Biology subjects

Harrison, L. B.

Publications and source records attributed to Harrison, L. B..

5 recordsLinked to original sources

bioRxiv2026

In vitro exposure to non-antipseudomonal antibiotics (NAPA) induces Pseudomonas aeruginosa resistance to antipseudomonal antibiotics (APA)

BackgroundPseudomonas aeruginosa readily evolves antimicrobial resistance through regulatory plasticity and stress-adaptive pathways. Clinically, antibiotics lacking intrinsic antipseudomonal activity are often favored with the assumption that they avoid selective pressure on P. aeruginosa. Whether subinhibitory exposure to such "non-antipseudomonal antibiotics" (NAPA) can nevertheless select for canonical resistance pathways remains incompletely defined. Methods: Three P. aeruginosa strains (ATCC 27853 and two bloodstream isolates) were serially passaged over 14 days in the presence of ertapenem, ceftriaxone, or moxifloxacin at one-third the baseline minimum inhibitory concentration (MIC). MICs for antipseudomonal antibiotics (meropenem, ceftazidime, ciprofloxacin) were measured at serial time points and after a 3-day antibiotic-free recovery (day 14). Whole-genome sequencing was performed longitudinally to identify mutations. ResultsNAPA exposure led to reproducible elevations in antipseudomonal MICs: ertapenem triggered up to a 29-fold increase in meropenem MIC, ceftriaxone up to a 31-fold rise in ceftazidime MIC, and moxifloxacin up to a 12-fold increase in ciprofloxacin MIC. Elevated MICs persisted on day 14 despite absence of further antibiotic pressure. Genomic analysis revealed convergent evolution of mutations in efflux regulator genes (nfxB, nalC, nalD, amrR) and the {beta}-lactamase-regulating gene dacB, emerging during periods of MIC escalation and mapping to regulatory pathways governing efflux and AmpC expression. ConclusionSubinhibitory exposure to antibiotics without intrinsic antipseudomonal activity reproducibly selected for heritable multidrug-resistant phenotypes in P. aeruginosa. Resistance arose through convergent evolution in regulatory genes classically associated with direct antipseudomonal antibiotic pressure, demonstrating that resistance architectures can be selected independent of target engagement and underscoring the inevitability of collateral resistance under antibiotic stress. ImportancePseudomonas aeruginosa is a major cause of hospital-acquired infections and is well known for its ability to develop antibiotic resistance. Clinicians often assume that antibiotics without activity against P. aeruginosa do not meaningfully influence its resistance behavior and are therefore safe choices when this organism is not the primary target. Our study challenges this assumption. We show that low-level exposure to such antibiotics is associated with increased resistance to key antipseudomonal drugs, even after the initial antibiotic exposure ends. Rather than arising from a single stable genetic change, resistance was accompanied by shifting genetic alterations in regulatory pathways that control drug efflux and {beta}-lactamase expression. These findings highlight how antibiotic exposure can broaden the evolutionary pathways available for resistance in unintended pathogens. Recognizing these indirect and population-level effects of antibiotic use may help inform more cautious antimicrobial prescribing strategies in clinical settings.

