Luke Diorio-Toth
Program: Computational and Systems Biology
Current advisor: Gautam Dantas, PhD
Undergraduate university: Carnegie Mellon University
Research summary
Microbes are everywhere. They live inside and on top of our bodies; they live in the natural environment as well as the environments we build for ourselves. Our interactions with those habitats affects those microbes, and negative perturbations to those habitats can promote selection for harmful bacteria. Perhaps the most serious risk we face is the increase in prevalence of antibiotic-resistant bacteria. Since the introduction of antibiotics in the mid-20th century, resistance in agricultural and clinical settings has increased, leading to an increase in morbidity and mortality of bacterial infections. Understanding the genomic context, time scale, and evolutionary trajectory of antibiotic resistance is crucial for predicting and mitigating their spread. In this work, I take a genomic approach to understanding antibiotic resistance through surveillance of existing threats in the environment, and future threats that may not be captured by current surveillance efforts.
The emergence of antibiotic resistance is a global phenomenon, and perhaps most troublesome in low-income and middle-income countries (LMICs). It is estimated that per-capital burden from antibiotic-resistant infections is highest in LMICs, but surveillance networks are not as complete as they are in high-income countries. To address this gap, I first examined the genotypic mechanisms of carbapenem resistance in Pseudomonas aeruginosa clinical isolates recovered from three hospitals in Pakistan. My genotypic and phenotypic analyses revealed that resistance to carbapenems – a critical tool in treating P. aeruginosa infection – was common. I found that these properties were present in both globally-disseminated and novel sequence types. Although phylogenomic background was correlated with overall antibiotic resistance gene (ARG) content, there was no correlation with the presence of high-risk carbapenemases. I next found that presence of multiple resistance mechanisms in the same genomes was associated with significantly higher resistance phenotype, suggesting that there is a selective benefit to acquiring redundant ARGs.
Hospitals are a critical environment for surveilling resident microbes. Pathogens from patients or healthcare workers can contaminate surfaces and transmit to a vulnerable patient. I next examined the contamination of hospital intensive care unit (ICU) sinks, a surface that has been linked to clinical outbreaks, to understand the time scales and dynamics of surface contamination. I recovered over 100 unique species and novel genomospecies and found that some taxa established long-term contamination across multiple ICU rooms, while others were more transient. I also found that bacteria recovered from ICU rooms were enriched in ARGs compared to non- hospital rooms. This ARG richness was maintained both by persistence of specific ARG-rich lineages as well as mobilizable resistance-conferring plasmids which were observed across multiple unrelated hosts.
Finally, I examine the evolution of a specific mechanism of tetracycline resistance – the tetracycline destructases (TDases). TDases are a family of flavoenzymes capable of selectively inactivating tetracyclines. Although they have a common function, they display a wide sequence diversity. To better understand the sequence-structure-function relationships of TDases I performed a deep mutational scan on tet(X7), a particularly active enzyme that has been identified in a clinical pathogen. I find a correlation between enzyme activity and residues that are critical for cofactor binding. I also find sites distal to the cofactor or substrate binding site which appear to mediate degradation, suggesting that there is complex allosteric effects that we do not fully understand. When comparing activity towards different substrates, I find that multiple residues proximal to the substrate binding site mediate high activity towards tigecycline. Taken together, these effects imply that tet(X7) has evolved a larger binding pocket to accommodate more diverse substrates compared to its evolutionary relatives.
Graduate publications
Blake KS, Kumar H, Loganathan A, Williford EE, Diorio-Toth L, Xue YP, Tang WK, Campbell TP, Chong DD, Angtuaco S, Wencewicz TA, Tolia NH, Dantas G. 2024 Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes. Commun Biol, 7(1):336.
Diorio-Toth L, Wallace MA, Farnsworth CW, Wang B, Gul D, Kwon JH, Andleeb S, Burnham CD, Dantas G. 2023 Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids. mSystems, ():Online ahead of print.
Diorio-Toth L, Irum S, Potter RF, Wallace MA, Arslan M, Munir T, Andleeb S, Burnham CD, Dantas G. 2022 Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance. Microbiol Spectr, 10(3):e0076622.
Stogios PJ, Bordeleau E, Xu Z, Skarina T, Evdokimova E, Chou S, Diorio-Toth L, D’Souza AW, Patel S, Dantas G, Wright GD, Savchenko A. 2022 Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family. Commun Biol, 5(1):263.
Sukhum KV, Diorio-Toth L, Dantas G. 2019 Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance. Clin Pharmacol Ther, 106(3):512-524.