Biology subjects

Parr, J. B.

Publications and source records attributed to Parr, J. B..

14 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↗

bioRxiv2026

Functional validation of the Plasmodium falciparum K13 C580Y mutation in recently collected Ethiopian isolates

Recent genomic investigation in Ethiopia identified the first detection of the Plasmodium falciparum kelch13 (K13) C580Y substitution in the Horn of Africa. To assess its functional impact, we introduced C580Y into two recently collected Ethiopian clinical isolates using CRISPR-Cas9 genome editing. Ring-stage survival assays showed significantly elevated in vitro dihydroartemisinin (DHA) survival in edited parasites relative to isogenic controls, demonstrating that C580Y confers artemisinin tolerance in contemporary Ethiopian parasite genetic backgrounds.

microbiology↗

bioRxiv2026

Malaria control and the unexpected spread of diagnostic-resistant Plasmodium falciparum in Peru

Plasmodium falciparum parasites with deletions of the histidine-rich protein 2 and 3 (hrp2 and hrp3) genes evade detection by common rapid diagnostic tests (RDTs) and pose a growing threat to malaria control. While these deletions have emerged in multiple regions globally, the evolutionary forces driving their spread remain unclear. Here, we analyze 1,215 P. falciparum samples collected between 2003 and 2018 in Loreto, Peru. This region experienced a major decline in malaria transmission following the Project for Malaria Control in Andean Border Areas (PAMAFRO) and now harbors a high proportion of hrp2/3 deleted parasites despite limited RDT use. Using molecular inversion probe (MIP) sequencing across > 2,000 genome-wide loci, we observed a marked reduction in genetic diversity, increased clonality, and fixation of parasites with deletions of both hrp2 and hrp3 genes (hrp2-/3-) over time. Identity-by-descent (IBD) analysis revealed rapid expansion of a single hrp2-/3- dominant lineage in the post-PAMAFRO period, consistent with clonal replacement after intense malaria control. Targeted sequencing of the hrp2/3 regions showed conserved deletion breakpoints across three different lineages, indicative of recombination of a common haplotype into distinct genetic backgrounds. To investigate the evolutionary forces driving the fixation of hrp2-/3- in Loreto, we simulated allele frequency trajectories under different selection coefficients. We found that fixation of hrp2-/3- due solely to genetic drift (selection coefficient s = 0) is unlikely; a selection coefficient of s [≥] 0.03 was required for fixation to occur consistently. However, our simulations also indicate that a genetic bottleneck caused by PAMAFRO increased the likelihood of fixation through drift by 4.5- to 17-fold depending on the population. These findings suggest that hrp2-/3- fixation was likely driven by a combination of demographic changes resulting from PAMAFRO and selective advantage unrelated to RDT use. Our results demonstrate how intensive malaria control efforts can reshape parasite populations and underscore the value of expanded genomic surveillance as countries move toward malaria elimination.

genetics↗

bioRxiv2026

Lineage-specific tprK diversification and Treponema pallidum transmission dynamics in Buenos Aires, Argentina

