Biology subjects

Rahman, A.

Publications and source records attributed to Rahman, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Colorectal cancers with distinct metastatic potential trigger divergent early T cell responses

Colorectal cancer (CRC) remains a leading cause of cancer mortality, with most cases refractory to immunotherapy. Distinguishing tumor-induced from steady-state mucosal T cell responses has been a critical barrier to understanding antitumor immunity in CRC. Using orthotopic transplantation of CRC organoids with and without metastatic potential, combined with temporal T cell fate-mapping, we show that non-metastatic tumors elicit early recruitment of CD8{beta} and CD4 T cells that acquired cytotoxic and Th1-like programs, whereas pro-metastatic tumors induce a naive-like, hypoactivated state. Tumor-infiltrating CD4+ T cells underwent clonal expansion, including clones recognizing microbial and dietary antigens. T cells in physical contact with tumor cells, identified by uLIPSTIC, were enriched for expanded and cytotoxic clones. Fate-mapped T cells from non-metastatic tumors suppressed tumor growth in an IFN-{gamma}-dependent manner, whereas pro-metastatic tumor-derived T cells failed to do so. Mechanistically, pro-metastatic tumors downregulated MHCII, and Ciita targeting in non-metastatic organoids reduced CD4 clonal expansion and led to tumor progression. Together, these findings define divergent early T cell trajectories associated with CRC metastatic potential, indicating that ineffective local immune engagement precedes metastatic dissemination.

immunology↗

bioRxiv2026

A ML-framework for the discovery of next-generation IBD targets using a harmonized single-cell atlas of patient tissue

Target discovery for IBD has traditionally relied on genetic associations, which lack the cellular resolution needed to identify novel, actionable, cell type-specific disease pathways. Here, we describe an integrated analytical and experimental framework that leverages harmonized single-cell data to systematically discover novel therapeutic strategies for IBD. We used AMICA DBTM, Immunais harmonized database of single-cell RNA datasets to construct a harmonized 1 million single-cell atlas of the human intestine. We applied a machine learning framework (Immune Patient Representation, IPR) to identify disease-associated transcriptional programs and cell type-specific gene targets. Candidate targets were prioritized using atlas-derived metrics, refined using custom criteria emphasizing translational actionability, and validated across independent clinical cohorts. Select candidates were evaluated in human primary-cell models reflecting the targets cell-type context. The IPR framework identified 85 disease-associated transcriptional programs and ranked 400 cell type-specific target genes across immune and stromal lineages. Disease-associated programs were interpreted using a structured AI-assisted reasoning framework for structured biological reasoning, linking them to IBD-relevant pathways and guiding the identification of novel, promising gene targets. Functional validation of two cell-type-specific candidates, PTGIR in myeloid cells and IL6ST in fibroblasts, confirmed the reduction of inflammatory and fibrotic pathways linked to IBD pathology. Multi-omic profiling and projection of in vitro phenotypes to patient datasets demonstrated the reversal of disease-associated programs via mechanisms distinct from those of existing biologics. Our single-cell anchored, machine-learning framework integrates in silico discovery with experimental validation, revealing new cell type-specific therapeutic opportunities and supporting a scalable approach for precision target discovery in IBD and other immune-mediated diseases.

bioinformatics↗

bioRxiv2026

PARP1 recruits SPRTN to DNA-protein crosslinks through a conserved poly-ADP-ribose binding domain.

DNA-protein crosslinks (DPCs) are toxic DNA lesions formed by the covalent attachment of proteins to DNA. Failure to resolve DPCs leads to genomic instability, premature aging, and cancer predisposition. Although multiple proteases and the 26S proteasome degrade DPCs, how these lesions are detected and marked for proteolysis remains unclear. Here, we show that poly-(ADP-ribose) polymerases (PARP1/2) sense DPCs and modify them with poly(ADP-ribose) (PAR) to promote repair via a SPRTN-Tdp1 axis. We discovered a Nudix homology domain (NHD) in SPRTN that mediates direct non-covalent PAR binding and is important for DPC repair. Loss of PARP1/2 activity or mutation of the SPRTN NHD leads to sustained DPCs. Single-molecule analysis revealed that SPRTN does not bind efficiently to the DPC, however after the addition of PARP1 in the presence of NAD+, SPRTN binding to the DPC was significantly increased. Our findings establish PARP1/2 enzymes as immediate DPC sensors, reveal PARylation as a signal marking DPCs for SPRTN-dependent degradation, and identify SPRTN as the first PARP-directed protease.

