Biology subjects

Whiley, D.

Publications and source records attributed to Whiley, D..

4 recordsLinked to original sources

bioRxiv2025

Evaluating a SNP calling pipeline for Mycobacterium leprae

Mycobacterium leprae is the causative agent of leprosy, a persisting disease characterised by skin lesions and peripheral nerve numbness. Attempts to sequence the genome have been challenged by its inability to be cultured on artificial media. Advances in DNA extraction and sequencing technologies have enabled molecular epidemiology to be introduced for M. leprae. However, a validated SNP calling pipeline does not currently exist. A ground truth of pairwise SNP differences was first created using Minimap2 and three complete genomes of M. leprae. Using simulated reads from each of these genomes and the others as a reference, we evaluated the precision and recall of short-read SNP calling using Snippy. Approximately 80% of SNPs were called with false positives only due to ambiguous bases in certain genomes. Repeat region masking was found to be unnecessary for M. leprae SNP calling, unlike for M. tuberculosis. We find that SNP calling from short reads is robust and highly accurate from M. leprae, showing promise as a tool for molecular epidemiology studies to increase case detection and inform leprosy control strategies.

genomics↗

bioRxiv2020

A comparison of ThinPrep-PreservCyt against four non-volatile transport media for HPV testing at or near the point of care.

IntroductionThe Xpert HPV Test (Cepheid, Sunnyvale, CA) is used at point-of-care for cervical screening in a number of low-and middle-income countries (LMIC). It is validated for use with ThinPrep-PreservCyt (Hologic, Marlborough, MA) transport medium which has a high methanol content and is therefore classified as a dangerous good for shipping; making cost, transportation and use challenging within LMIC. Therefore, we compared the performance of ThinPrep against four non-volatile commercially available media for HPV point-of-care testing. MethodsTen-fold serial dilutions were prepared using three HPV cell lines each positive for 16, 18 or 31 and with each suspended in five different media types. The media types consisted of Phosphate Buffered Saline (Thermo Fischer Scientific, Waltham, MA, USA), Sigma Virocult (Medical Wire & Equipment, Wiltshire, England), MSwab (Copan, Brescia BS, Italy) Xpert Transport Media (Cepheid, Sunnyvale, USA) and ThinPrep-PreservCyt (Hologic Inc., Marlborough, MA). ResultsA total of 105 HPV Xpert tests were conducted in a laboratory setting, with 7 ten-fold dilutions of each of the 3 HPV genotypes tested in all 5 media types. The lowest HPV ten-fold dilution detected for any media, or cell line was the fifth dilution. Mswab was the only media to detect HPV to the 5th dilution across all three cell types. DiscussionMswab transport media may be a suitable alternative to ThinPrep for Xpert HPV point of care testing and increase HPV detection. A field-based, head to head comparison of both media types using the Xpert HPV assay is warranted to confirm these laboratory-based findings.

microbiology↗

bioRxiv2019

Prospective evaluation of beta-lactamase detection in penicillin susceptible Staphylococcus aureus by interpretation of the penicillin disc edge

Penicillin susceptible Staphylococcus aureus (PSSA) may occasionally be encountered as a cause of complicated S. aureus infection, such as endocarditis or bloodstream infections. Clinicians may choose to treat these patients with penicillin over a semi-synthetic penicillin derivative, such as flucloxacillin or oxacillin, due to a favourable Pk/Pd profile. In this study, we prospectively evaluated the penicillin disc (1-IU) method for detection of blaZ, with interpretation of the penicillin edge according to EUCAST recommendations. 472 PSSA isolates were collected between September 2014 to December 2015 from three clinical microbiology laboratories in Queensland, Australia. Initial antimicrobial susceptibility testing was performed by the Vitek 2 system. Real-time PCR for blaZ was performed following phenotypic testing with the 1-IU penicillin disc and the PCR used as the gold standard for detection of penicillinase. The prevalence of blaZ amongst the isolates was 7%. The sensitivity, specificity, positive predictive value and negative predictive value of the penicillin disc method was 97%, 95%, 61% and 100% when compared to blaZ PCR. In summary, the penicillin disc zone size and edge interpretation is a reliable method for detection of blaZ in S. aureus isolates that otherwise test susceptible to penicillin by Vitek 2 AST.

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↗