Extreme flooding is one of the major risk factors for human health, and it can significantly influence the microbial communities and enhance the mobility of infectious disease agents within the affected areas. The flood crisis in 2018 was one of the severe natural calamities recorded in the southern state of India (Kerala) that significantly affected its economy and ecological habitat. We utilized a combination of shotgun metagenomics and bioinformatics approaches to understand the bacterial profile and the abundance of pathogenic and antibiotic-resistant bacteria in extremely flooded areas of Kuttanad, Kerala (4–10 feet below sea level). Here we report the bacterial profiles of flooded sites that are abundant with virulent and resistant bacteria. The flooded sites were heavily contaminated with faecal contamination indicators such as Escherichia coli and Enterococcus faecalis and multidrug-resistant strains of Pseudomonas aeruginosa, Salmonella typhi/typhimurium, Klebsiella pneumoniae, Vibrio cholerae. The resistome of the flooded sites contains 103 known resistant genes, of which 38% are plasmid-encoded, where most of them are known to be associated with pathogenic bacteria. Our results reveal an overall picture of the bacterial profile and resistome of sites following a devastating flood event, which might increase the levels of pathogens and its associated risks.

Quantitative determination of neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) is paramount in immunodiagnostics, vaccine efficacy testing, and immune response profiling among the vaccinated population. Cost-effective, rapid, easy-to-perform assays are essential to support the vaccine development process and immunosurveillance studies. We describe a bead-based screening assay for S1-neutralization using recombinant fluorescent proteins of hACE2 and SARS-CoV2-S1, immobilized on solid beads employing nanobodies/metal-affinity tags. Nanobody-mediated capture of SARS-CoV-2-Spike (S1) on agarose beads served as the trap for soluble recombinant ACE2-GFPSpark, inhibited by neutralizing antibody. The first approach demonstrates single-color fluorescent imaging of ACE2-GFPSpark binding to His-tagged S1-Receptor Binding Domain (RBD-His) immobilized beads. The second approach is dual-color imaging of soluble ACE2-GFPSpark to S1-Orange Fluorescent Protein (S1-OFPSpark) beads. Both methods showed a good correlation with the gold standard pseudovirion assay and can be adapted to any fluorescent platforms for screening.

Extreme flooding is one of the major risk factors for human health, and it can significantly influence the microbial communities and enhance the mobility of infectious disease agents within its affected areas. The flood crisis in 2018 was one of the severe natural calamities recorded in the southern state of India (Kerala) that significantly affected its economy and ecological habitat. We utilized a combination of shotgun metagenomics and bioinformatics approaches for understanding microbiome disruption and the dissemination of pathogenic and antibiotic-resistant bacteria on flooded sites. Here we report, altered bacterial profiles at the flooded sites having 77 significantly different bacterial genera in comparison with non-flooded mangrove settings. The flooded regions were heavily contaminated with faecal contamination indicators such as Escherichia coli and Enterococcus faecalis and resistant strains of Pseudomonas aeruginosa, Salmonella Typhi/Typhimurium , Klebsiella pneumoniae, Vibrio cholerae and Staphylococcus aureus . The resistome of the flooded sites contains 103 resistant genes, of which 38% are encoded in plasmids, where most of them are associated with pathogens. The presence of 6 pathogenic bacteria and its susceptibility to multiple antibiotics including ampicillin, chloramphenicol, kanamycin and tetracycline hydrochloride were confirmed in flooded and post-flooded sites using traditional culture-based analysis followed by 16S rRNA sequencing. Our results reveal altered bacterial profile following a devastating flood event with elevated levels of both faecal contamination indicators and resistant strains of pathogenic bacteria. The circulation of raw sewage from waste treatment settings and urban area might facilitate the spreading of pathogenic bacteria and resistant genes.