Biology subjects

Payne, M.

Publications and source records attributed to Payne, M..

At least 19 recordsLinked to original sources

bioRxiv2026

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

By 2050, almost half of the global population will be at risk of mosquito-borne disease. Effective response requires monitoring both pathogen transmission and vector abundance, yet these are typically assessed using separate assays with limited taxonomic breadth. Here we present COSMOS (COmprehensive Sequencing for MOSquito-borne disease), a targeted metagenomics workflow designed to reconstruct pathogen genomes and mosquito community composition directly from mixed field-collected samples. Over three annual rounds of a major Australian surveillance program, we evaluated >120,000 mosquitoes in 219 traps, with 98.7% agreement with surveillance data across seven monitored arboviruses, and additional detections of Sindbis virus and the state's first detection of encephalitic Little Sussex virus. Of 137 viral detections, 101 yielded near-complete genomes (>90% coverage) at median 95x depth. Using an accompanying computational workflow, COSMOS quantified mosquito composition, matching entomological estimates of reported vector species (CCC 0.78-0.89). Joint analysis of virus and vector composition identified structured mosquito communities associated with spatial and temporal environmental variation, allowing the ecological context of arbovirus detections to be characterised. Detections during the Murray Valley encephalitis virus outbreak in 2023 were concentrated within a narrowly defined mosquito-community space corresponding to rural communities dominated by the inland S-AUS sub-lineage of Culex annulirostris. Integrated vector-pathogen metagenomics provides ecological and evolutionary context for arbovirus activity within a single scalable workflow for surveillance and outbreak response.

microbiology↗

bioRxiv2026

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

Deep metagenomic sequencing is increasingly used for lineage profiling of complex biological mixtures, including applications such as wastewater virus surveillance and microbiome profiling. For profiling, sequence read sets are compared against a database of reference sequences to identify component genetic lineages, and estimate their relative abundance. However, there is currently a lack of clarity regarding the impact of two ubiquitous features of biological mixtures on compositional profiling: (1) population diversity, where reads contain genetic diversity not represented in the reference set, and (2) the presence of high sequence similarity between references, which causes ambiguity in read assignment. Here we show, using both simulated and real data, that performance of two commonly used tools for lineage profiling, KMA and Kallisto, is differently affected by sample-reference distance and the presence of highly similar competing reference sequences. Increasing sample-reference distance reduced read assignment for both tools, but more strongly for Kallisto, which led to directional bias in abundance estimates when distance differed between mixture components. In contrast, when sample-reference distance was low, Kallisto more specifically discriminated between highly similar competing references, whereas KMA was less able to partition reads accurately between them. This specificity-sensitivity trade-off was reflected in real datasets: KMA produced more accurate abundance estimates for mosquito COX1 mixtures, whereas Kallisto performed better for mixtures of closely related SARS-CoV-2 lineages, although neither tool fully resolved the most similar SARS-CoV-2 variants. Tool choice is therefore dependent on the degree of expected sample-reference distance and inter-reference distance within datasets.

bioinformatics↗

bioRxiv2026

Rhizobacterial Biosensors Spatially Map Natural and Engineered Sucrose Exudation

Root exudation mediates the delivery of plant primary and secondary metabolites into soil, where they regulate plant-microbe interactions and terrestrial carbon cycling. Conventional exudate analyses quantify total root-released carbon yet obscure the spatial origin and rhizosphere influence of individual compounds. Here, we develop a rhizobacterial biosensor platform, named Suc-MAPP, to map local exudate profiles along the surface of colonized root tissues. Focusing on sucrose, we engineered sfGFP-based, sucrose-responsive gene circuits in Pseudomonas putida KT2440 for live imaging of exudate concentrations in the micromolar range. These biosensors reveal spatially structured sucrose exudation patterns across eudicots and monocots and implicate photoassimilated source-sink dynamics as a major determinant. We further apply this platform to phenotype exudation modulated by synthetic gene circuitry in Arabidopsis thaliana, identifying genetic design rules for graded sucrose release and quantifying how engineered export sculpts rhizosphere assembly of a defined bacterial community. Together, these results establish programmable rhizobacterial biosensors as tools to spatially resolve plant-environment carbon exchange in situ and provide a framework for extending this approach to diverse exudate targets.

