scholarly journals Ethnically diverse urban transmission networks of Neisseria gonorrhoeae without evidence of HIV serosorting

2019 ◽  
Vol 96 (2) ◽  
pp. 106-109
Author(s):  
Jayshree Dave ◽  
John Paul ◽  
Thomas Joshua Pasvol ◽  
Andy Williams ◽  
Fiona Warburton ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Ethnic Groups ◽  
Antimicrobial Susceptibility ◽  
Sequence Data ◽  
Small Sample ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequencing Data ◽  
Transmission Networks ◽  
Hiv Serosorting

ObjectiveWe aimed to characterise gonorrhoea transmission patterns in a diverse urban population by linking genomic, epidemiological and antimicrobial susceptibility data.MethodsNeisseria gonorrhoeae isolates from patients attending sexual health clinics at Barts Health NHS Trust, London, UK, during an 11-month period underwent whole-genome sequencing and antimicrobial susceptibility testing. We combined laboratory and patient data to investigate the transmission network structure.ResultsOne hundred and fifty-eight isolates from 158 patients were available with associated descriptive data. One hundred and twenty-nine (82%) patients identified as male and 25 (16%) as female; four (3%) records lacked gender information. Self-described ethnicities were: 51 (32%) English/Welsh/Scottish; 33 (21%) white, other; 23 (15%) black British/black African/black, other; 12 (8%) Caribbean; 9 (6%) South Asian; 6 (4%) mixed ethnicity; and 10 (6%) other; data were missing for 14 (9%). Self-reported sexual orientations were 82 (52%) men who have sex with men (MSM); 49 (31%) heterosexual; 2 (1%) bisexual; data were missing for 25 individuals. Twenty-two (14%) patients were HIV positive. Whole-genome sequence data were generated for 151 isolates, which linked 75 (50%) patients to at least one other case. Using sequencing data, we found no evidence of transmission networks related to specific ethnic groups (p=0.64) or of HIV serosorting (p=0.35). Of 82 MSM/bisexual patients with sequencing data, 45 (55%) belonged to clusters of ≥2 cases, compared with 16/44 (36%) heterosexuals with sequencing data (p=0.06).ConclusionWe demonstrate links between 50% of patients in transmission networks using a relatively small sample in a large cosmopolitan city. We found no evidence of HIV serosorting. Our results do not support assortative selectivity as an explanation for differences in gonorrhoea incidence between ethnic groups.

scholarly journals MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5895 ◽  
Author(s):  
Thomas Andreas Kohl ◽  
Christian Utpatel ◽  
Viola Schleusener ◽  
Maria Rosaria De Filippo ◽  
Patrick Beckert ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Sequencing Data ◽  
Desktop Computer

Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source.

scholarly journals Rapid statistical methods for inferring intra- and inter-hospital transmission of nosocomial pathogens from whole genome sequence data

2018 ◽  
Author(s):  
Marianne Aspbury ◽  
James Sciberras ◽  
Jukka Corander ◽  
Sion C. Bayliss ◽  
Tjibbe Donker ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genome Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Bacterial Pathogens ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Transmission Networks ◽  
Genome Sequence Data ◽  
Hospital Transmission

AbstractWhole genome sequence (WGS) data for bacterial pathogens can provide evidence as to the source of nosocomial infection, and more specifically the ability to distinguish between intra- and inter-hospital transmission. This is currently achieved either through using SNP thresholds, which can lack statistical robustness, or by constructing phylogenetic trees, which can be computationally expensive and difficult to interpret. Here we compare two alternative statistical approaches using 1022 genomes of methicillin resistantStaphylococcus aureus(MRSA) clone ST22. In 71% of cases both methods predict the same hospital origin, which is also supported by the ML tree. Robust assignments are divided approximately equally between intra-hospital transmission and inter-hospital transmission. Our approaches are rapid and produce intuitive output that could inform on immediate infection control priorities, as well as providing long-term data on inter-hospital transmission networks. We discuss the strengths and weakness of our methods, and the generalisability of this approach.One Sentence SummaryWe present rapid statistical methods for distinguishing intra- versus inter-hospital transmission of bacterial pathogens using whole genome sequence data; these methods do not require the use of SNP thresholds or the generation and interpretation of phylogenetic trees.

scholarly journals Population genomics of East Asian ethnic groups

Hereditas ◽  
2020 ◽  
Vol 157 (1) ◽  
Author(s):  
Ziqing Pan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Ethnic Groups ◽  
Population Genomics ◽  
Sequence Data ◽  
East Asian ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

scholarly journals Characteristics of Salmonella recovered from stools of children enrolled in the Global Enteric Multicenter Study