molecular biology↗

bioRxiv2025

Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa

Oat (Avena sativa L.) is a globally important cereal cultivated for both livestock feed and human nutrition. However, its productivity is increasingly constrained by both biotic and abiotic stresses, exacerbated by rapid climate change. To support the development of dual-usage, stress-resilient and high-yielding cultivars adapted to subtropical agroecologies, we evaluated the genetic structure and agronomic performance of a 169-member oat association panel. This panel was phenotyped for key vegetative, forage feed quality and grain related traits across three subtropical locations in Sub-Saharan Africa (SSA) over two growing seasons and genotyped using Genotyping-by-Sequencing (GBS). Diversity analysis, based on filtered SNPs, showed moderate genetic diversity (He = 0.39 and PIC = 0.3), and population structure analysis identified two main sub-groups with varying degrees of admixture, suggesting gene flow among different groups. Genome-wide association analysis uncovered 42 SNPs significantly associated with sixteen traits (false discovery rate, FDR, <0.05), along with 46 candidate genes located near these loci. Notably, candidate genes associated with seed traits included a homolog of rice OsAK3, encoding adenylate kinase, and a UDP-glucosyltransferase homologous to rice GSA1, both previously shown to regulate grain size. These genes were located near QTL linked to seed length, width, and thousand-grain weight. Another key candidate, encoding a subunit of the ESCRT-II complex (VPS25), was identified near a separate QTL and is implicated in intracellular trafficking, endosperm development, and overall seed quality. By illuminating the genetic architecture of economically important traits and identifying molecular markers linked to yield, quality and resilience, this study provides valuable genomic resources to support genomics-based breeding aimed at developing climate-resilient, productive oats varieties adapted to sub-tropical agro-ecologies.

genomics↗

bioRxiv2025

Autoantibody origins in lupus and in relapse post CAR-T therapy

Anti-CD19 chimeric antigen receptor (CAR)-T therapy induces profound remissions in lupus by depleting B cells, challenging the longstanding view that treatment-resistant disease is sustained by long-lived plasma cells. Additionally, emerging relapses highlight the need to understand how pathogenic autoantibodies arise. Using molecular antibody tagging in mice with human monogenic lupus variants, we reveal that autoantibody-producing cell cohorts are long-lived but plasma cells are short-lived, requiring continuous replenishment from proliferating precursors. The spleen acts as a major plasma cell reservoir, with perivascular localization conserved in mice and lupus patients. Relapse after anti-CD19 CAR-T occurred through newly-generated B cells rather than treatment-resistant clones. Plasma cell depletion by anti-BCMA CAR-T failed to eliminate some precursors that become autoantibody-secreting. These findings demonstrate that continuous B cell-to-plasma cell differentiation, not intrinsic plasma cell longevity, sustains pathogenic antibody responses in lupus, supporting a potential benefit of adjunctive therapies after CAR-T, particularly in genetically predisposed patients.

immunology↗

bioRxiv2025

EGGS: Empirical Genotype Generalizer for Samples

SummaryWe introduce Empirical Genotype Generalizer for Samples (EGGS) which accepts empirical genotypes with missing data and replicates the distribution of missing genotypes along the empirical segment in other replicates. The empirical segment must have a number of sites less than the replicate. In addition, EGGS can remove phase, remove polarization, simulate deamination, simulate sequencing error, create pseudohaploids, and convert between Variant Call Format (VCF), ms-style replicates, and EIGENSTRAT/ANCESTRYMAP. When producing VCF files, EGGS is not limited to biallelic sites and assumes all samples are diploid. Availability and ImplementationEGGS is written in the C programming language. Precompiled executables, source code, the manual, and the analysis conducted in the paper are available at https://github.com/TQ-Smith/EGGS