synthetic biology↗

bioRxiv2025

Multilevel HierCC typing scheme for global genomic epidemiology and antimicrobial resistance surveillance of Campylobacter jejuni

Campylobacter jejuni is the most common bacterial cause of human gastroenteritis around the world. The disease burden and financial cost associated with C. jejuni pose significant challenges to the global public health system. A stable, scalable and standardised typing scheme is essential for epidemiological and AMR surveillance for prevention and control of C. jejuni infections. We curated and assembled a C. jejuni global whole genome sequencing (WGS) dataset of 63,012 publicly available Illumina short-read genomes. A C. jejuni global cgMLST scheme with 1161 core loci was developed using a representative subset of 2,587 genomes. HierCC clustering of the cgMLST profiles was performed for all levels and suitable HierCC levels were selected to enable epidemiological analysis. Antimicrobial resistance (AMR) prediction was performed using AbritAMR. A HierCC cluster was classified as a resistant cluster if [≥]80% of the isolates were resistant to at least one antibiotic.We selected 9 HierCC levels (HC2, HC4, HC6, HC12, HC19, HC55, HC100, HC167 and HC264) to form the multilevel HierCC scheme. The multilevel design allowed natural and genetically discrete clusters to be described consistently at both global and local scale. We showcased the utility of the scheme with identification of country and continent specific clusters at HC264 to HC19 levels and differentiation of animal host specific (specialist) from human infection (generalist) clusters at HC264 to HC55 levels. In the USA dataset from 2016 to 2022, a total of 276 resistant clusters were identified with 22 resistant clusters increasing in frequence in recent years. An increased prevalence of C. jejuni carrying 50S_L22 mutations in the USA was observed from 2016 to 2022, suggesting continuing selection pressure from macrolide use in the farm animals. We developed a novel multilevel HierCC typing scheme to standardise AMR surveillance and provide flexible typing resolution for both short- and long-term epidemiological investigations of C. jejuni at global and local levels.

microbiology↗

bioRxiv2025

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogenic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet to be expressed they must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA present in multiple copies (up to nine) in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes and is enriched in E. coli strains that carry the locus of enterocyte effacement (LEE). We show that HnrS directly base-pairs with the ribosome-binding site of the hha mRNA, repressing its translation and thereby reducing Hha-enhanced H-NS silencing. This counter-silencing de-represses the LEE type III secretion system and concomitantly represses motility. Transcriptomic profiling further revealed that HnrS indirectly activates genes involved in nitrate/nitrite respiration and nitric oxide resistance, metabolic pathways that contribute to survival in the inflamed gastrointestinal tract. Deletion of hnrS reduced expression of nitrate reductase genes and impaired actin pedestal formation on host epithelial cells. Our results indicate that prophage-encoded, multicopy hnrS provides a counter-silencing mechanism that reduces Hha-H-NS repression at specific virulence loci. This likely enables expression of horizontally acquired genes without broadly disrupting the core H-NS regulon. HnrS illustrates how mobile genetic elements deploy sRNAs to counteract xenogenic silencing and promote virulence gene expression, enhancing colonisation of the host. Importance statementHorizontally acquired genes are often silenced to protect bacterial genomes, but this defence also limits the expression of new traits. We identify a prophage-encoded small RNA, HnrS, that counteracts this restriction by repressing the xenogenic silencer Hha, lifting Hha-H-NS-mediated repression of virulence and metabolic genes. HnrS activates the locus of enterocyte effacement, nitrate/nitrite respiration, and nitric oxide resistance--pathways that help E. coli survive and colonise the inflamed gut. Our findings reveal an RNA-based counter-silencing mechanism encoded by mobile genetic elements, showing how phages can reprogram bacterial regulatory networks to promote adaptation and pathogenicity.

microbiology↗

bioRxiv2025

Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon Insertion in vivo.