microbiology↗

bioRxiv2025

Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae

Hypotheses concerning the ecology and evolution of bacteria commonly relate to the presence and abundance of species in various settings and conditions. Shotgun metagenomics may address these hypotheses, which previously relied on PCR or culture. However, the problem of determining the presence/absence of a given species of interest is not trivial, particularly when closely related species are present in the reference database or metagenomic sample. Reference-based methods to detect species-level taxa mostly rely on thresholding of aligned reads or mapped k-mers or derivative metrics like genomic coverage, and create a trade-off between recall/completeness and precision/purity. New methods for species-level profiling (YACHT, metapresence and sylph) have recently been published. Here we test the performance of these methods, along with Kraken2/bracken and MetaPhlAn4, to detect related species of interest using simulated metagenomic samples from genomes in the families Mycobacteriaceae and Neisseriaceae, which contain closely related genomes. Among methods tested, metapresence, when used with an alignment quality filter, and sylph offer the best overall performance. Sylph maintains high precision but requires a depth of coverage greater than approximately 0.1x to reliably detect a genomes presence. Metapresence has a lower limit of detection of hundreds of reads but this is balanced against relatively lower precision. Both methods are relatively robust to the presence of reads from genomes outside the groups of interest. We demonstrate the application of these methods in two real-world datasets: a mycobacterial community in a drinking water system and the community of Neisseriaceae present in the human oral cavity. ImportanceDetecting which bacterial species of interest are present in a given sample is fundamental to studies of microbial ecology and evolution, and to applied microbiology (e.g. clinical diagnostics). Culture-dependent and independent (e.g. PCR) approaches are increasingly complemented by metagenomic approaches, but methods to accurately identify specific low-abundance species-level genomes in a shotgun metagenomic sample are still being refined. Here we comprehensively test YACHT, Kraken2/bracken, metapresence, MetaPhlAn4, and sylph using two simulated datasets of bacterial families, Mycobacteriaceae and Neisseriaceae that contain closely related species. Our simulations exploit natural genomic diversity to create a challenging benchmark. We demonstrate that metapresence and sylph perform best, with the former being well-suited to low-biomass host-associated datasets, and the latter with environmental metagenomic samples. This study is the first extensive benchmark of these methods for this use case, and demonstrates these methods can accurately identify closely related species of interest.

bioinformatics↗

bioRxiv2024

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars - Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.

genomics↗

bioRxiv2023

An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows

Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these referents do not capture the complete structural variation now known to be present in the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent in H37Rv such as the TbD1 and RvD4496/RD7/RD713 regions in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence into a standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC. Data SummaryThe MTBC0 sequence, is available in the online data supplement in FASTA format at https://github.com/lukebharrison/MTBC0. Included with the MTBC0 sequence in the data supplement are: the reference-free alignment of MTBC closed genomes in hierarchical alignment (HAL) format, control files for cactus, annotations for H37Rv and L8, a BED file of regions excluded from SNP calls lifted over onto MTBC0, as well as the scripts used to call SNPs and the phylogenetic trees generated in this article. All previously published sequence data is available at the NCBI nucleotide and SRA databases, accession number for sequences used in this manuscript are available in Supplementary Tables 1 and 2. Impact StatementThis article describes an imputed ancestral genomic sequence (MTBC0) at the base of the MTBC for use as a reference sequence for Mycobacterium tuberculosis genomic workflows. Widely used reference sequences are limited to the structural diversity present in H37Rv, a lineage 4 isolate. MTBC0 obviates this limitation by incorporating the structural variation present at the base of the Mycobacterium tuberculosis complex (MTBC) by encompassing a wide sample of human and animal lineages including newly discovered lineages (L8, M. orygis). Use of MTBC0 enables the mapping of more reads and calling of more SNPs and allows for the investigation of structural variation not present in the current used reference sequences within this important group of animal and human pathogens.

microbiology↗

bioRxiv2020

Harnessing tumor immune ecosystem dynamics to personalize radiotherapy

Radiotherapy is a pillar of cancer care and augments the response to immunotherapies. However, little is known regarding the relationships between the tumor immune ecosystem (TIES) and intrinsic radiosensitivity, and a pressing question in oncology is how to optimize radiotherapy to improve patient responses to immune therapies. To address this challenge, we profiled over 10,000 primary tumors for their metrics of radiosensitivity and immune cell infiltrate (ICI), and applied a new integrated in silico model that mimics the dynamic relationships between tumor growth, ICI flux and the response to radiation. We then validated this model with a separate cohort of 59 lung cancer patients treated with radiotherapy. These analyses explain radiation response based on its effect on the TIES and quantifies the likelihood that radiation can promote a shift to anti-tumor immunity. Dynamic modeling of the relationship between tumor radiosensitivity and the TIES may provide opportunity to personalize combined radiation and immunotherapy approaches.

cancer biology↗