bioinformatics↗

bioRxiv2025

Selection scans and downstream analysis with selscan

Summary statistics based on Extended Haplotype Homozygosity (EHH) are widely used for inferring positive selection in genomes as a result of their ease of use, computational efficiency, and interpretability. These various summary statistics can be applied to single populations or to pairs of populations, can be used with a genetic recombination map or without, and can be applied to phased or unphased data. Although these statistics are straightforward to compute, there lacks clear descriptions on how they relate to one another, how they should be used, and how their resulting outputs should be interpreted. Here, we provide a comprehensive introduction to selection statistics as they are implemented in the widely used software, selscan. In addition to this detailed guide, we implement enhanced normalization procedures and support for gene-based analyses, enabling users to translate selection signals captured by these statistics into gene-level interpretations using BED annotation files, facilitating biologically meaningful insights. We demonstrate the behavior of such statistics on simulated data and highlight best practices by performing an example downstream analysis on data from the 1000 Genomes Project using new features in selscan v3.0. We hope these guidelines will foster reproducibility in the evolutionary genomics community. Precompiled executables and source code for selscan v3.0 can be found at https://github.com/szpiech/selscan.

evolutionary biology↗

bioRxiv2025

RNA Pol I activity maintains chromatin condensation and the H3K4me3 gradient essential for oogenesis, independent of ribosome production

Oogenesis requires extensive and dynamic chromatin remodeling that primes gene promoters for later transcriptional activation during embryonic development. Here, we uncover a pivotal, non-canonical role for RNA Polymerase I (Pol I) in driving these chromatin state transitions during Caenorhabditis elegans oogenesis. Using the auxin-inducible degron system to selectively deplete either Pol I catalytic subunits or ribosome assembly factors, we disentangle the consequences of impaired nucleolar integrity from reductions in ribosome biogenesis. Strikingly, although disrupting ribosome assembly caused minimal effects on oocyte production, loss of Pol I activity led to widespread changes in chromatin accessibility, a dampening of the distal-proximal H3K4me3 gradient required for oogenesis, reduced synapsis, and elevated ATM/ATR phosphorylation, resulting in fewer but significantly larger oocytes. Despite their promoters becoming more accessible, oogenesis genes did not show large changes in steady-state mRNA, consistent with transcriptional repression prior to fertilization. Instead, Pol I depletion prematurely remodeled oogenic chromatin, through a misdirection of H3K4me3 deposition towards promoters normally primed for zygotic genome activation. These findings reveal an epigenetic gating function for nucleolar integrity in oocyte maturation: Pol I preserves three-dimensional chromatin organization and maintains proper spatiotemporal regulation of histone modifications, independent of ribosome production. Given the evolutionary conservation of nucleolar dynamics and histone modifications during gametogenesis, our work suggests that nucleolar stress, whether from environmental factors, aging, or genetic disorders, could broadly compromise fertility by disrupting oogenic chromatin priming. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/652530v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@9b95bforg.highwire.dtl.DTLVardef@844eb5org.highwire.dtl.DTLVardef@4b7a79org.highwire.dtl.DTLVardef@155ca31_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Evolutionary Influences on Local Patterns of Genetic Relatedness

Dimensionality reduction methods, such as Principal Components Analysis (PCA) or Multi-dimensional Scaling (MDS), when applied to genomic data, help to visualize the relatedness of individuals in lower dimensional space and are ubiquitous in population-genetic studies. These analyses use genome-wide patterns of variation to provide an "average" picture of genetic structure and relatedness. However, evolutionary processes result in different patterns of relationship among samples in local genomic regions as compared to the genome-wide aggregate. Recently, these local patterns of relatedness have been used to identify regions under selection and inverted segments. Here, we propose a unifying method to dissect these local deviations in genetic relatedness. Our method, Local Decomposition and Similarity to All Regions (LODESTAR), uses Procrustes Analysis to assess the similarity between local MDS results computed using pairwise allele sharing distances or a set of user-defined points. Given two sets of points, Procrustes Analysis computes the optimal rotation and scaling that fits one set of points onto the other, while maintaining the relative relationship between points within both sets. We use the Procrustes statistic to measure the similarity between the two sets of points. We show how this method can be used to explore local relatedness patterns that mirror sampling geography or population stratification by performing Procrustes analysis between local relatedness plots and coordinates representing sampling geography or between local relatedness plots and the genome-wide relatedness plot, respectively. In addition, we show how the variance of samples in lower-dimensional space can capture regions lacking population structure and inverted segments.

