Biology subjects

Marathe, N. P.

Publications and source records attributed to Marathe, N. P..

5 recordsLinked to original sources

bioRxiv2025

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome

Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) can colonise humans, animals, and various environments, and frequently cause nosocomial and community-acquired infections in humans. While plasmid-borne AMR genes are prevalent in clinical strains, the diversity, distribution, and association of plasmids encoding AMR and virulence across ecological niches remain poorly characterised. Understanding the traits governing successful plasmid transmission within and between ecological niches is critical for developing effective AMR prevention strategies. Here, we characterise the diversity and distribution of KpSC plasmids and identify potential niche associations of AMR, heavy metal resistance, virulence factors, and plasmid clusters. We analysed the plasmidome (i.e. total genetic content attributable to plasmids) of 578 whole-genome sequenced KpSC isolates collected in Norway between 2001-2020 from human (n=453), terrestrial animal (n=102), and marine (n=23) sources. Plasmids from complete hybrid assemblies were annotated and clustered to evaluate the plasmid diversity and content across niches. Additionally, the representativeness of this plasmid collection was determined by clustering with a global collection of 8656 circularised KpSC plasmids. In total, 1415 circularised plasmids were identified and grouped according to rearrangement distance using Pling, resulting in 130 clusters (containing >1 plasmid), of which 36% (n=47) contained plasmids from >1 niche. The plasmids exhibited significant diversity, as 37% (n=524) remained singletons after clustering. AMR and virulence genes existed across diverse clusters and singletons, but predominantly resided on 120-250 kbp conjugative or mobilisable plasmids harbouring various transposable elements. The human niche exhibited a significantly higher prevalence of plasmids with AMR genes compared to animal or marine niches (p<0.001), whereas the animal niche displayed a significantly higher prevalence of virulence-encoding plasmids compared to human or marine niches (p<0.001), which was largely due to an enrichment of iuc3 plasmids in pigs. The high diversity of the KpSC plasmids underscores the dynamic nature of plasmid evolution, driven by horizontal gene transfer, and selective pressures. The presence of variable clusters, marked by high genetic diversity, indicates a dynamic plasmidome capable of rapid adaptation to environmental pressures through the acquisition and rearrangement of accessory genes.

microbiology↗

bioRxiv2024

Identification of clinical carbapenemases, 478 novel β-lactamases and putative seven new bacterial phyla from wastewater contaminated high arctic fjord sediments.

Arctic microbiota is enigmatic and highly underexplored. With the aim of understanding the resistome and microbiota of high-Arctic fjord sediments and the effect of wastewater discharge on sediment microbiota, we analysed sediments using metagenomics. We show presence of 888 clinically relevant antibiotic resistance genes including genes coding resistance against last-resort antibiotics such as carbapenems, colistin, vancomycin, linezolid and tigecycline in sediment microbiota. Using computational models, 478 novel {beta}-lactamases belonging to 217 novel {beta}-lactamases families were revealed in sediment microbiota from Adventfjorden in Svalbard. We identified hosts for 69 novel gene families and showed that these genes are widespread in the Arctic environment. Further, in 644 metagenome-assembled genomes (MAGs) from sediment metagenomes >97% belong to novel taxa, representing seven putative novel phyla. These MAGs encoded important functions like nutrient cycling and methane metabolism etc. Our study demonstrated mixing of human associated bacteria and Arctic sediment microbiota. It provides the first comprehensive dataset of the distribution and diversity of novel microbes and {beta}-lactamases in the high Arctic sediments.

microbiology↗

bioRxiv2024

Identification of Novel FosX Family Determinants from Diverse Environmental Samples

ObjectivesThis study aimed to identify novel fosfomycin resistance genes across diverse environmental samples, ranging in levels of anthropogenic pollution. We focused on fosfomycin resistance, and given its increasing clinical importance, explored the prevalence of these genes within different environmental contexts. MethodsMetagenomic DNA was extracted from wastewater and sediment samples collected from sites in India, Sweden, and Antarctica. Class 1 integron gene cassette libraries were prepared, and resistant clones were selected on fosfomycin-supplemented media. Long-read sequencing was performed, followed by bioinformatics analysis to identify novel fosfomycin resistance genes. The genes were cloned and functionally characterized in E. coli, and the impact of phosphonoformate on the enzymes was assessed. ResultsFour novel fosfomycin resistance genes were identified. Phylogenetic analysis placed these genes within the FosX family, a group of metalloenzymes that hydrolyse fosfomycin without thiol conjugation. The genes were subsequently renamed fosE2, fosI2, fosI3, and fosP. Functional assays confirmed that these genes conferred resistance to fosfomycin in E. coli, with with MIC ranging from 32 g/ml to 256g/ml. Unlike FosA/B enzymes, these FosX-like proteins were resistant to phosphonoformate inhibitory action. A fosI3 homolog was identified in Pseudomonas aeruginosa, highlighting potential clinical relevance. ConclusionsThis study expands the understanding of fosfomycin resistance by identifying new FosX family members across diverse environments. The lack of phosphonoformate inhibition underscores the clinical importance of these poorly studied enzymes, which warrant further investigation, particularly in pathogenic contexts.

microbiology↗

bioRxiv2024

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed. Utilising 3,255 whole-genome sequenced isolates from human, animal and marine sources collected during 2001-2020 in Norway, we showed the KpSC populations in different niches were distinct but overlapping. Notably, human infection isolates showed greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives ([≤]22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. Infection prevention measures are essential to limit transmission within human clinical settings and reduce disease burden. However, as colonisation often precedes infection, preventing transmission that leads to colonisation, e.g. transmission between animals and humans in the community, and in the food chain, could also be beneficial.

microbiology↗

bioRxiv2022

Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics

Pseudomonas aeruginosa is an opportunistic pathogen with increasing incidence of multidrug-resistant strains, including resistance to last-resort antibiotics, such as carbapenems. Resistances are often due to complex interplays of naturally and acquired resistance mechanisms that are enhanced by its remarkably large regulatory network. This study describes the proteomic responses of two carbapenem-resistant P. aeruginosa strains of high-risk clones ST235 and ST395 to subminimal inhibitory concentrations (sub-MICs) of meropenem by identifying differentially expressed proteins and pathways. Strain CCUG 51971, carries a VIM-4 metallo-{beta}-lactamase or classical carbapenemase, and strain CCUG 70744 carries no known acquired carbapenem-resistance genes and exhibits non-classical carbapenem-resistance. Each strain was cultivated with different sub-MICs of meropenem, and analyzed, using quantitative shotgun proteomics, based on tandem mass tag (TMT) isobaric labeling followed by nano-liquid chromatography tandem-mass spectrometry. Exposure of both strains to sub-MICs meropenem resulted in hundreds of differentially expressed proteins, including {beta}-lactamases, proteins associated with transport, peptidoglycan metabolism, cell wall organization, and regulatory proteins. Strain CCUG 51971 showed up-regulation of intrinsic {beta}-lactamases and VIM-4 carbapenemase, while CCUG 70744 exhibited a combination of up-regulated intrinsic {beta}-lactamases, efflux pumps, penicillin-binding proteins and down-regulation of porins. All components of the H1 type VI secretion system were up-regulated in strain CCUG 51971. Enrichment analyses revealed multiple metabolic pathways affected in both strains. Sub-MICs of meropenem cause marked changes in the proteomes of carbapenem-resistant strains of P. aeruginosa exhibiting different resistance mechanisms, involving a wide range of proteins, many uncharacterized, which might play a role in the susceptibility of P. aeruginosa to meropenem.

microbiology↗