by causing when infected with trh+ environmental isolates. The expression of the trh, VopC, and VopA genes during infection showed a significant upregulation. This suggests the presence of virulence traits among V. parahaemolyticus that could threaten public health.

Functional insights of antibiotic resistance mechanism in Helicobacter pylori: Driven by gene interaction network and centrality-based nodes essentiality analysis.

Increased antibiotic resistance in Helicobacter pylori (H. pylori), a major human pathogen, constitutes a substantial threat to human health. Understanding the pathophysiology and development of antibiotic resistance can aid our battle with the infections caused by H. pylori. The aim of this study is to discover the high-impact key regulatory mechanisms and genes involved in antimicrobial drug resistance (AMR). In this study, we constructed a functional gene interaction network by integrating multiple sources of data related to antibiotic resistant genes (number-77) from H. pylori. The gene interaction network was assortative, with a hierarchical, scale-free topology enriched in a variety of gene ontology (GO) categories and KEGG pathways. Using an iterative clustering methodology, we identified a number of communities in the AMR gene network that comprised nine genes (sodB, groEL, gyrA, recA, polA, tuf, infB, rpsJ, and gyrB) that were present at the deepest level and hence were key regulators of AMR. Further, an antibiotic-resistant gene network-based centrality analysis revealed superoxide dismutase (sodB) as a bottleneck node in the network. Our findings suggested that sodB is critically enriched in the cellular response to oxidative stress, removal of superoxide radicals, cellular oxidant detoxification processes, cellular component biogenesis, response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process and reactive oxygen species metabolic process. We demonstrated how the sodB, which are involved in the response to reactive oxygen species, urea metabolic process, nitrogen cycle metabolic process, reactive oxygen species metabolic process, regulated by Fur gene/proteins, claim a major authority over regulation and signal propagation in the AMR.

The mutational analysis unveils the distribution of G614 genotype of SARS-CoV-2in different Indian states and its association with case fatality rate of COVID-19

Pan genomic analysis of the global SARS-CoV-2 isolates has resulted in the identification of several regions of increased genetic variation but there is absence of research on its association with the clinical outcome. The present study fills the vacuum and does mutational analysis of genomic sequence of Indian SARS-CoV-2 isolates. Results reveal the existence of non-synonymous G614 spike protein mutation in 61.45% of the total study genome along with three other mutations. Further, temporal variation in the frequencies of G614 genotype in the country is observed. The examination of the probable association of G614 genotype with COVID-19 severity shows that CFR G614 genotype in India is positively and strongly correlated. It appears that the clinical outcome of the COVID-19 cases in India are significantly and adversely affected by the increasing trend in the G614 genotype; which needs to be addressed combining both laboratory experiments and epidemiological investigations.

Occurrence of antibiotic resistance among Gram negative bacteria isolated from effluents of fish processing plants in and around Mangalore.

The presence of antibiotic-resistant bacteria in seafood not only poses a serious health risk for the consumers but also contributes to the spread of these antibiotic-resistant bacteria in the natural environments through the effluents discharged from the fish processing plants. The aims of this study were to isolate Gram-negative bacteria from the effluents of fish processing plants in and around Mangalore, India and to profile their antibiotic resistance pattern. Maximum resistance was seen for ampicillin (40.78%) followed by tetracycline (40.22%) and nitrofurantoin (29.05%). Further, the detection of genes that contribute to antibiotic resistance revealed the presence of sulfonamide resistance genes (sul1 and sul2) and extended spectrum ß-lactamase genes (bla CTX-M, bla TEM) in a few isolates. The presence of such bacteria in fish processing effluents is a matter of great concern because they can contribute significantly to the antibiotic resistance in the natural environment. It is imperative that seafood processing plants follow the safe disposal of effluents in order to reduce or eliminate the antibiotic resistance menace.

Draft Genome Sequence of Multidrug Resistant Salmonella enterica serovar Weltevreden Isolated from Seafood.

Salmonella enterica subsp. enterica serovar Weltevereden is the most frequent serovar isolated from Asia. Here, we report a draft genome sequence of multidrug resistant Salmonella Weltevreden 9 isolated from seafood. Whole-genome of this isolate and annotation will help enhance the understanding of this pathogenic multidrug-resistant serovar.