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.

Background SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants. Results Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 49 distinct amino acid substitutions in contact and non-contact amino acid residues. Molecular phylogenetic analysis suggested independent emergence of RBD mutants. Structural mapping of these mutations on the SARS-CoV-2 Wuhan reference strain RBD and structural comparison with RBDs from bat-CoV, SARS-CoV, and pangolin-CoV, all bound to human or mouse ACE2, revealed several changes in the interfacial interactions in all three binding clusters. Interestingly, interactions mediated via N487 residue in cluster-I and Y449, G496, T500, G502 residues in cluster-III remained largely unchanged in all RBD mutants. Further analysis showed that these interactions are evolutionarily conserved in sarbecoviruses which use ACE2 for entry. Importantly, despite extensive changes in the interface, RBD-ACE2 stability and binding affinities were maintained in all the analyzed mutants. Taken together, these findings reveal how SARS-CoV-2 uses its RBD residues to constantly remodel the binding interface. Conclusion Our study broadly signifies understanding virus-host binding interfaces and their alterations during pandemic. Our findings propose a possible interface remodelling mechanism used by SARS-CoV-2 to escape deleterious mutations. Future investigations will focus on functional validation of in-silico findings and on investigating interface remodelling mechanisms across sarbecoviruses. Thus, in long run, this study may provide novel clues to therapeutically target RBD-ACE2 interface for pan-sarbecovirus infections.

SARS-CoV-2, the causative agent of COVID-2019 pandemic is an RNA virus prone to mutations.Information on mutations within the circulating strains of the virus is pivotal to understand disease spread and dynamics. Here, we analyse the mutations associated with 2,954 globally reported high quality genomes of SARS-CoV-2 with special emphasis on genomes of viral strains from India.Molecular phylogenetic analysis suggests that SARS-CoV-2 strains circulating in India form five distinct phyletic clades designated R1-R5. These clades categorize into the previously reported S, G as well as a new unclassified subtype. A detailed analysis of gene encoding the Spike (S) protein in the strains across the globe shows non-synonymous mutations on 54 amino acid residues. Among these, we pinpoint 4 novel mutations in the region that interacts with human ACE2 receptor (RBD). Further in silico molecular docking analyses suggest that these RBD mutations could alter the binding affinity of S-protein with ACE2 that may lead to changes in SARS-CoV-2 infectivity. Strikingly, one of these RBD mutations (S438F) is unique to a subset within the R4 clade suggesting intrinsic S-protein variations in strains currently circulating in India. Together, our findings reveal a unique pattern of SARS-CoV-2 evolution that may alert vaccine and therapeutic development.

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 2 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.

Background The environmental microbiome has a direct influence on human health and disease. Previous reports suggest that urbanization and anthropogenic activities can alter natural microbial flora and potentially spread infectious disease-causing agents by emergence of pathogenic strains of bacteria. The nature of microbes present in urban settings and the flow of genetic elements between environmental and clinically relevant pathogenic bacteria, however, remains largely unknown. Results To unravel the bacterial diversity and resistome profile of multiple hotspot setups of a tropical urban system such as transport hubs, wet markets, hospital surroundings, waste dumps, and urban coastal area (beaches) metagenomics analyses of sediment samples from around Thiruvananthapuram city were done. Our study revealed the presence of 3,735 species belonging to 46 phyla of bacteria and archaea. The phylum Pseudomonadota was the most abundant bacterial community, followed by Bacteriodota and Actinomycetota. The genus Cloacibacterium had the highest overall relative abundance, while Pseudomonas was the most prevalent bacterial genus in hospital surroundings and coastal area (beaches) settings. We identified 291 antimicrobial resistance genes (ARGs) in the urban resistome, conferring resistance to more than 15 drug classes. The hospital settings had the highest number of ARGs across different drug classes. From the culturomics microcosm setups, we reconstructed 62 high-quality metagenome-assembled genomes (MAGs) which shows high resemblance to pathogenic bacterias such as Klebsiella pneumoniae, Escherichia coli and Acinetobacter baumannii etc. The ARGs detected in these genomes include genes encoding antibiotic-modifying enzymes (ArnT, eptA, eptB), beta-lactamase (ampC, ampC1, ampH), transcription regulating proteins (KpnE, KpnF, KpnG), efflux pumps (oqxA, oqxB). Furthermore, eight MAGS belonging to Acinetobacter kookii, Acinetobacter pitti, Acinetobacter baumannii, Acinetobacter gerneri, Escherichia coli, Klebsiella pneumoniae and Klebsiella quasipneumoniae were found to contain virulence factors such as siderophores (acinetobactin, aerobactin, enterobactin etc.), capsule, secretion systems belonging to type III group) (T3SS, TTSS etc) or type II (T2SS), fimbriae (type 3 and I), efflux pump (AdeFGH), or quorum sensing (abaR) associated with pathogenicity. Conclusions The study provides insights into bacterial composition, antimicrobial resistance, and virulence potential in urban environments, highlighting the importance of monitoring and managing antimicrobial resistance in urban ecosystems.