BackgroundSyphilis rates are rising globally, with increases in congenital syphilis in South America particularly concerning. The characterization of contemporary South American Treponema pallidum (Tp) strains is crucial to syphilis vaccine development, yet few genomic epidemiology studies have focused on this region. Here, we performed whole genome sequencing (WGS) of Tp from Buenos Aires, Argentina, as well as deep sequencing of the hypervariable tprK locus, which is critical to Tp immune evasion. MethodsPeople with primary, secondary, or congenital syphilis were enrolled at two clinics in Buenos Aires between October 2018 and January 2023, including individuals associated with intra-household transmission. Hybrid capture WGS was performed and a core genome phylogeny generated. K-mer-based methods using full-length tprK PacBio long reads were used to uncover differences in diversity and detect Tp transmission. FindingsTp genomes were recovered from 70 individuals in Buenos Aires and primarily belonged to globally dominant SS14 sublineage-1 and Nichols sublineage-8, as did Tp from Brazil (n=8). Peruvian samples (n=3) all belonged to sublineage-1. Two individuals from Argentina had co-infections with Nichols- and SS14-lineage strains. Macrolide resistance via A2058G occurred in 27/70 (38.6%) samples. Across 56 samples, tprK allelic diversity was significantly increased in secondary syphilis, oral lesions, and SS14-lineage strains compared to primary syphilis, anogenital lesions, and Nichols-lineage strains, respectively. Increased diversity in SS14-lineage strains is driven by an enhanced repertoire of V7-specific donor sequences. tprK sequences from intra-household transmissions were more similar than unrelated samples with identical core genomes. InterpretationTp circulating in South America is closely related to dominant global sublineages. Increased tprK diversity in the SS14 lineage may influence Tps ability to escape host immunity. tprK profiling is a promising tool to elucidate syphilis transmission networks. This study underscores the utility of genomics to yield insights into Tp pathogenesis. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAlthough whole genome sequencing (WGS) and genomic epidemiology have contributed to an understanding of the global diversity of Treponema pallidum (Tp), very few strains from South America have been sequenced to date. On January 6th, 2026, we performed a PubMed search including terms "syphilis genomic epidemiology", "South America", "Treponema pallidum", and "Argentina". We excluded studies of ancient Tp samples found in South American archeological sites. A single Tp sample from Argentina was originally sequenced in 2016 and included in subsequent analyses of global diversity. Nine Peruvian samples were previously sequenced in a study of global diversity on six continents. Thirty-three samples from Cali, Colombia were predominantly SS14-lineage and genotypic macrolide resistance was found in half of strains. Additionally, studies of Tp in Buenos Aires using a multi-locus sequence typing approach have shown circulation of strains belonging to both Nichols and SS14 lineages, with an increasing rate of macrolide resistance over time. Five previous studies have examined tprK in clinical specimens and consistently shown increased tprK diversity in specimens associated with secondary syphilis compared to primary syphilis lesions. One study has shown that loss of tprK donor cassettes is associated with reduced tprK diversity, consistent with results from in vitro experiments. A single study has shown that tprK sequence content is more similar in samples with a suspected epidemiologic link, though no prior studies have looked at tprK diversity in the context of known syphilis transmission events. Added value of this studyThis study is the first to use WGS to comprehensively examine Tp transmission in a large South American city, yielding 96 samples from 70 individuals. We also add the first contemporary Tp genomes from Brazil. In contrast to findings from England, Australia, and other high-income countries, no Tp sublineages are associated with demographic groups or sexual networks in Buenos Aires. Two of seventy patients were co-infected with both Nichols- and SS14-lineage strains, showing the previously unappreciated frequency of conditions that permit inter-strain recombination-driven diversification of Tp. This study also reveals novel aspects of Tp pathogenesis, including lineage-specific differences in tprK diversity. We also develop methods for the analysis of tprK relatedness between samples and demonstrate that tprK sequences are more similar in samples from individuals within intra-household syphilis transmission chains compared to those from epidemiologically unrelated individuals. Implications of all the available evidenceTp strains circulating in Buenos Aires are genetically similar to those circulating worldwide and in Brazil and Peru but are noteworthy for the low (but rising) rate of macrolide resistance. Lineage-specific patterns of tprK antigenic variation could result in differences between Nichols- and SS14-lineage strains interactions with the host immune system. Finally, we show that tprK profiling holds promise to identify samples from within a syphilis transmission chain and could play an important role in public health.

microbiology↗

bioRxiv2025

Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of Treponema pallidum outer membrane proteins

Knowledge of Treponema pallidum subspecies pallidum (TPA) outer membrane protein (OMP) sequence variability is essential for understanding spirochete proliferation within endemic populations as well as design of a globally effective syphilis vaccine. Our group has identified extracellular loops (ECLs) of TPA BamA (TP0326) and members of the FadL family (TP0548, TP0856, TP0858, TP0859, and TP0865) as potential components of a multivalent vaccine cocktail. As part of a consortium to explore TPA strain diversity, we mapped the variability of BamA and FadL orthologs in 186 TPA strains from Malawi, China and Colombia onto predicted 3D structures. The 186 genomes fell into eight subclades (five Nichols-, three SS14-lineage) with substantial geographic restriction. Single nucleotide variants accounted for the large majority of proteoforms, with variability notably higher within the Nichols-lineage strains. Most mutations were in regions of the proteins predicted to be extracellular and harboring B cell epitopes. We observed a striking difference in the degree of variability between the six OMPs, suggesting that these proteins are following divergent evolutionary paths. Concatenation of OMP sequences recapitulated the phylogenetic structure of the TPA strains, effectively segregating within clades and largely clustering by subclades. Lastly, we noted that BamA and FadL candidate ECL vaccinogens previously shown to elicit antibodies that kill treponemes during in vitro cultivation are well conserved. Taken as a whole, our study establishes a structural-phylogenetic approach for analyzing the forces shaping the host-pathogen interface in syphilis within endemic populations while informing selection of vaccine targets. IMPORTANCESyphilis remains a major global health concern, reinforcing the need for a safe and effective vaccine. Understanding the variability of TPA OMPs is essential for tracking pathogen evolution and informing vaccine design. Here, we analyzed the variability of six TPA OMPs in 186 strains from Malawi, China, and Colombia, identifying protein-specific evolutionary patterns. Most mutations were localized in extracellular regions and, notably, appeared to correlate with the phylogenetic structure of TPA. Despite OMP heterogeneity, several candidate vaccinogens remained highly conserved, reinforcing their potential as globally effective vaccine targets. Our study establishes a structural-phylogenetic framework for dissecting the forces shaping the host-spirochete interface within endemic populations and provides a foundation for designing a globally effective syphilis vaccine.

