Biology subjects

Hicks, J. A.

Publications and source records attributed to Hicks, J. A..

4 recordsLinked to original sources

bioRxiv2026

Validation of a molecular workflow for Cochliomyia hominivorax (New World screwworm) identification in field samples

Cochliomyia hominivorax, New world Screwworm (NWS), has become a reemerging veterinary concern in the United States due to the recent northward expansion of fly detections as far as northern Mexico. Rapid, accurate and validated detection pipelines need to be developed in the case of an incursion into the United States. Confirmatory cases are evaluated by morphological identification with no paired test to verify identifications. With the frequency of submissions of non-ideal samples, particularly from fly traps, a molecular tool would be necessary for species identification. In this manuscript, we develop and assess a pipeline including three real-time PCR assays targeting the ribosomal RNA and five sets of Sanger primers targeting the mitochondrial genome that would be used as a paired tool with morphological identification. Two of the assessed real-time PCR assays are highly specific, sensitive and repeatable requiring <1 copy per reaction for detection. Four of the five Sanger primer sets were assessed, optimized and results evaluated for potential use in preliminary geographic analysis of specimens. This workflow will expedite screening of samples, provide a method to verify results using different tools and help understand genetic variations within the mitochondria for NWS outbreaks.

molecular biology↗

bioRxiv2025

Initial identification of genomic islands in Taylorella equigenitalis and Taylorella asinigenitalis and their distribution in isolates from around the world

Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), is endemic in several countries throughout the world and impacts the global movement of horses. It presents with symptoms ranging from non-clinical to endometritis, vaginitis, and acute infertility in females while males remain asymptomatic. Studies of the disease have focused primarily on understanding pathology, transmission dynamics, diagnostics, and phenotypic and genotypic characteristics. The goal of this study was to establish a more comprehensive global phylogenetic structure and generate reference-quality genomes for each major clade of the tree where such data were absent. Seven of these genomes along with 44 other publicly available genome assemblies, including Taylorella asinigenitalis, were then used to predict genomic islands. Exploration of the NCBI annotations in the genomic islands indicate links to virulence and ecological fitness. An additional 97 T. equigenitalis and 48 T. asinigenitalis short-read isolates from this study and 215 publicly available genomes were used to examine distribution of each genomic island across the phylogenetic tree for evidence of horizontal movement. The stability of these genomic islands in their natural environment was evaluated utilizing 141 isolates recovered from a recent CEM outbreak in the United States. The results obtained in this study demonstrate mobile genomic islands in T. equigenitalis genomes, sites of concern for their contribution to the potential virulence of the organism.

microbiology↗

bioRxiv2023

An accurate and interpretable model to predict antimicrobial resistance in One Health settings

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

bioinformatics↗

bioRxiv2021

Antimicrobial Resistance and Genomic Characterization of Salmonella Dublin Isolates in Cattle from the United States.

Salmonella enterica subspecies enterica serovar Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S. Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S. Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S. Dublin isolates (n=140) were selected from submissions to the NVSL for Salmonella serotyping (2014 - 2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S. Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to betalactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(3)-Ib and aph(6)-Id (96.4%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyrA. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S. Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S. Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S. Dublin isolates may provide valuable insight on increased virulence observed in humans.

microbiology↗