Biology subjects

Bowcutt, B.

Publications and source records attributed to Bowcutt, B..

4 recordsLinked to original sources

bioRxiv2026

Fluoroquinolone resistance-conferring gyrA variants alter the fitness cost and potentiate the resistance of the zoliflodacin resistance mutation gyrB D429N in Neisseria gonorrhoeae

Neisseria gonorrhoeae is a major public health concern due to its high global prevalence and rapid evolution of antibiotic resistance. A first-in-class topoisomerase inhibitor, zoliflodacin (a spiropyrimidinetrione) recently received FDA approval for treatment of gonorrhea, but its potential for cross-resistance with another topoisomerase inhibitor, the fluoroquinolone antibiotic ciprofloxacin, remains poorly understood. Here, we investigated how genetic diversity in the fluoroquinolone target gyrA influences the resistance and fitness effects of the zoliflodacin resistance mutation gyrBD429N. We constructed an isogenic panel of N. gonorrhoeae to determine how the resistance and fitness effects of the gyrBD429N mutation are modulated by the most common ciprofloxacin resistance-associated variants in gyrA. In the presence of gyrBD429N, the zoliflodacin minimum inhibitory concentration (MIC) was 2-4-fold higher in strains that also contained ciprofloxacin resistance-associated gyrA alleles, and the gyrBD429N mutation reciprocally increased ciprofloxacin MICs of these strains 3-6-fold. Fitness cost of the gyrBD429N mutation varied from modest to severe across gyrA backgrounds, with the largest cost in ciprofloxacin resistant gyrA91F/95G and gyrA91F/95N backgrounds and comparatively minimal cost in the ciprofloxacin resistant gyrA91F/95A background. These results demonstrate the capacity for epistatic interactions among resistance-associated gyrA and gyrB mutations, underscoring the need for genomic surveillance to monitor high-risk combinations of resistance determinants as new therapies are deployed.

microbiology↗

bioRxiv2026

Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa

Viruses are crucial components of microbial communities, both phage that infect bacterial community members as well as pathogenic and other eukaryotic viruses. However, they remain unobserved by most current technologies, due to combinations of experimental and analytical factors. To address the latter, we developed the BAQLaVa algorithm for high-resolution profiling of >120,000 viral species (viral genome bins, VGBs) via reference-based metagenome (MGX) or metatranscriptome (MTX) alignment to complementary nucleotide markers and proteome sets. In comprehensive benchmarking, BAQLaVa substantially outperformed alternatives, achieving species-level recall and precision regularly over 90%. We applied BAQLaVa to MGX and MTX samples from the HMP2 IBDMDB cohort to identify previously undescribed viral perturbations in inflammatory bowel diseases. Most notably, virome diversity was reduced in tandem with bacterial diversity during inflammation, in contrast to previous findings based on a narrower range of viral detection. A subset of viruses were enriched during IBD, associated with carriage of abortive infection anti-defense systems such as AbiL and PD-{lambda}-2, as well as genes involved in the regulation of lysogeny. Leveraging the corresponding viral profiles, we also inferred phage-host relationships using scalable co-occurrence and covariation signals, even in the absence of host references or genome annotations. By enabling high sensitivity and specificity viral profiling from metagenomes or metatranscriptomes, BAQLaVa provides a scalable framework for virome epidemiology and systematic analysis of virus-host interactions.

bioinformatics↗

bioRxiv2026

Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae

Neisseria gonorrhoeae is a sexually transmitted bacterial pathogen that deploys multiple mechanisms to evade the immune system, including rapid variation in surface antigens. One of the most abundant and diverse antigens is the Opacity (Opa) protein, a surface protein that mediates gonococcal attachment to host receptors. Studies of Opa diversity and evolution have been limited by the inability of short-read sequencing to resolve the multiple copies of opa in each genome, preventing a comprehensive understanding of antigenic variation for vaccine design and immunology studies. We assembled a dataset of 219 complete genomes from diverse clinical isolates using long-read sequencing and developed bioinformatics and phylogenetics tools to assess opa variation quantitatively. Each genome had on average 7 distinct opa alleles at 9 to 12 opa loci, and almost all isolates had at least one pair of identical or near-identical opa genes. Fewer opa genes were in frame, and thus inferred to be expressed, than expected due to chance. While genomic distance between isolates correlated with overall opa allele sequence similarity, opa genes were on average 74 times more diverse than the rest of the genome. One opa locus evolved more rapidly than the other loci. There was little evidence that interspecies recombination contributed to N. gonorrhoeae opa diversity. Our findings reveal a continuously evolving opa repertoire that leads to diverse opa alleles even in closely related strains and indicate that there are likely unknown biological factors modulating opa expression. Author SummaryThe rising levels of antibiotic resistance in Neisseria gonorrhoeae make controlling the spread of this sexually transmitted pathogen a public health priority. N. gonorrhoeae rapidly varies surface proteins to evade recognition by the human adaptive immune system. Understanding how these proteins evolve may help us design better vaccines and control measures for curbing the spread of gonorrhea. One of the most abundant surface proteins is the Opacity protein (Opa), which helps N. gonorrhoeae bind to host cells upon colonization. Research efforts to understand the evolution of Opa have been limited because it is encoded by multiple genes in the genome that are not resolved by short-read sequencing technologies. Here, we resolved the genes that encode Opa using a dataset of 132 publicly available complete genomes and 87 genomes that we completed using long-read sequencing of diverse clinical isolates. We found that Opa evolves rapidly to generate different versions of the protein in the same isolate, but very few of these protein versions appear expressed. We also found evidence that there may be other, uncharacterized mechanisms that control how these proteins evolve over longer timescales.

evolutionary biology↗

bioRxiv2023

Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle

Intramammary (IMM) ceftiofur treatment is commonly used in dairy farms to prevent mastitis, though its impact on the cattle gut microbiome and selection of antibiotic-resistant bacteria has not been elucidated. Herein, we enrolled 40 healthy dairy cows after lactation: 20 were treated with IMM ceftiofur (Spectramast(R)DC) and a non-antibiotic internal teat sealant (bismuth subnitrate) and 20 (controls) received only bismuth subnitrate. Fecal samples were collected before (day -1) and after treatment (weeks 1, 2, 3, 5, 7, and 9) for bacterial quantification and metagenomic next-generation sequencing. Overall, 90% and 24% of the 278 samples had Gram-negative bacteria with resistance to ampicillin and ceftiofur, respectively. Most of the cows treated with ceftiofur did not have an increase in the number of resistant bacteria; however, a subset (25%) shed higher levels of ceftiofur-resistant bacteria for up to 2 weeks post-treatment. At week 5, the antibiotic-treated cows had lower microbiome abundance and richness, whereas a greater abundance of genes encoding extended-spectrum {beta}-lactamases (ESBLs), CfxA, ACI-1, and CMY, was observed at weeks 1, 5 and 9. Moreover, the contig and network analyses detected associations between {beta}-lactam resistance genes and phages, mobile genetic elements, and specific genera. Commensal bacterial populations belonging to Bacteroidetes most often possessed ESBL genes followed by members of Enterobacteriaceae. This study highlights variable, persistent effects of IMM ceftiofur treatment on the gut microbiome and resistome in dairy cattle. Antibiotic-treated cattle had an increased abundance of specific taxa and genes encoding ESBL production that persisted for 9 weeks, while fecal shedding of ESBL-producing Enterobacteriaceae varied across animals. Together, these findings highlight the need for additional studies that identify factors linked to shedding levels and the dissemination and persistence of resistance determinants on dairy farms in different geographic locations.

microbiology↗