The piggyBac transposase enables robust forward genetic screens in mice. Further, fusions of piggyBac with specific transcription factors (TFs) enables recovery of recoverable transposons (Calling Cards) for recording location of DNA binding events in vitro and in vivo. Such applications would be enhanced by engineering inducible transposases, such that timing of recording could be precisely controlled in vivo, as has been previously developed in vitro. Here, we tested two approaches for applying inducible Calling Cards (iCC) in the murine brain. We engineered knock-ins of inducible versions of two TFs: Jun, an immediate early gene that serves as a proxy for neural activity, and Sp1, a promiscuous binder of CpG unmethylated regions that indicates active promoters. We fused hyperPiggyBac transposase and a tamoxifen-inducible domain (ERT2) to these TFs and tested the system for efficacy and temporal control of insertions, both in vitro and in vivo. Jun-iCC mice developed normally with no behavioral abnormalities, showed tamoxifen-dependent recording, and captured neural activity during pharmacologically induced seizures. Jun-iCC yields relatively low numbers of insertions, likely due to the transient expression of Jun. In contrast, Sp1-iCC provided substantially higher insertion numbers, but transgenic animals exhibited developmental abnormalities, including reduced viability, anophthalmia, and reduced body weight, suggesting that ERT2 domains may sequester Sp1 and thus significantly impact development. Nonetheless, these inducible Calling Cards mouse lines enable drug-inducible integration of transposon cargo into specific loci in the living mouse. SIGNIFICANCE STATEMENTTransposases, like the more widely used recombinases (Cre, Flp, etc.), enable the integration of a variety of DNA sequences into the genome, but without dependence on LoxP sites. However, few mouse reagents exist for transposases. Cre has been adapted to be drug-inducible, as well as activity-regulated (e.g., FOS-TRAP). Thus, additional applications would become available if transposases could also be drug-controlled and activity-dependent. Further, there may be benefits to targeting integration to specific genomic region types (e.g., promotors). Here, we report results testing mouse lines for two drug-inducible transposase fusions to transcription factors (TF) - the promoter binding SP1, and activity dependent Jun. Both allowed genomic integration, with viability, efficiency, inducibility and targeting varying by TF-fusion.

neuroscience↗

bioRxiv2025

Single nucleus multiomic atlas of human dorsal root ganglia reveals the contribution of non-neuronal cell types to pain

Sensory neurons residing in dorsal root ganglia (DRG) transmit sensory information such as pain, itch, touch, pressure and bodily position to the central nervous system. The activity of sensory neurons is regulated by non-neuronal cell types in the DRG, including satellite glial cells (SGCs), immune cells and fibroblasts. Dysregulated gene expression in DRG cells contributes to sensory nervous system disorders such as chronic pain. Understanding the genetic underpinnings of these conditions requires dissecting transcriptional regulation in human tissue. In this study, we profiled transcriptomic and chromatin accessibility landscapes from postmortem human DRG (hDRG) samples at single-nucleus level. We demonstrate that sequencing depth significantly impacts downstream analysis, with deeper sequencing yielding more detected cells and features, improved data integration, refined clustering and annotation, and more accurate scientific interpretations. We identified nine major cell types, defined their molecular signatures, and mapped cis-regulatory landscapes. Integration of gene expression with chromatin accessibility enabled peak-gene association and transcriptional network analyses, revealing transcription factors, their target genes, regulatory elements and potential partners that cooperatively drive cell-type-specific gene expression programs. This integrative approach identified cell types, genes, and cis-regulatory regions potentially driving pain conditions. Our unbiased genome-wide analysis not only recovered known pain-related genes but also highlighted novel candidate genes and regulatory regions implicated in pain mechanisms. Importantly, our results demonstrate that non-neuronal cells, including endothelial cells, fibroblasts, macrophages, and SGCs, play critical roles in pain pathogenesis and should be investigated as therapeutic targets. One Sentence SummaryOur work provides a comprehensive single-nucleus multi-omic atlas of human dorsal root ganglia, uncovering novel cell-type-specific regulatory mechanisms and candidate therapeutic targets for pain, thereby directly advancing translational insights into human sensory disorders and chronic pain pathogenesis.

