Biology subjects

Forde, B.

Publications and source records attributed to Forde, B..

5 recordsLinked to original sources

bioRxiv2022

Systematic benchmarking of all-in-one microbial SNP calling pipelines

Clinical and public health microbiology is increasingly utilising whole genome sequencing (WGS) technology and this has lead to the development of a myriad of analysis tools and bioinformatics pipelines. Single nucleotide polymorphism (SNP) analysis is an approach used for strain characterisation and determining isolate relatedness. However, in order to ensure the development of robust methodologies suitable for clinical application of this technology, accurate, reproducible, traceable and benchmarked analysis pipelines are necessary. To date, the approach to benchmarking of these has been largely ad-hoc with new pipelines benchmarked on their own datasets with limited comparisons to previously published pipelines. In this study, Snpdragon, a fast and accurate SNP calling pipeline is introduced. Written in Nextflow, Snpdragon is capable of handling small to very large and incrementally growing datasets. Snpdragon is benchmarked using previously published datasets against six other all-in-one microbial SNP calling pipelines, Lyveset, Lyveset2, Snippy, SPANDx, BactSNP and Nesoni. The effect of dataset choice on performance measures is demonstrated to highlight some of the issues associated with the current available benchmarking approaches. The establishment of an agreed upon gold-standard benchmarking process for microbial variant analysis is becoming increasingly important to aid in its robust application, improve transparency of pipeline performance under different settings and direct future improvements and development. Snpdragon is available at https://github.com/FordeGenomics/SNPdragon. Impact statementWhole-genome sequencing has become increasingly popular in infectious disease diagnostics and surveillance. The resolution provided by single nucleotide polymorphism (SNP) analyses provides the highest level of insight into strain characteristics and relatedness. Numerous approaches to SNP analysis have been developed but with no established gold-standard benchmarking approach, choice of bioinformatics pipeline tends to come down to laboratory or researcher preference. To support the clinical application of this technology, accurate, transparent, auditable, reproducible and benchmarked pipelines are necessary. Therefore, Snpdragon has been developed in Nextflow to allow transparency, auditability and reproducibility and has been benchmarked against six other all-in-one pipelines using a number of previously published benchmarking datasets. The variability of performance measures across different datasets is shown and illustrates the need for a robust, fair and uniform approach to benchmarking. Data SummaryO_LIPreviously sequenced reads for Escherichia coli O25b:H4-ST131 strain EC958 are available in BioProject PRJNA362676. BioSample accession numbers for the three benchmarking isolates are: O_LIEC958: SAMN06245884 C_LIO_LIMS6573: SAMN06245879 C_LIO_LIMS6574: SAMN06245880 C_LI C_LIO_LIAccession numbers for reference genomes against the E. coli O25b:H4-ST131 strain EC958 benchmark are detailed in table 2. C_LIO_LISimulated benchmarking data previously described by Yoshimura et al. is available at http://platanus.bio.titech.ac.jp/bactsnp (1). C_LIO_LISimulated datasets previously described by Bush et al. is available at http://dx.doi.org/10.5287/bodleian:AmNXrjYN8 (2). C_LIO_LIReal sequencing benchmarking datasets previously described by Bush et al. are available at http://dx.doi.org/10.5287/bodleian:nrmv8k5r8 (2). C_LI O_TBL View this table: org.highwire.dtl.DTLVardef@f2446corg.highwire.dtl.DTLVardef@16a299corg.highwire.dtl.DTLVardef@d1c7a5org.highwire.dtl.DTLVardef@8a3cbaorg.highwire.dtl.DTLVardef@198f455_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONReference genomes used in the EC958 benchmarking dataset and the percent identity against the three included samples. C_TABLECAPTION C_TBL

bioinformatics↗

bioRxiv2022

A gut commensal protozoa remotely shapes a lung niche for asthma-promoting eosinophils.