2021 ◽  
Author(s):  
Irene N Kasumba ◽  
Caisey V Pulford ◽  
Blanca M Perez-Sepulveda ◽  
Sunil Sen ◽  
Nurulla Sayed ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Multicenter Study ◽  
Antimicrobial Susceptibility ◽  
Sequence Data ◽  
Sub Saharan Africa ◽  
Whole Genome Sequence ◽  
Diffusion Method ◽  
Whole Genome ◽  
Disk Diffusion Method ◽  
Severe Diarrhea

Abstract Background The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of non-typhoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates. Methods Salmonella isolated from children with MSD or diarrhea-free controls were identified by classical clinical microbiology and serotyped using antisera and/or whole genome sequence data. We evaluated antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. Salmonella Typhimurium sequence types were determined using multi-locus sequence typing and whole genome sequencing was performed to assess the phylogeny of ST313. Results Out of 370 Salmonella-positive individuals, 190 (51.4%) were MSD cases and 180 (48.6%) were diarrhea-free controls. The most frequent Salmonella serovars identified were Salmonella Typhimurium, serogroup O:8 (C2-C3), serogroup O:6,7 (C1), Salmonella Paratyphi B Java and serogroup O:4 (B). The prevalence of NTS was low but similar across sites, regardless of age, and was similar amongst both cases and controls except in Kenya, where Salmonella Typhimurium was more commonly associated with cases than controls. Phylogenetic analysis showed that these Salmonella Typhimurium isolates, all ST313, were highly genetically related to isolates from controls. Generally, Salmonella isolates from Asia were resistant to ciprofloxacin and ceftriaxone but African isolates were susceptible to these antibiotics. Conclusion Our data confirms that NTS is prevalent, albeit at low levels, in Africa and South Asia. Our findings provide further evidence that multi-drug resistant Salmonella Typhimurium ST313 can be carried asymptomatically by humans in sub-Saharan Africa.

scholarly journals KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

2017 ◽  
Author(s):  
Jungeun Kim ◽  
Jessica A. Weber ◽  
Sungwoong Jho ◽  
Jinho Jang ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Sequence Data ◽  
Copy Number Variations ◽  
Genetic Variations ◽  
Korean Population ◽  
National Standard ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Personal Genome ◽  
Whole Genome ◽  
Sequencing Data

AbstractHigh-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations. Herein, we report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals with an average coverage depth of 31×. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project data when prioritizing disease-causing variants. CNV analyses revealed gene losses related to bone mineral densities and duplicated genes involved in brain development and fat reduction. Finally, KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.

scholarly journals Training workshop on Mycobacterium whole genome sequence data analysis

2019 ◽  
Vol 24 ◽  
Author(s):  
Yonas Kassahun Hirutu ◽  
Mesert D Bayeleygne ◽  
Adey F Desta ◽  
Tewodros Tariku ◽  
Markos Abebe
Keyword(s):  
Life Science ◽  
Sequence Data ◽  
Addis Ababa ◽  
Whole Genome Sequence ◽  
Next Generation Sequencing Data ◽  
Whole Genome ◽  
Training Workshop ◽  
Sequencing Data ◽  
Training Initiative ◽  
Generation Sequencing

Basic bioinformatics training workshop conducted at Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia. This report describes a bioinformatics training initiative started at AHRI aiming to support life science researchers and postgraduates in handling next-generation sequencing data.

scholarly journals Accurate Phasing of Pedigree Genotypes Using Whole Genome Sequence Data

2017 ◽  
Author(s):  
A.N. Blackburn ◽  
M.Z. Kos ◽  
N.B. Blackburn ◽  
J.M. Peralta ◽  
P. Stevens ◽  
...  
Keyword(s):  
Error Rate ◽  
Sequence Data ◽  
Software Implementation ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Genotype Data ◽  
Whole Genome ◽  
Genotyping Error ◽  
Sequencing Data ◽  
Missing Genotypes