evolutionary biology↗

bioRxiv2025

Immunogenicity and Structural Features of a Stabilized Clade-C HIV-1 Env Derived from a Pediatric Elite-neutralizer

The envelope (Env) glycoprotein derived from circulating viruses in elite-neutralizers (who naturally develop broadly neutralizing antibodies (bNAbs)), serves as potential template for HIV-1 vaccine design. Herein, we report the structure and immunogenicity of soluble clade-C HIV-1 Env trimer (330) derived from a pediatric elite-neutralizer (AIIMS_330). Using SOSIP, NFL and ferritin-nanoparticle (NP) platforms, we engineered immunogens that preserved native-like Env conformation, exhibited high thermostability and nanomolar affinity for diverse bNAbs, with minimal reactivity to non-neutralizing antibodies. Cryo-EM structure solved at 5 [A] resolution of 330-SOSIP trimer-autologous bNAb 44m complex revealed interactions at GDIR motif, N332 supersite along with additional contacts at E293, K337, K446 and glycans N326, N442, N448, as compared to our previously reported BG505-44m structure. Rabbit immunizations with soluble and NP-displayed formats elicited autologous, and heterologous neutralization of tier-1 clade-C viruses. Herein we define a structurally resolved HIV-1 clade C Env that supports multivalent vaccine strategies and provides mechanistic insights toward rational HIV-1 immunogen design.

immunology↗

bioRxiv2025

Privacy-Preserving Generative AI Framework for Synthetic Multimodal Eye Movement Data

Eye movements, such as nystagmus, saccades, and smooth pursuit, provide valuable information about neurological function but have limited publicly accessible datasets due to patient privacy concerns. To address this, we leverage generative AI to create realistic videos of artificial eye movement, eliminating the need for real patient data. These synthetic datasets have shown performance comparable to actual patient data in clinical tasks. Our generated videos will be openly shared, facilitating broader research and advancement in neurologic and neuro-ophthalmic AI applications.

bioengineering↗

bioRxiv2025

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans

Haplotype-based statistics are widely used for finding genomic regions under positive selection. At the heart of many such statistics is the computation of extended haplotype homozygosity (EHH), which captures the decay of homozygosity away from a focal site. This computation, repeated for potentially millions of sites, is computationally demanding, as it involves tracking counts of unique haplotypes iteratively over long genomic distances and across many individuals. Because of these computational challenges, existing tools do not scale well when applied to large-scale population datasets, such as the 1000 Genomes Project, or the UK Biobank with 500,000 individuals. Optimizing computation becomes crucial when data sets grow large, especially when handling large sample sizes or generating training data for machine learning algorithms. https://github.com/szpiech/selscan Here, we propose a dynamic programming algorithm that substantially improves runtime and memory usage over existing tools on both real and simulated data. On real phased data, we achieve 5-50x speedup with minimal memory footprint. Our simulations show an even more pronounced performance gap with large populations (up to 15x speedup and 46x memory reduction). EHH-based statistics designed for unphased genotypes run an order of magnitude faster, and multi-parameter support results in 20x runtime improvement. Source code and binaries are available at https://github.com/szpiech/selscan as selscan v2.1.

genomics↗

bioRxiv2025

Excessive Postnatal Smooth Muscle Differentiation in a Lung Specific Model of TBX4-related Pulmonary Hypertension