neuroscience↗

bioRxiv2025

A multi-omic atlas of human autonomic and sensory ganglia implicates cell types in peripheral neuropathies

The human peripheral nervous system (PNS) consists of many ganglia including sympathetic ganglia (SG) and dorsal root ganglia (DRG). These ganglia house the cell bodies of diverse PNS neurons that transmit autonomic and sensory signals, as well as a much larger number of non-neuronal cells. However, the molecular and cellular diversity of these human PNS cell types and their implications in human disease remain elusive. By generating an integrated single-cell multi-omic atlas of human SG and DRG, we provide comprehensive transcriptional and epigenomic landscapes of various cell types in these peripheral ganglia. While the major cell types and their cell-type-specific transcriptional and epigenomic features are similar between human SG and DRG, we identify key differences between SG and DRG cell types. These differences highlight the distinct molecular and cellular mechanisms underlying their specific functions. We also profiled key genomic regulatory networks that govern cell-type-specific gene expression in these peripheral ganglia. Moreover, by mapping the expression and chromatin accessibility of disease-associated genes in human SG and DRG, we identify cell types that may underlie various peripheral neuropathies. This atlas serves as a valuable resource for understanding the intricate cell-type-specific molecules and interactions in the human PNS and their implications in human health and diseases.

neuroscience↗

bioRxiv2025

Human sensory neurons exhibit cell-type-specific, pain-associated differences in intrinsic excitability and expression of SCN9A and SCN10A

Despite major advances in pain science, the approval of novel therapeutics has been slow. A major cause for the lack of new analgesics may be fundamental biological differences between humans and model organisms used in preclinical research. Large-scale transcriptional profiling efforts on human dorsal root ganglia (hDRG) have now identified at least 22 distinct neuronal subtypes; however, a significant knowledge gap exists in ascribing functional phenotypes to these diverse neuronal populations. In this study, we use Patch-seq recordings in hDRG to link electrical properties to transcriptionally defined cell types. First, through unbiased clustering of electrophysiological properties from 228 hDRG neurons, we identify three electrophysiological subtypes (E-types). Next, we show that E-types can be mapped onto specific transcriptional classes (T-types) of hDRG neurons. We find that donors pain history is associated with E-type-specific differences in electrical properties, some of which may be associated with higher expression of voltage-gated sodium channels, NaV1.7 and NaV1.8. These results highlight the importance of using multimodal profiling to better understand human sensory neuron biology and may help reveal novel therapeutic targets driving chronic pain. TeaserMapping electrical properties to transcriptional profiles of human sensory neurons offers new insights into pain neurobiology

neuroscience↗

bioRxiv2025

Expression of Fibroblast Growth Factor Receptor 3 (FGFR3) in the Human Peripheral Nervous System: Implications for the Putative Pathogenic Role of FGFR3 Autoantibodies in Neuropathy

IntroductionAutoantibodies to the Fibroblast Growth Factor Receptor 3 (FGFR3-AAbs) have been associated with idiopathic sensory-predominant neuropathy. The pathogenicity of FGFR3-AAbs in this disorder is unknown. Pathogenic mechanisms of autoantibodies in other dysimmune neuropathies commonly involve their direct binding to antigens on either neurons or glia. The expression of FGFR3 in the human peripheral nervous system is unknown. Therefore, as an initial step toward clarifying the pathogenicity of FGFR3-AAbs, we characterized the expression of FGFR3 in nerve (hNerve), dorsal root ganglia (hDRG) and spinal cord (hSC) in human. MethodsFGFR3 mRNA was assayed via in situ hybridization (ISH) on post-mortem sections of hNerve, hDRG and hSC, and by re-analysis of RNA-sequencing data from hDRG. FGFR3 protein was assayed in these tissues using capillary electrophoretic immunoassays (CEIA) with several validated anti-FGFR3 antibodies. ResultsFGFR3 mRNA was not detected in hNerve or hDRG but was abundant in hSC by ISH. FGFR3 protein was absent from hNerve and hDRG by CEIA but was moderately expressed in hSC. DiscussionA direct pathogenic mechanism of FGFR3-AAbs in sensory neuropathy would require the expression of FGFR3 in either neurons or non-neuronal cells in nerve or DRG. Using multiple methods, we did not detect FGFR3 expression at the mRNA or protein levels in these tissues. Given the absence of FGFR3 from hNerve and hDRG, it is improbable that FGFR3-AAbs cause direct damage to the neural components involved in neuropathy and thus are unlikely to be pathogenic, although indirect mechanisms via non-neural cells cannot be excluded.