AbstractPhasing, the process of predicting haplotypes from genotype data, is an important undertaking in genetics and an ongoing area of research. Phasing methods, and associated software, designed specifically for pedigrees are urgently needed. Here we present a new method for phasing genotypes from whole genome sequencing data in pedigrees: PULSAR (Phasing Using Lineage Specific Alleles / Rare variants). The method is built upon the idea that alleles that are specific to a single founding chromosome within a pedigree, which we refer to as lineage-specific alleles, are highly informative for identifying haplotypes that are identical-by-decent between individuals within a pedigree. Through extensive simulation we assess the performance of PULSAR in a variety of pedigree sizes and structures, and we explore the effects of genotyping errors and presence of non-sequenced individuals on its performance. If the genotyping error rate is sufficiently low PULSAR can phase > 99.9% of heterozygous genotypes with a switch error rate below 1 x 10-4 in pedigrees where all individuals are sequenced. We demonstrate that the method is highly accurate and consistently outperforms the long-range phasing approach used for comparison in our benchmarking. The method also holds promise for fixing genotype errors or imputing missing genotypes. The software implementation of this method is freely available.

scholarly journals Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

2019 ◽  
Author(s):  
Allison L. Hicks ◽  
Nicole Wheeler ◽  
Leonor Sánchez-Busó ◽  
Jennifer L. Rakeman ◽  
Simon R. Harris ◽  
...  
Keyword(s):  
Machine Learning ◽  
Antibiotic Resistance ◽  
Antibiotic Susceptibility ◽  
Sequence Data ◽  
Model Performance ◽  
Outcome Data ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

AbstractPrediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics. However, there has been no systematic evaluation of factors that may influence performance of such models, how they might apply to and vary across clinical populations, and what the implications might be in the clinical setting. Here, we performed a meta-analysis of seven large Neisseria gonorrhoeae datasets, as well as Klebsiella pneumoniae and Acinetobacter baumannii datasets, with whole genome sequence data and antibiotic susceptibility phenotypes using set covering machine classification, random forest classification, and random forest regression models to predict resistance phenotypes from genotype. We demonstrate how model performance varies by drug, dataset, resistance metric, and species, reflecting the complexities of generating clinically relevant conclusions from machine learning-derived models. Our findings underscore the importance of incorporating relevant biological and epidemiological knowledge into model design and assessment and suggest that doing so can inform tailored modeling for individual drugs, pathogens, and clinical populations. We further suggest that continued comprehensive sampling and incorporation of up-to-date whole genome sequence data, resistance phenotypes, and treatment outcome data into model training will be crucial to the clinical utility and sustainability of machine learning-based molecular diagnostics.Author SummaryMachine learning-based prediction of antibiotic resistance from bacterial genome sequences represents a promising tool to rapidly determine the antibiotic susceptibility profile of clinical isolates and reduce the morbidity and mortality resulting from inappropriate and ineffective treatment. However, while there has been much focus on demonstrating the diagnostic potential of these modeling approaches, there has been little assessment of potential caveats and prerequisites associated with implementing predictive models of drug resistance in the clinical setting. Our results highlight significant biological and technical challenges facing the application of machine learning-based prediction of antibiotic resistance as a diagnostic tool. By outlining specific factors affecting model performance, our findings provide a framework for future work on modeling drug resistance and underscore the necessity of continued comprehensive sampling and reporting of treatment outcome data for building reliable and sustainable diagnostics.

scholarly journals Genome-scale profiling reveals noncoding loci carry higher proportions of concordant data

2021 ◽  
Author(s):  
Robert Literman ◽  
Rachel Schwartz
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Coding Sequences ◽  
Evolutionary Forces ◽  
Tree Inference ◽  
Intergenic Regions

Abstract Many evolutionary relationships remain controversial despite whole-genome sequencing data. These controversies arise in part due to challenges associated with accurately modeling the complex phylogenetic signal coming from genomic regions experiencing distinct evolutionary forces. Here we examine how different regions of the genome support or contradict well-established hypotheses among three mammal groups using millions of orthologous parsimony-informative biallelic sites [PIBS] distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages among locus types (e.g. coding sequences, introns, intergenic regions), and contrasted PIBS utility over evolutionary timescales. Sites derived from noncoding sequences provided more data and proportionally more concordant sites compared with those from coding sequences [CDS] in all clades. CDS PIBS were also predominant drivers of tree incongruence in two cases of topological conflict. PIBS derived from most locus types provided surprisingly consistent support for splitting events spread across the timescales we examined, although we find evidence that CDS and intronic PIBS may, respectively and to a limited degree, inform disproportionately about older and younger splits. In this era of accessible whole genome sequence data, these results (1) suggest benefits to more intentionally focusing on noncoding loci as robust data for tree inference, and (2) reinforce the importance of accurate modeling, especially when using CDS data.

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