Heterozygous TBX4 variants are the second most common genetic cause of pediatric pulmonary hypertension (PH), yet the mechanisms underlying the pathophysiology of TBX4-related lung disease remain poorly understood. We developed a lung mesenchyme-specific Tbx4 loss of function (Tbx4cKO) mouse model that bypasses embryonic lethality to investigate TBX4-related lung disease. Echocardiography of adult Tbx4cKO mice demonstrated significant hemodynamic changes consistent with PH. Three-dimensional whole-mount analysis of embryonic day 18.5 lungs revealed reduced lobe volumes and decreased distance between pleural edges and muscularized vessels. In adult Tbx4cKO lungs, high-resolution spatial quantitation identified extensive vascular remodeling characterized by significant medial thickening, distal muscularization of small diameter arteries, and extension of muscularized vessels into normally non-muscularized subpleural zones. Contrary to previous reports suggesting vascular simplification with Tbx4 loss, our comprehensive three-dimensional approach demonstrated an elaborated arterial tree with pathologic muscularization. Additional heterozygous loss of Tbx5 (Tbx4cKO;Tbx5het) exacerbated vascular phenotypes without worsening hemodynamic parameters. We also documented dysregulated airway smooth muscle patterning and prominent subpleural smooth muscle bands that share molecular features with myofibroblasts and airway smooth muscle cells, echoing pathologic findings in human TBX4 syndrome lung tissue. Collectively, our findings identify TBX4 as a critical suppressor of smooth muscle differentiation across multiple pulmonary compartments. This model recapitulates key features of human TBX4 syndrome and reveals mild developmental underpinnings with subsequent progressive postnatal smooth muscle dysregulation, highlighting a postnatal window during which therapeutic regulation of mesenchymal differentiation may be beneficial.

genetics↗

bioRxiv2025

VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog

Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.

microbiology↗

bioRxiv2025

Future flooding tolerant rice germplasm: resilience afforded beyond Sub1A gene

Developing high-yielding, flood-tolerant rice varieties is essential for enhancing productivity and livelihoods in flood-prone ecologies. We explored genetic avenues beyond the well-known SUB1A gene to improve flood resilience in rice. We screened a collection of 6,274 elite genotypes from IRRIs germplasm repository for submergence and stagnant flooding tolerance over multiple seasons and years. This rigorous screening identified 89 outstanding elite genotypes, among which thirty-seven exhibited high submergence tolerance, surpassing the survival rate of SUB1A introgression genotypes by 40-50%. Thirty-five genotypes showed significant tolerance to stagnant flooding, and 17 demonstrated dual tolerance capabilities, highlighting their adaptability to varying flood conditions. The genotypes identified have a broader genetic diversity and harbor 86 key QTLs and genes related to traits such as grain quality, grain yield, herbicide resistance, and various biotic and abiotic traits, highlighting the richness of the identified elite collection. Besides germplasm, we introduce an innovative breeding approach called Transition from Trait to Environment (TTE). TTE leverages a parental pool of high-performing genotypes with complete submergence tolerance to drive population improvement and enable genomic selection in the flood breeding program. Our approach of TTE achieved a remarkable 65% increase in genetic gain for submergence tolerance, with the resulting fixed breeding genotypes demonstrating exceptional performance in flood-prone environments of India and Bangladesh. The elite genotypes identified herein represent invaluable genetic resources for the global rice research community. By adopting the TTE approach, which is trait agonistic, we establish a robust framework for developing more resilient genotypes using advanced breeding tools. Plain Language SummaryTo address climate challenges, an urgent focus is necessary to identify and develop flood-tolerant rice varieties, particularly for flood-prone ecosystems across Asia and Africa. We screened 6,274 elite genotypes from IRRIs germplasm and identified 89 promising lines with improved tolerance to submergence and stagnant flooding. Among these, 37 demonstrated 40-50% greater submergence tolerance than SUB1A introgression lines, 35 exhibited stagnant flooding tolerance, and 17 showed dual tolerance. These genotypes contain 86 key QTLs and genes associated with yield, grain quality, and biotic and abiotic tolerance traits. A new breeding strategy, the Transition from Trait to Environment (TTE) approach, was developed. We achieved a genetic gain of 65% for submergence tolerance in rice using this method. The newly identified germplasm provides invaluable genetic resources for the global rice research community to develop flood-tolerant rice genotypes. Core ideas The SUB1A gene, enabling rice to survive underwater for 14 days, marked a significant breakthrough. We have identified elite genotypes with submergence tolerance significantly surpassing the SUB1A gene-mediated tolerance. The diverse elite genotypes identified harbor 86 key genes and QTLs that affect various traits positively. Developed a unique breeding strategy for implementing population improvement in challenging environments. The new breeding strategy demonstrated a genetic gain of 65% for submergence tolerance.

