Biology subjects

Palace, S. G.

Publications and source records attributed to Palace, S. G..

9 recordsLinked to original sources

bioRxiv2026

In vitro evaluation of the activity of pairwise combinations of zoliflodacin, gepotidacin, and ciprofloxacin against Neisseria gonorrhoeae

Two new antibiotics, zoliflodacin and gepotidacin, were recently approved for the treatment of urogenital gonorrhea. While combination therapy could, in principle, delay the emergence and spread of resistance, doing so depends on the absence of antagonism between the co-administered drugs. Using in vitro checkerboard testing, we observed no evidence of antagonism for all pairwise combinations of zoliflodacin, gepotidacin, and ciprofloxacin, including in strains with elevated ciprofloxacin MICs.

microbiology↗

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

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↗

bioRxiv2025

Zoliflodacin and gepotidacin cross-resistance in Neisseria gonorrhoeae

Resistance to zoliflodacin, a first-in-class antibiotic for gonorrhea treatment, can occur through gyrBD429N, but this mutations impact on fitness and resistance to other topoisomerase targeting drugs, including gepotidacin, have been unclear. Here, we show that gyrBD429N confers cross-resistance to gepotidacin in some clinical isolates and that its fitness effect varies with strain back-ground. These findings inform strategies for introducing the new topoisomerase inhibitors into clinical use and for surveillance of resistance.

microbiology↗

bioRxiv2025

Quantifying the impact of genetic determinants of antibiotic resistance on bacterial lineage dynamics

The dynamics of antimicrobial resistance in bacterial populations are informed by the fitness impact of genetic determinants of resistance and antibiotic pressure. However, estimates of real-world fitness impact have been lacking. To address this gap, we developed a hierarchical Bayesian phylodynamic model to quantify contributions of resistance determinants to strain success in a 20-year collection of Neisseria gonorrhoeae isolates. Fitness contributions varied with antibiotic use, and genetic pathways to phenotypically identical resistance conferred distinct fitness effects. These findings were supported by in vitro and experimental infection competition. Quantifying these fitness contributions to lineage dynamics reveals opportunities for investigation into other genetic and environmental drivers of fitness. This work thus establishes a method for linking pathogen genomics and antibiotic use to define factors shaping ecological trends.

microbiology↗

bioRxiv2024

Linkage-based ortholog refinement in bacterial pangenomes with CLARC

Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [https://github.com/IndraGonz/CLARC] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by more than 30% and improved evolutionary predictions based on accessory gene frequencies. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.

bioinformatics↗

bioRxiv2024

Axial asymmetry organizes division plane orthogonality in Neisseria gonorrhoeae

For rod-shaped bacterial model organisms, the division plane is defined by the geometry of the cell. However, for Neisseria gonorrhoeae, a coccoid organism that most commonly exists as a diplococcus and that possesses genes coding for rod-based cell division systems, the relationship between cell geometry and division is unclear. Here, we characterized the organization of N. gonorrhoeae division using a combination of fluorescent probes, genetics, and time-lapse microscopy. We found that the planes of successive cell divisions are orthogonal and temporally overlapping, thereby maintaining diplococcal morphology. Division takes place perpendicular to a subtle long-axis in each coccus. In keeping with the ParABS and the MinCDE systems reading the long-axis of rod-shaped bacteria, in the coccoid N. gonorrhoeae, ParB segregates along this subtle long-axis and cells lacking minCDE have severe morphological consequences, including an inability to perform orthogonal division and aberrant assembly of the division plane at the cell poles. Taken together, this stresses the central role of even slight dimensional asymmetry as a general organizational principle in bacterial cell division.

microbiology↗

bioRxiv2019

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates

Increasing Neisseria gonorrhoeae resistance to ceftriaxone, the last antibiotic recommended for empiric gonorrhea treatment, poses an urgent public health threat. However, the genetic basis of reduced susceptibility to ceftriaxone is not completely understood: while most ceftriaxone resistance in clinical isolates is caused by target site mutations in penA, others lack these mutations. Here, we show that penA-independent ceftriaxone resistance has evolved multiple times through distinct mutations in rpoB and rpoD. We identify five mutations in these genes that each increase resistance to ceftriaxone, including one mutation that arose independently in two lineages, and show that clinical isolates from multiple lineages are a single nucleotide change from ceftriaxone resistance. These RNA polymerase mutations result in large-scale transcriptional changes without altering susceptibility to other antibiotics, reducing growth rate, or deranging cell morphology. These results underscore the unexpected diversity of pathways to resistance and the importance of continued surveillance for novel resistance mutations.

microbiology↗

bioRxiv2018

Gain of Function Analysis Reveals Non-Redundant Roles for the Yersinia pestis Type III Secretion System Effectors YopJ, YopT, and YpkA

Virulence of Yersinia pestis in mammals requires the type III secretion system, which delivers seven effector proteins into the cytoplasm of host cells to undermine immune responses. All seven of these effectors are conserved across Y. pestis strains, but three - YopJ, YopT, and YpkA - are apparently dispensable for virulence. Some degree of functional redundancy between effector proteins would explain both observations. Here, we use a combinatorial genetic approach to define the minimal subset of effectors required for full virulence in mice following subcutaneous infection. We found that a Y. pestis strain lacking YopJ, YopT, and YpkA is attenuated for virulence in mice, and that addition of any one of these effectors to this strain increases lethality significantly. YopJ, YopT, and YpkA likely contribute to virulence via distinct mechanisms. YopJ is uniquely able to cause macrophage cell death in vitro and to suppress accumulation of inflammatory cells to foci of bacterial growth in deep tissue, whereas YopT and YpkA cannot. The synthetic phenotypes that emerge when YopJ, YopT, and YpkA are removed in combination provide evidence that each enhances Y. pestis virulence, and that YopT and YpkA act through a mechanism distinct from that of YopJ.

microbiology↗