neuroscience↗

bioRxiv2025

Small molecule-mediated targeted protein degradation of voltage-gated sodium channels involved in pain

The voltage-gated sodium channels (VGSC) NaV1.8 and NaV1.7 (NaVs) have emerged as promising and high-value targets for the development of novel, non-addictive analgesics to combat the chronic pain epidemic. In recent years, many small molecule inhibitors against these channels have been developed. The recent successful clinical trial of VX-548, a NaV1.8-selective inhibitor, has spurred much interest in expanding the arsenal of subtype-selective voltage-gated sodium channel therapeutics. Toward that end, we sought to determine whether NaVs are amenable to targeted protein degradation with small molecule degraders, namely proteolysis-targeting chimeras (PROTACs) and molecular glues. Here, we report that degron-tagged NaVs are potently and rapidly degraded by small molecule degraders harnessing the E3 ubiquitin ligases cereblon (CRBN) and Von Hippel Lindau (VHL). Using LC/MS analysis, we demonstrate that PROTAC-mediated proximity between NaV1.8 and CRBN results in ubiquitination on the 2nd intracellular loop, pointing toward a potential mechanism of action and demonstrating the ability of CRBN to recognize a VGSC as a neosubstrate. Our foundational findings are an important first step toward realizing the immense potential of NaV-targeting degrader analgesics to combat chronic pain.

neuroscience↗

bioRxiv2024

Global genomic dissection of antimicrobial resistance in Salmonella Typhimurium

Salmonella Typhimurium (STm) is a globally prevalent pathogen. We compiled a dataset comprising [~]65,000 publicly available STm isolates and analysed the predicted-resistance to 15 key antibiotics. Additionally, we typed all isolates using a standardized typing method, multilevel genome typing (MGT), and characterised the resistance profiles by MGT sequence types (ST). We identified 407 MGT STs wherein at least 80% of the isolates were non-susceptible to at least one antibiotic. For the key antibiotics prescribed for severe salmonellosis, we identified three ciprofloxacin non-susceptible MGT STs, and eight cefotaxime non-susceptible MGT STs in the last two years of the dataset (2021-2022). While the ciprofloxacin non-susceptible MGT STs comprised isolates predominantly from the UK; only one cefotaxime non-susceptible MGT ST comprised isolates predominantly from UK and associated with swine, with others from USA, and associated with cattle and poultry. Integration of AMR predictions with MGT strain typing provides sharable, standardised, and specific identification and tracking of resistant isolates. This integrated analysis presents a unique approach for the global surveillance of antimicrobial resistance and resistant strains.

microbiology↗

bioRxiv2024

Characterising Staphylococcus aureus genomic epidemiology with Multilevel Genome Typing.

