Shotgun Metagenomics Unravels the Bacterial Diversity, Resistome Profile and Genetic Exchange in a Tropical Urban Environment

Abstract

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.