Biology subjects

Saund, K.

Publications and source records attributed to Saund, K..

5 recordsLinked to original sources

bioRxiv2021

Strain variation in Clostridioides difficile toxin activity associated with genomic variation at both PaLoc and non-PaLoc loci

Clinical disease from Clostridioides difficile infection can be mediated by two toxins and their neighboring regulatory genes encoded within the five-gene pathogenicity locus (PaLoc). We provide several lines of evidence that the toxin activity of C. difficile may be modulated by genomic variants outside of the PaLoc. We used a phylogenetic tree-based approach to demonstrate discordance between toxin activity and PaLoc evolutionary history, an elastic net method to show the insufficiency of PaLoc variants alone to model toxin activity, and a convergence-based bacterial genome-wide association study (GWAS) to identify correlations between non-PaLoc loci with changes in toxin activity. Combined, these data support a model of C. difficile disease wherein toxin activity may be strongly affected by many non-PaLoc loci. Additionally, we characterize multiple other in vitro phenotypes relevant to human infections including germination and sporulation. These phenotypes vary greatly in their clonality, variability, convergence, and concordance with genomic variation. Lastly, we highlight the intersection of loci identified by GWAS for different phenotypes and clinical severity. This strategy to identify the overlapping loci can facilitate the identification of genetic variation linking phenotypic variation to clinical outcomes. IMPORTANCEClostridioides difficile has two major disease mediating toxins, A and B, encoded within the pathogenicity locus (PaLoc). In this study we demonstrate via multiple approaches that genomic variants outside of the PaLoc are associated with changes in toxin activity. These genomic variants may provide new avenues of exploration in the hunt for novel disease modifying interventions. Additionally, we provide insight into the evolution of several additional phenotypes also critical to clinical infection such as sporulation, germination, and growth rate. These in vitro phenotypes display a range of responses to evolutionary pressures and as such vary in their appropriateness for certain bacterial genome wide association study approaches. We used a convergence-based association method to identify the genomic variants most correlated with both changes in these phenotypes and disease severity. These overlapping loci may be important to both bacterial function and human clinical disease.

microbiology↗

bioRxiv2020

hogwash: Three Methods for Genome-Wide Association Studies in Bacteria

Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene- or pathway-analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub. DATA SUMMARYO_LIhogwash is available from GitHub under the MIT license (https://github.com/katiesaund/hogwash) and can be installed using the R commands install.packages("devtools") devtools::install_github("katiesaund/hogwash") C_LIO_LIThe simulated data used in this manuscript and the code to generate it are available from GitHub (https://github.com/katiesaund/simulate_data_for_convergence_based_bGWAS) C_LI IMPACT STATEMENTWe introduce hogwash, an R package with three methods for bacterial genome-wide association studies. There are two methods for handling binary phenotypes, including an implementation of PhyC(1), as well as one method for handling continuous phenotypes. We formulate novel indices quantifying the relationship between phenotype convergence and genotype convergence on a phylogenetic tree. These indices shape an intuitive understanding for the ability of hogwash to detect significant intersections of phenotype convergence and genotype convergence and how to interpret hogwash outputs.

microbiology↗

bioRxiv2019

prewas: Data pre-processing for more informative bacterial GWAS

While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior to their use in bacterial genome-wide association studies (bGWAS). Three nuances of variant pre-processing that impact downstream identification of genetic associations include the separation of variants at multiallelic sites, separation of variants in overlapping genes, and referencing of variants relative to ancestral alleles. Here we demonstrate the importance of these variant pre-processing steps on diverse bacterial genomic datasets and present prewas, an R package, that standardizes the pre-processing of multiallelic sites, overlapping genes, and reference alleles before bGWAS. This package facilitates improved reproducibility and interpretability of bGWAS results. Prewas enables users to extract maximal information from bGWAS by implementing multi-line representation for multiallelic sites and variants in overlapping genes. Prewas outputs a binary SNP matrix that can be used for SNP-based bGWAS and will prevent the masking of minor alleles during bGWAS analysis. The optional binary gene matrix output can be used for gene-based bGWAS which will enable users to maximize the power and evolutionary interpretability of their bGWAS studies. Prewas is available for download from GitHub. DATA SUMMARYO_LIprewas is available from GitHub under the MIT License (URL: https://github.com/Snitkin-Lab-Umich/prewas) and can be installed using the command devtools::install_github("Snitkin-Lab-Umich/prewas") C_LIO_LICode to perform analyses is available from GitHub under the MIT License (URL: https://github.com/Snitkin-Lab-Umich/prewas_manuscript_analysis) C_LIO_LIAll genomes are publicly available on NCBI (see Table S1 for more details) C_LI O_TBL View this table: org.highwire.dtl.DTLVardef@137f5b6org.highwire.dtl.DTLVardef@e4a12dorg.highwire.dtl.DTLVardef@11b2a3org.highwire.dtl.DTLVardef@1e71da1org.highwire.dtl.DTLVardef@4a7286_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable S1:C_FLOATNO O_TABLECAPTIONSources for bacterial datasets C_TABLECAPTION C_TBL IMPACT STATEMENTIn between variant calling and performing bacterial genome-wide association studies (bGWAS) there are many decisions regarding processing of variants that have the potential to impact bGWAS results. We discuss the benefits and drawbacks of various variant pre-processing decisions and present the R package prewas to standardize single nucleotide polymorphism (SNP) pre-processing, specifically to incorporate multiallelic sites and prepare the data for gene-based analyses. We demonstrate the importance of these considerations by highlighting the prevalence of multiallelic sites and SNPs in overlapping genes within diverse bacterial genomes and the impact of reference allele choice on gene-based analyses.