Staphylococcus aureus is a major source of both hospital and community acquired infections, and is the leading source of skin and soft tissue infections worldwide. Advances in whole genome sequencing (WGS) technologies have recently generated large volumes of S. aureus WGS data. The timely classification of S. aureus WGS data with genomic typing technologies has the potential to describe detailed genomic epidemiology at large and small scales. In this study, a multilevel genome typing (MGT) scheme comprised of 8 levels of multilocus sequence typing schemes of increasing resolution was developed for S. aureus and used to analyse 50,481 publicly available genomes. Application of MGT to S. aureus epidemiology was showcased in three case studies. Firstly, the population structure of the globally disseminated sequence type ST8 were described by MGT2, which was compared with Spa typing. Secondly, MGT was used to characterise MLST ST8 - PFGE USA300 isolates that colonised multiple body sites of the same patient. Unique STs from multiple MGT levels were able to group isolates of the same patient, and the highest resolution MGT8 separated isolates within a patient that varied in predicted antimicrobial resistance. Lastly, MGT was used to describe the transmission of MLST ST239 - SCCmec III throughout a single hospital. MGT STs were able to describe both isolates that had spread between wards and also isolates that had colonised different reservoirs within a ward. The S. aureus MGT describes large- and small-scale S. aureus genomic epidemiology with scalable resolutions using stable and standardised ST assignments. The S. aureus MGT database is online (https://mgtdb.unsw.edu.au/staphylococcus) and is capable of tracking new and existing clones to facilitate the design of new strategies to reduce the global burden of S. aureus related diseases.

microbiology↗

bioRxiv2023

Larval swimming in the sea anemone Nematostella vectensis is sensitive to a broad light spectrum and exhibits a wavelength-dependent behavioral switch

In nearly all animals, light sensing mediated by opsin visual pigments is important for survival and reproduction. Eyeless light-sensing systems, though vital for many animals, have received relatively less attention than forms with charismatic or complex eyes. Despite no single light sensing organ, the sea anemone Nematostella vectensis, has 29 opsin genes and multiple light-mediated behaviors throughout development and reproduction, suggesting a deceptively complex light-sensing system. To characterize one aspect of this light-sensing system, we analyzed larval swimming behavior at high wavelength resolution across the ultraviolet and visual spectrum. N. vectensis larvae respond to light at least from 315 to 650 nm, which is a broad sensitivity range even compared to many animals with complex eyes. Swimming in the water column is induced by ultraviolet (UV) and violet wavelengths until 420 nm. Between 420 and 430 nm a behavioral switch occurs where at wavelengths longer than 430 nm, larvae respond to light by swimming down. Swimming down toward the substrate is distinct from light avoidance, as animals do not exhibit positive or negative phototaxis at any wavelength tested. At wavelengths longer than 575 nm, animals in the water column take increasingly longer to respond and this behavior is more variable until 650 nm where larval response is no different from the dark, suggesting these longer wavelengths lie outside of their sensitivity range. Larval swimming is the only motile stage in the life history of N. vectensis, and increased swimming activity in the water column could lead to greater dispersal range in potentially damaging shallow environments with short-wavelength light exposure. Longer wavelength environments may indicate more suitable substrates for metamorphosis into the polyp stage, where the individual will remain for the rest of its life. Future work will test whether this robust behavior is mediated by multiple opsins.

animal behavior and cognition↗

bioRxiv2023

Multiple parallel expansions of bilaterian-like phototransduction gene families in the eyeless Anthozoa

Opsin-mediated phototransduction cascades in photoreceptor cells are primarily responsible for light-mediated behaviors in animals. Although some visual cascades are well-studied, phototransduction mediated by non-visual opsins and in non-model animal lineages are poorly characterized. In the Cnidaria (jellyfish, corals, sea anemones etc.), the sister group to Bilateria (vertebrates, arthropods, mollusks etc.), limited evidence suggests some overlap with bilaterian phototransduction. This raises the question of whether phototransduction pathways arose a single time early in animal evolution or if light signaling cascades have evolved multiple times. These evolutionary patterns remain obscured because almost nothing is known about phototransduction in a major group within Cnidaria, the eyeless Anthozoa (corals, sea anemones, sea pens etc.). To better understand whether bilaterian-like phototransduction could be present in Anthozoa, we phylogenetically characterized 63 genes in 12 protein families known to be crucial in two types of bilaterian phototransduction in the sea anemone Nematostella vectensis. Using high quality genomic data from N. vectensis, we took a candidate gene approach to find phototransduction genes and characterize their expression in development and regeneration. We found that N. vectensis possesses the core suite of proteins for both r-opsin and c-opsin mediated phototransduction. In addition, several new gene subfamilies were identified, particularly in the G protein subunits and TRP channels, and many were anthozoan-specific. We identified a novel G protein subunit family, which we call GVI, and characterized its expression in N. vectensis with in situ hybridization. This expansion of phototransduction genes correlates with a large anthozoan-specific radiation in opsin number, suggesting possible coevolution of receptor and signaling diversity in Anthozoa. While further functional experiments on these genes are needed, our findings are in line with the hypothesis that the common ancestor of Eumetazoa had at least two related phototransduction cascades which then further diversified in each animal lineage.

