Biology subjects

Hennelly, C. M.

Publications and source records attributed to Hennelly, C. M..

3 recordsLinked to original sources

bioRxiv2026

Microbial community profiles of genital and non-genital skin lesions from Ghana

Skin ulcers, such as those observed in cases of the non-venereal disease yaws and the venereal disease syphilis, are traditionally diagnosed based on their anatomical location and visible appearance. Yet various evidence suggests that the pathogens that cause these ulcers may not be restricted to genital or non-genital body sites. We explored this by profiling the bacterial communities of genital and non-genital skin ulcers collected in Ghana using 16S rRNA gene amplicon sequencing. Swab samples were collected from 156 clinically diagnosed skin lesions (110 non-genital and 46 genital). The V1-V2 region of the 16S rRNA gene was sequenced to characterize bacterial communities. Microbial diversity, community composition, differential abundance, and associations between lesion diversity and common skin bacteria were analysed using bioinformatics and statistical methods. Following quality filtering, 135 samples were retained, revealing 23 bacterial phyla, 143 families, and 406 genera. Alpha diversity indicated similar bacterial richness and diversity in genital and non-genital skin lesions. Beta diversity analyses indicated differences between genital and non-genital lesions, accompanied by significant differences in within group dispersion. A log2 fold change analysis evidenced genital lesions were enriched in Gardnerella, whereas non-genital lesions showed more abundance of Staphylococcus, Streptococcus, Corynebacterium, Bradyrhizobium, and Pelomonas. Clinically important genera, including Treponema, Haemophilus, and Mycobacterium, were also detected, even in samples with low sequencing depths. Statistical modelling indicated that greater microbial diversity was associated with intermediate abundances of common skin taxa, particularly Corynebacteriaceae, Micrococcaceae, Cutibacterium, and Staphylococcaceae, thereby attesting the presence of polymicrobial communities in skin ulcers. Overall, genital and non-genital skin lesions showed similar microbial diversity but differed in composition. Our findings support the view of skin lesions as ecological niches containing diverse bacterial communities rather than being consistently dominated by a single bacterial taxon. They provide a basis for investigating possible polymicrobial interactions in skin ulcers.

microbiology↗

bioRxiv2022

High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

Sequencing of most Treponema pallidum (T. pallidum) genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modelling of TP0470 suggested that the eight residue repeats form an extended -helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged {beta}- sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.

microbiology↗

bioRxiv2020

A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, speciation, and drug-resistance genotyping

CRISPR-based diagnostics are a new class of highly sensitive and specific assays with multiple applications in infectious disease diagnosis. SHERLOCK, or Specific High-Sensitivity Enzymatic Reporter UnLOCKing, is one such CRISPR-based diagnostic that combines recombinase polymerase pre-amplification, CRISPR-RNA base-pairing, and LwCas13a activity for nucleic acid detection. We developed SHERLOCK assays for malaria capable of detecting all Plasmodium species known to cause malaria in humans and species-specific detection of P. vivax and P. falciparum, the species responsible for the majority of malaria cases worldwide. We validated these assays against parasite genomic DNA and achieved analytical sensitivities ranging from 2.5-18.8 parasites per reaction. We further tested these assays using a diverse panel of 123 clinical samples from the Democratic Republic of the Congo, Uganda, and Thailand and pools of Anopheles mosquitoes from Thailand. When compared to real-time PCR, the P. falciparum assay achieved 94% sensitivity and 94% specificity in clinical samples. In addition, we developed a SHERLOCK assay capable of detecting the dihydropteroate synthetase (dhps) single nucleotide variant A581G associated with P. falciparum sulfadoxine-pyrimethamine resistance. Compared to amplicon-based deep sequencing, the dhps SHERLOCK assay achieved 73% sensitivity and 100% specificity when applied to a panel of 43 clinical samples, with false-negative calls only at lower parasite densities. These novel SHERLOCK assays have potential to spawn a new generation of molecular diagnostics for malaria and demonstrate the versatility of CRISPR-based diagnostic approaches. One-sentence summaryNovel malaria SHERLOCK assays enabled robust detection, speciation, and genotyping of Plasmodium spp. in diverse samples collected in Africa and Asia.

molecular biology↗