microbiology↗

bioRxiv2025

Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border

Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collected Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.

microbiology↗

bioRxiv2024

Development and utilization of Treponema pallidum expressing green fluorescent protein to study spirochete-host interactions and antibody-mediated clearance: expanding the toolbox for syphilis research.

Syphilis is a sexually transmitted infection caused by the highly invasive and immunoevasive spirochetal pathogen Treponema pallidum subsp. pallidum (TPA). Untreated syphilis can lead to infection of multiple organ systems, including the central nervous system. The alarming increase in syphilis cases globally underscores the importance of developing novel strategies to understand the complexities of syphilis pathogenesis. In this study, we took advantage of recent advances in in vitro cultivation and genetic manipulation of syphilis spirochetes to engineer a TPA strain that constitutively expresses green fluorescent protein (GFP). GFP+ TPA grew identically to the Nichols parent strain in vitro and exhibited wild-type infectivity in the rabbit model. We then used the GFP+ strain to visualize TPA interactions with host cells during co-cultivation in vitro, within infected rabbit testes, and following opsonophagocytosis by murine bone marrow-derived macrophages. Development of fluorescent strain also enabled us to develop a flow cytometric-based assay to assess antibody-mediated damage to the spirochetes fragile outer membrane (OM), demonstrating dose-dependent growth inhibition and OM disruption in vitro. Notably, we observed greater OM disruption of GFP+ TPA with sera from immune rabbits infected with the TPA Nichols strain compared to sera generated against the genetically distinct SS14 strain. These latter findings highlight the importance of OM protein-specific antibody responses for clearance of TPA during syphilitic infection. The availability of fluorescent TPA strains paves the way for future studies investigating spirochete-host interactions as well as functional characterization of antibodies directed treponemal OM proteins, the presumptive targets for protective immunity. ImportanceSyphilis, a sexually transmitted infection caused by Treponema pallidum (TPA), remains a pressing threat to global public health. TPA has a remarkable and still poorly understood ability to disseminate rapidly from the site of inoculation and establish persistent infection throughout the body. Recent advances in in vitro cultivation and genetic manipulation of syphilis spirochetes enabled the development of fluorescent TPA. In the study, we generated and characterized an infectious TPA strain that constitutively expresses green fluorescent protein and used this strain to visualize interaction of TPA with host cells and functionally characterize antibodies directed against treponemal outer membrane proteins. Most notably, we assessed the ability of surface-bound antibodies to inhibit growth of TPA in vitro and/or disrupt the spirochetes fragile outer membrane. Fluorescent TPA strains provide a powerful new tool for elucidating host-pathogen interactions that enable the syphilis spirochete to establish infection and persistent long-term within its obligate human host.

microbiology↗

bioRxiv2024

Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health

BackgroundTargeted amplicon sequencing is a powerful and efficient tool for interrogating the Plasmodium falciparum genome, generating actionable data from infections to complement traditional malaria epidemiology. For maximum impact, genomic tools should be multi-purpose, robust, sensitive, and reproducible. MethodsWe developed, characterized, and implemented MAD4HatTeR, an amplicon sequencing panel based on Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing, along with a bioinformatic pipeline for data analysis. Additionally, we introduce an analytical approach to detect gene duplications and deletions from amplicon sequencing data. Laboratory control and field samples were used to demonstrate the panels high sensitivity and robustness. ResultsMAD4HatTeR targets 165 highly diverse loci, focusing on multiallelic microhaplotypes, key markers for drug and diagnostic resistance (including duplications and deletions), and csp and potential vaccine targets. The panel can also detect non-falciparum Plasmodium species. MAD4HatTeR successfully generated data from low-parasite-density dried blood spot and mosquito midgut samples, and detected minor alleles at within-sample allele frequencies as low as 1% with high specificity in high-parasite-density dried blood spot samples. Gene deletions and duplications were reliably detected in mono- and polyclonal controls. Data generated by MAD4HatTeR were highly reproducible across multiple laboratories. ConclusionsThe successful implementation of MAD4HatTeR in five laboratories, including three in malaria-endemic African countries, showcases its feasibility and reproducibility in diverse settings. MAD4HatTeR is thus a powerful tool for research and a robust resource for malaria public health surveillance and control.