The gut microbiome influences chronic inflammation of the airways via the gut-lung axis. However, causal connections between microbes and their host, including the underlying mechanisms for this phenomenon remain largely unknown. Here, we show that colonization with the gut commensal protozoa, Tritrichomonas musculis (T.mu), remotely shapes the lung immune landscape and exacerbates allergic airway inflammation. We demonstrate that colonization with T.mu mediates the T and B cell-dependent accumulation and activation of inflammatory group 2 innate lymphoid cells in the lungs to constitute a tripartite immune network that serves as a niche for lung eosinophils. Animals colonized with T.mu show severely exacerbated allergic inflammation in the airways and reveal a new protozoan-driven gut-lung axis that remotely shapes the lung immune network to potentiate chronic pulmonary inflammation. One-Sentence SummaryA gut microbe exacerbates asthma severity by promoting lung eosinophilia through a tripartite lymphocyte immune network.

immunology↗

bioRxiv2021

Excessive inflammatory and metabolic responses to acute SARS-CoV-2 infection are associated with a distinct gut microbiota composition

Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and associated clinical sequelae requires well-coordinated metabolic and immune responses that limit viral spread and promote recovery of damaged systems. In order to understand potential mechanisms and interactions that influence coronavirus disease 2019 (COVID-19) outcomes, we performed a multi-omics analysis on hospitalised COVID-19 patients and compared those with the most severe outcome (i.e. death) to those with severe non-fatal disease, or mild/moderate disease, that recovered. A distinct subset of 8 cytokines and 140 metabolites in sera identified those with a fatal outcome to infection. In addition, elevated levels of multiple pathobionts and lower levels of protective or anti-inflammatory microbes were observed in the faecal microbiome of those with the poorest clinical outcomes. Weighted gene correlation network analysis (WGCNA) identified modules that associated severity-associated cytokines with tryptophan metabolism, coagulation-linked fibrinopeptides, and bile acids with multiple pathobionts. In contrast, less severe clinical outcomes associated with clusters of anti-inflammatory microbes such as Bifidobacterium or Ruminococcus, short chain fatty acids (SCFAs) and IL-17A. Our study uncovered distinct mechanistic modules that link host and microbiome processes with fatal outcomes to SARS-CoV-2 infection. These features may be useful to identify at risk individuals, but also highlight a role for the microbiome in modifying hyperinflammatory responses to SARS-CoV-2 and other infectious agents.

immunology↗

bioRxiv2019

Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit

BackgroundKlebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which sources of transmission can be challenging to elucidate. We describe the use of whole genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-{beta}-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. MethodsCeftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read (Illumina) and long-read (MinION, Oxford Nanopore Technologies) sequencing was used to confirm species taxonomy, define antimicrobial resistance genes and determine phylogenetic relationships using single nucleotide polymorphism (SNP) profiling. ResultsA total of 21 organisms (10 patient-derived and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from baby bath drains and multiple detergent dispensing bottles were either identical or closely related by SNP comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk-expressing equipment. No new cases were identified once the detergent bottles were removed and the baby baths decommissioned. ConclusionsEnvironmental reservoirs may be an important source in outbreaks of multi-drug resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses. Key pointsO_LIK. michiganensis can be misidentified as K. oxytoca and is probably under-recognized as a nosocomial pathogen C_LIO_LIWhole genome sequencing of neonatal and environmental isolates during an outbreak of ESBL-producing K. michiganensis confirmed contaminated detergent and sinks to be the source C_LI

microbiology↗

bioRxiv2017

Use of whole genome sequencing to investigate an outbreak of gonorrhoea among females in urban New South Wales, Australia, 2012 to 2014.

Increasing rates of gonorrhoea have been observed among urban heterosexuals within the Australian state of New South Wales (NSW). Here, we applied whole genome sequencing (WGS) to better understand transmission dynamics. Ninety-four isolates of a particular N. gonorrhoeae genotype (G122) associated with female patients (years 2012 to 2014) underwent phylogenetic analysis using core single nucleotide polymorphisms (SNPs). Context for genetic variation was provided by including an unbiased selection of 1,870 N. gonorrhoeae genomes from a recent United Kingdom (UK) study. NSW genomes formed a single clade, with the majority of isolates belonging to one of five clusters, and comprised patients of varying age groups. Intra-patient variability was less than 7 core SNPs. Several patients had indistinguishable core SNPs, suggesting a common infection source. These data have provided an enhanced understanding of transmission of N. gonorrhoeae among urban heterosexuals in NSW, Australia, and highlight the value of using WGS in N. gonorrhoeae outbreak investigations.

epidemiology↗