evolutionary biology↗

bioRxiv2023

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

Bordetella pertussis is responsible for the respiratory infectious disease pertussis (or whooping cough), which causes one of the most severe diseases in infants, although it can be prevented by whole cell and acellular vaccines. The recent resurgence of pertussis is partially due to pathogen adaptation to vaccines as well as resistance to antimicrobials. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health. Although there is increased genomics based typing, a genomic nomenclature for this pathogen has not been well established. Here, we implemented the Multilevel Genome Typing (MGT) system for B. pertussis with five levels of resolution, which provide targeted typing of relevant lineages as well as discrimination of closely related strains at the finest scale. The low resolution levels can describe the distribution of alleles of major vaccine antigen genes such as ptxP, fim3, fhaB and prn as well as temporal and spatial trends within the B. pertussis global population. Mid-resolution levels enables typing of antibiotic resistant lineages and Prn deficient lineages within the ptxP3 clade. High resolution levels can capture small-scale epidemiology such as local transmission events and has comparable resolution to existing genomic methods of strain relatedness assessment. The scheme offers stable MGT type assignments aiding harmonisation of typing and communication between laboratories. The scheme is available at www.mgtdb.unsw.edu.au/pertussis/ is regularly updated from global data repositories and accepts public data submissions. The MGT scheme provides a comprehensive, robust, and scalable system for global surveillance of B. pertussis.

microbiology↗

bioRxiv2023

Bradykinin receptor expression and bradykinin-mediated sensitization of human sensory neurons

Bradykinin is a peptide implicated in inflammatory pain in both humans and rodents. In rodent sensory neurons, activation of B1 and B2 bradykinin receptors induces neuronal hyperexcitability. Recent evidence suggests that human and rodent dorsal root ganglia (DRG), which contain the cell bodies of sensory neurons, differ in the expression and function of key GPCRs and ion channels; whether BK receptor expression and function are conserved across species has not been studied in depth. In this study, we used human DRG tissue from organ donors to provide a detailed characterization of bradykinin receptor expression and bradykinin-induced changes in the excitability of human sensory neurons. We found that B2 and, to a lesser extent, B1 receptors are expressed by human DRG neurons and satellite glial cells. B2 receptors were enriched in the nociceptor subpopulation. Using patch-clamp electrophysiology, we found that acute bradykinin increases the excitability of human sensory neurons, while prolonged exposure to bradykinin decreases neuronal excitability in a subpopulation of human DRG neurons. Finally, our analyses suggest that donors history of chronic pain and age may be predictors of higher B1 receptor expression in human DRG neurons. Together, these results indicate that acute BK-induced hyperexcitability, first identified in rodents, is conserved in humans and provide further evidence supporting BK signaling as a potential therapeutic target for treating pain in humans.

neuroscience↗

bioRxiv2023

SaLTy: a novel Staphylococcus aureus Lineage Typer

Staphylococcus aureus asymptomatically colonises 30% of humans and in 2017 was associated with 20,000 deaths in the USA alone. Dividing S. aureus into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus WGS when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5,000 genomes and 99.12% (4,956/5,000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (n=21,173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCCmec) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCCmec and the four largest lineages varied in SCCmec over time. Classifying isolates into SaLTy lineages, which were further SCCmec typed, allowed SaLTy to describe high-level MRSA epidemiology We provide SALTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SALTy is highly accurate and can quickly analyse large amounts of S. aureus WGS. SALTy will aid the characterisation of S. aureus populations and the ongoing surveillance of sub-groups that threaten human health.

microbiology↗