genomics↗

bioRxiv2022

Genomic insights into Plasmodium vivax population structure and diversity in central Africa

Plasmodium vivax malaria has not traditionally been a major concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility that P. vivax is evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. In this study, we perform whole genome sequencing of a new P. vivax isolate from the Democratic Republic of the Congo (DRC) and assess how this central African isolate fits into the global context of this species. We use population genomics methods to show that P. vivax from DRC is similar to other African parasite populations and is not closely related to the non-human primate parasite P. vivax-like. SignificanceThe second most common malaria species to infect humans, Plasmodium vivax, is not considered a major threat to human health in central Africa because people in this region frequently have a genetic variant that prevents the P. vivax species from being able to cause illness. Recent research shows that P. vivax can be found in individuals who should be immune, but there is insufficient data to understand why. Our study investigates the genome of one P. vivax sample collected from central Africa to show that the DRC population is closely related to other P.vivax populations in Africa.

evolutionary biology↗

bioRxiv2022

Non-allelic homologous recombination driven translocation explains histidine-rich protein 3 deletion mechanism in Plasmodium falciparum

Most malaria rapid diagnostic tests (RDTs) detect Plasmodium falciparum histidine-rich protein 2 (PfHRP2) and PfHRP3, but deletions of pfhrp2 and phfrp3 genes make parasites undetectable by RDTs. We analyzed 19,313 public whole-genome-sequenced P. falciparum field samples to understand these deletions better. Pfhrp2 deletion only occurred by chromosomal breakage with subsequent telomere healing. Pfhrp3 deletions involved loss from pfhrp3 to the telomere and showed 3 patterns: no other associated rearrangement with evidence of telomere healing at breakpoint (Asia; Pattern 13-TARE1); associated with duplication of a chromosome 5 segment containing multidrug-resistant-1 gene (Asia; Pattern 13-5++); and most commonly, associated with duplication of a chromosome 11 segment (Americas/Africa; Pattern 13-11++). We confirmed a 13-11 hybrid chromosome with long-read sequencing, consistent with a translocation product arising from recombination between large interchromosomal ribosome-containing segmental duplications. Within most 13-11++ parasites, the duplicated chromosome 11 segments were identical. Across parasites, multiple distinct haplotype groupings were consistent with emergence due to clonal expansion of progeny from intrastrain meiotic recombination. Together, these observations suggest negative selection normally removes 13-11++ pfhrp3 deletions, and specific conditions are needed for their emergence and spread including low transmission, findings that can help refine surveillance strategies.

genomics↗

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

Analysis of Treponema pallidum strains from China using improved methods for whole-genome sequencing from primary syphilis chancres

Whole-genome sequencing (WGS) of Treponema pallidum subsp. pallidum (TPA) has been constrained by the lack of in vitro cultivation methods for isolating spirochetes from patient samples. We built upon recently developed enrichment methods to sequence TPA directly from primary syphilis chancre swabs collected in Guangzhou, China. By combining parallel, pooled whole-genome amplification (ppWGA) with hybrid selection, we generated high quality genomes from four of eight chancre-swab samples and two of two rabbit-passaged isolates, all subjected to challenging storage conditions. This approach enabled the first WGS of Chinese samples without rabbit passage and provided insights into TPA genetic diversity in China.

genomics↗

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↗

bioRxiv2019

The Impact of Antimalarial Resistance on the Genetic Structure of Plasmodium falciparum in the DRC

The Democratic Republic of the Congo (DRC) harbors 11% of global malaria cases, yet little is known about the spatial and genetic structure of the parasite population in that country. We sequenced 2537 Plasmodium falciparum infections, including a nationally representative population sample from DRC and samples from surrounding countries, using molecular inversion probes - a novel high-throughput genotyping tool. We identified an east-west divide in haplotypes known to confer resistance to chloroquine and sulfadoxine-pyrimethamine. Furthermore, we identified highly related parasites over large geographic distances, indicative of gene flow and migration. Our results were consistent with a background of isolation by distance combined with the effects of selection for antimalarial drug resistance. This study provides a high-resolution view of parasite genetic structure across a large country in Africa and provides a baseline to study how implementation programs may impact parasite populations.

genomics↗