plant biology↗

bioRxiv2025

Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion

Multipartite bacterial genome organization can confer advantages including coordinated gene regulation and faster genome replication but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the lab model strain C58, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria (CFBP) and identified two strains with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed both replication origins remain active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres are essential. Importantly, the site-specific recombinases XerCD are required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains. ImportanceMost bacterial genomes are monopartite with a single, circular chromosome. But some species, like Agrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches including pathogenesis or symbiosis. Multipartite genomes confer certain advantages, however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage of A. tumefaciens strain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two environmental isolates of A. tumefaciens containing fused chromosomes derived from a different route, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings help us better understand how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification.

microbiology↗

bioRxiv2025

Dirt floors and domestic animals are associated with soilborne exposure to antimicrobial resistant E. coli in rural Bangladeshi households

Soil can harbor enteropathogens and antimicrobial-resistant organisms in settings with domestic animals. We enrolled 49 households with young children (28 soil floors, 21 concrete floors) in Bangladesh and recorded animal ownership/management. Staff swabbed the floor of childrens sleeping area with a sterile sponge and collected floor dust and a child hand rinse. We used IDEXX QuantiTray/2000 with and without cefotaxime supplementation to enumerate cefotaxime-resistant and generic E. coli. There was 8.0 g/m2 of dust on soil floors vs. 0.2 g/m2 on concrete floors (p-value=0.005). We detected E. coli on 100% of soil vs. 86% of concrete floors and cefotaxime-resistant E. coli on 89% of soil vs. 43% of concrete floors (p-values<0.05). Cefotaxime-resistant E. coli prevalence on floors was 36% in compounds without animals, 79% in compounds with animals and 100% if animals stayed indoors overnight or the floor had animal feces; associations were strongest for chickens. In multivariable models, generic and cefotaxime-resistant E. coli counts were 1.5-2 log higher on soil vs. concrete floors, and counts on floors and child hands were 0.17-0.24 log higher for every 10 additional chickens owned (p-values<0.05). Efforts to mitigate infections and antimicrobial resistance in low-income countries should test flooring improvements and hygienic animal management. SynopsisIn rural Bangladeshi households, generic and cefotaxime-resistant E. coli were more common on soil floors than concrete floors and among households with higher cohabitation intensity with domestic animals, especially chickens.

microbiology↗

bioRxiv2025

A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology

Whole genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary relationships. Recent improvements in Oxford Nanopore long-read sequencing have made its use attractive for genomic epidemiology. However, the accuracy and optimal strategy for analysis of Nanopore reads remains to be determined. We compared the use of Illumina short reads and Oxford Nanopore long reads for genome assembly and variant calling of phytopathogenic bacteria. We generated short- and long-read datasets for diverse phytopathogenic Agrobacterium strains. We then analyzed these data using multiple pipelines designed for either short or long reads and compared the results. We found that assemblies made from long reads were more complete than those made from short-read data and contained few sequence errors. Variant calling pipelines differed in their ability to accurately call variants and infer genotypes from long reads. Results suggest that computationally fragmenting long reads can improve the accuracy of variant calling in population-level studies. Using fragmented long reads, pipelines designed for short reads were more accurate at recovering genotypes than pipelines designed for long reads. Further, short- and long-read datasets can be analyzed together with the same pipelines. These findings show that Oxford Nanopore sequencing is accurate and can be sufficient for microbial pathogen genomics and epidemiology. Ultimately, this enhances the ability of researchers and clinicians to understand and mitigate the spread of pathogens. ImportanceGenome assembly and variant calling are important steps in microbial population studies and epidemiology. Most variant calling and genotyping pipelines are designed for Illumina short sequencing reads. Oxford Nanopore Technology long-read sequencing results in more complete genome assemblies but has historically been of lower quality. Here, we show that Nanopore long reads are now of sufficient quality for bacterial whole genome assembly and epidemiology. We benchmarked the accuracy of multiple variant-calling pipelines with short and long reads. Using an optimized variant calling approach, variant calls and genotypes inferred from long reads are as accurate as those inferred from short reads. Importantly, we found that gold-standard variant calling pipelines designed for short reads are also accurate with long reads when long reads are first fragmented into shorter sequences. This finding allows researchers to incorporate the advantages of Nanopore sequencing for genome assembly, while maintaining high accuracy for epidemiology and population analysis.

genomics↗