bioinformatics↗

bioRxiv2019

Evidence that vertical transmission of the vaginal microbiota can persist into adolescence

BackgroundFactors that influence vaginal microbiota composition, including its source, are not well understood. To determine if vaginal microbiota transmission from mother to daughter at birth influences the human vaginal microbiota composition in adolescence, we investigated the relationship between the vaginal microbiota of 13 mother/daughter pairs and the daughters birth mode. ResultsBased on analysis of bacterial 16S rRNA gene sequences, the vaginal microbiotas of mother/daughter pairs were more similar to each other if the daughter was born by vaginal delivery rather than by C-section. Additionally, genome sequences from an important member of the vaginal microbiota, Lactobacillus crispatus, isolated from one mother/daughter pair in which the daughter was born by vaginal delivery, were highly similar. ConclusionsBoth community-level analysis and isolate genome sequence analysis are consistent with birth-mode dependent transmission and persistence of at least some members of the vaginal microbiota. ImportanceThe composition of the human vaginal microbiota is related to many aspects of health from infection susceptibility to preterm birth. Our study provides evidence that transmission of vaginal bacteria from mother to daughter at birth may be an important factor influencing vaginal microbiota composition into adolescence.

microbiology↗

bioRxiv2019

Outbreak of murine infection with Clostridium difficile associated with the administration of a pre- and peri-natal methyl-donor diet

Between October 2016 and June 2017, a C57BL/6J mouse colony that was undergoing a pre- and peri-natal methyl-donor supplementation diet intervention to study the impact of parental nutrition on offspring susceptibility to disease was found to suffer from an epizootic of unexpected deaths. Necropsy revealed the presence of severe colitis, and further investigation linked these outbreak deaths to a Clostridium difficile strain of ribotype 027 we term 16N203. C. difficile infection (CDI) is associated with antibiotic use in humans. Current murine models of CDI rely on antibiotic pretreatment to establish clinical phenotypes. In this report, the C. difficile outbreak occurs in F1 mice linked to alterations in the parental diet. The diagnosis of CDI in the affected mice was confirmed by cecal/colonic histopathology, presence of C. difficile bacteria in fecal/colonic culture, and detection of C. difficile toxins. F1 mice from parents fed the methyl-supplementation diet also had significantly reduced survival (p<0.0001) than F1 mice from parents fed the control diet. When we tested the 16N203 outbreak strain in an established mouse model of antibiotic-induced CDI, we confirmed that this strain is pathogenic. Our serendipitous observations from this spontaneous outbreak of C. difficile in association with a pre- and perinatal methyl-donor diet suggest the important role diet may play in host defense and CDI risk factors.\n\nImportanceClostridium difficile infection (CDI) has become the leading cause of infectious diarrhea in hospitals worldwide, owing its preeminence to the emergence of hyperendemic strains, such as ribotype 027 (RT027). A major CDI risk factor is antibiotic exposure which alters gut microbiota, resulting in the loss of colonization resistance. Current murine models of CDI also depend on pretreatment of antibiotics of animals to establish disease. The outbreak we report here is unique in that the CDI occurred in mice with no antibiotic exposure and is associated to a pre- and peri-natal methyl-supplementation donor diet intervention study. Our investigation subsequently reveals that the outbreak strain we term 16N203 is an RT027 strain, and this isolated strain is also pathogenic in an established murine model of CDI (with antibiotics). Our report of this spontaneous outbreak offers additional insight into the importance of environmental factors, such as diet, and CDI susceptibility.

epidemiology↗