Biology subjects

Annavajhala, M. K.

Publications and source records attributed to Annavajhala, M. K..

3 recordsLinked to original sources

bioRxiv2026

Interconnected reservoirs of multidrug-resistant bacteria and plasmids within the hospital built environment

Hospital sinks and wastewater streams are hotspots for contamination and colonization with multidrug-resistant Gram-negative bacteria (MDR-GNB). However, longitudinal studies investigating the population dynamics of environmental MDR-GNB and links between patients and the environment are lacking, especially in non-outbreak settings. Here we aimed to characterize the diversity and abundance of MDR-GNB across the hospital built environment and evaluate their relationship with clinical isolates. We performed nanopore sequencing on MDR-GNB cultured from sink drains (n=523) and wastewater (n=146) at a New York City hospital between March-August 2023. Using comparative genomics and plasmid clustering analyses, we assessed spatial and longitudinal strain and plasmid dynamics and quantified relatedness to historical clinical isolates from the same hospital (n=602). Sink drains (54-73%) and wastewater (100%) demonstrated widespread, longitudinal colonization with MDR-GNB, driven primarily by carbapenem-resistant GNB including opportunistic organisms and Enterobacterales encoding blaKPC. While bacterial colonization was largely niche-specific, we identified both MDR-GNB strains and resistance plasmids that were shared between clinical and environmental sources, as well as differing dynamics between clinical and wastewater versus sink drain samples. This study supports the role of the hospital environment as an important reservoir for clinically-relevant MDR-GNB, but highlights differences across environmental sites which may impact surveillance approaches.

microbiology↗

bioRxiv2022

Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir

Nirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful in reducing hospitalization or death due to COVID-191,2. However, as SARS-CoV-2 has evolved to become resistant to other therapeutic modalities3-9, there is a concern that the same could occur for nirmatrelvir. Here, we have examined this possibility by in vitro passaging of SARS-CoV-2 in increasing concentrations of nirmatrelvir using two independent approaches, including one on a large scale in 480 wells. Indeed, highly resistant viruses emerged from both, and their sequences revealed a multitude of 3CL protease mutations. In the experiment done at a larger scale with many replicates, 53 independent viral lineages were selected with mutations observed at 23 different residues of the enzyme. Yet, several common mutational pathways to nirmatrelvir resistance were preferred, with a majority of the viruses descending from T21I, P252L, or T304I as precursor mutations. Construction and analysis of 13 recombinant SARS-CoV-2 clones, each containing a unique mutation or a combination of mutations showed that the above precursor mutations only mediated low-level resistance, whereas greater resistance required accumulation of additional mutations. E166V mutation conferred the strongest resistance (~100-fold), but this mutation resulted in a loss of viral replicative fitness that was restored by compensatory changes such as L50F and T21I. Structural explanations are discussed for some of the mutations that are proximal to the drug-binding site, as well as cross-resistance or lack thereof to ensitrelvir, another clinically important 3CL protease inhibitor. Our findings indicate that SARS-CoV-2 resistance to nirmatrelvir does readily arise via multiple pathways in vitro, and the specific mutations observed herein form a strong foundation from which to study the mechanism of resistance in detail and to inform the design of next generation protease inhibitors.

microbiology↗

bioRxiv2020

Meta-azotomics of engineered wastewater treatment processes reveals differential contributions of established and novel models of N-cycling

The application of metagenomics and metatranscriptomics to field-scale engineered biological nitrogen removal (BNR) processes revealed a complex N-cycle network (the meta-azotome) therein in terms of microbial structure, potential and extant function. Autotrophic nitrification bore the imprint of well-documented Nitrosomonas and Nitrospira in most systems. However, in select BNR processes, complete ammonia oxidizing bacteria, comammox Nitrospira, unexpectedly contributed more substantially to ammonia oxidation than canonical ammonia oxidizing bacteria, based on metatranscriptomic profiling. Methylotrophic denitrification was distinctly active in methanol-fed reactors but not in glycerol-fed reactors. Interestingly, glycerol metabolism and N-reduction transcript signatures were uncoupled, possibly suggesting the role of other carbon sources in denitrification emanating from glycerol itself or from upstream process reactors. In sum, the meta-azotome of engineered BNR processes revealed both traditional and novel mechanisms of N-cycling. Similar interrogation approaches could potentially inform better design and optimization of wastewater treatment and engineered bioprocesses in general.

systems biology↗