Biology subjects

Sait, M.

Publications and source records attributed to Sait, M..

6 recordsLinked to original sources

bioRxiv2025

Comprehensive public health surveillance identifies novel human cryptosporidiosis subtypes and genetic diversity associated with swimming pool outbreaks in Australia, Victoria (2018-2024)

Cryptosporidium and Giardia are major causes of gastrointestinal illness globally. In Australia, cryptosporidiosis is a nationally notifiable disease, yet molecular characterisation of clinical cases is rarely performed, limiting the capacity to identify outbreaks, trace sources and assess zoonotic risk. During 2024 there was a 273% cases increase in Australia, the third country with the highest increase. We present the first comprehensive molecular investigation of human Cryptosporidium and Giardia infections in the state of Victoria, Australia. We analysed faecal samples collected between 2018 and 2024. Positive samples were subtyped and parasite load was estimated. Of the 2,330 samples tested, 225 were positive for Cryptosporidium and nine for Giardia. Seven Cryptosporidium species and 24 subtypes were identified, including multiple novel or regionally unique subtypes. C. hominis was the predominant species (85%), and three subtypes associated with 11 recreational water outbreaks in 2024. Based on spatiotemporal overlap and subtypes, 52 cases were inferred to represent undetected outbreak-associated infections. Several C. parvum subtypes reflected probable zoonotic transmission, two subtypes were associated with a childcare and camp outbreak. Six C. hominis subtypes and eight subtypes overall were reported for the first time in Australia. Globally novel subtypes of C. occultus, C. fayeri and C. meleagridis in human hosts is reported. The study reveals high diversity of Cryptosporidium subtypes in human infections in Victoria. This study demonstrates the potential for molecular surveillance to inform public health interventions when integrated with epidemiological data. These findings support One Health approaches to outbreak detection and source attribution. IMPORTANCECryptosporidium is a nationally notifiable pathogen in Australia, yet routine genotyping is not performed, limiting outbreak detection and source attribution. This study represents the first large-scale molecular surveillance of human Cryptosporidium and Giardia infections in southern Australia. By integrating species- and subtype-level typing with epidemiological metadata, we demonstrate the substantial diversity of infective lineages, including several novel or zoonotic genotypes. Our findings highlight the critical role of molecular tools in tracking transmission pathways, supporting outbreak investigation and informing public health responses. These data provide a foundation for incorporating routine genotyping into national surveillance strategies for parasitic enteropathogens. This study presents the first epidemiological study of the 2024 outbreaks in Australia. The global comparison of cases during this period also highlights potential large-scale disease dynamic of public health importance.

molecular biology↗

bioRxiv2025

Extensive endemic transmission of multidrug resistant Mycobacterium tuberculosis in Bhutan: A retrospective genomic-epidemiological study

Despite decreasing overall tuberculosis notifications, the proportion of multidrug-resistant tuberculosis (MDR-TB) cases are increasing in Bhutan. While most MDR-TB cases are diagnosed among patients in the bordering districts and the capital, current diagnostic tests are limited in their ability to differentiate between the recurrent introductions and local transmission. For the first time, we conducted a retrospective genomic-epidemiological study to provide insights into the population structure, genotypic resistance patterns, and explore recent transmission of drug-resistant TB in Bhutan. Whole genome sequencing was performed on randomly selected drug-resistant and drug-sensitive TB isolates from Bhutan, collected between 2018-2022 at Microbiological Diagnostic Unit Public Health Laboratory in Melbourne, Australia. We investigated drug resistance mutations, and genomic clustering of cases using different single nucleotide polymorphisms (SNPs) thresholds. Of the 203 sequences that passed the quality control, 126 (62.1%) were MDR-TB and 15 (7.4%) were isoniazid-resistant TB. There were four different circulating lineages, with most sequences belonging to lineage 2 (86.2%). Using a SNP-threshold of [≤]12 SNPs, 71% of sequences formed 12 genomic clusters. Surprisingly, the largest cluster included of 88% of all MDR-TB sequences and spanned the entire study period. These cases were highly clonal (mean pairwise SNP-distance of 10, range 0-25). Phylogenetic analysis with publicly available international sequence data showed that this MDR-TB cluster formed a distinct clade. The major burden of MDR-TB in Bhutan appears to be due to recent local transmission of cases resulting in a large, single endemic cluster. This information will be critical for TB control program in Bhutan to tackle the major burden of MDR-TB through enhanced contact tracing of this MDR-TB clade. Additionally, this genomic data will be valuable to regional neighbours to monitor for dissemination of the strain. This study highlights the significant value of investing in TB genomics in resource limited settings globally to gain actionable insights into transmission dynamics.

genomics↗

bioRxiv2023

Bringing TB genomics to the clinic: A comprehensive pipeline to predict antimicrobial susceptibility from genomic data, validated and accredited to ISO standards.

BackgroundWhole genome sequencing (WGS) is increasingly contributing to the clinical management of tuberculosis. Whilst the availability of bioinformatic tools for analysis and clinical reporting of Mycobacterium tuberculosis sequence data is improving, However, there remains a need for accessible, flexible bioinformatic tools that can be easily tailored for clinical reporting needs in different settings and are suitable for accreditation to international standards. MethodsWe developed tbtAMR, a flexible yet comprehensive tool for analysis of Mycobacterium tuberculosis genomic data, including inference of phenotypic susceptibility and lineage calling. Validation was undertaken using local and publicly-available real-world data (phenotype and genotype) and synthetic genomic data to determine the appropriate quality control metrics and extensively validate the pipeline for clinical use. FindingstbtAMR accurately predicted lineages and phenotypic susceptibility for first- and second-line drugs, with equivalent computational and predictive performance compared to other bioinformatics tools currently available. tbtAMR is flexible with modifiable criteria to tailor results to users needs. InterpretationThe tbtAMR tool is suitable for use in clinical and public health microbiology laboratory settings, and can be tailored to specific local needs by non-programmers. We have accredited this tool to ISO standards in our laboratory, and it has been implemented for routine reporting of AMR from genomic sequence data in a clinically relevant timeframe. Reporting templates, validation methods and datasets are provided to offer a pathway for laboratories to adopt and seek their own accreditation for this critical test, to improve the management of tuberculosis globally. FundingVictorian Government Department of Health; Australian National Health and Medical Research Council and Medical Research Futures Fund. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for studies using the search terms: "Mycobacterium tuberculosis", "clinical", "bioinformatics", "genomics", "drug resistance (OR antimicrobial)", published prior to 31st July 2024 without language restrictions (n=258). We considered all studies from this search that used genomics to infer likely drug-resistance in M. tuberculosis. Many of these studies highlight the challenges in making meaningful interpretations from genomic data for the purpose of inferring AMR for clinical applications. Despite the development of bioinformatics tools and compilation of catalogues of resistance conferring mutations, few of these studies directly address the challenges specific to implementation of a whole genome sequencing (WGS) and bioinformatics pipelines to deliver validated and accredited results for use in clinical applications and none provide sustainable solutions. Added value of this studyTo the best of our knowledge, this study is the first to detail practical solutions to challenges to validating and accrediting the routine inference of AMR from WGS data for clinical applications for treatment of M. tuberculosis. We developed, validated and accredited a bioinformatics tool, tbtAMR, which is robust and flexible, using a data-driven approach to inferring resistance, allowing for simple customisation of behaviour on a large collection of in-house data supplemented with publicly available data. Furthermore, we have made this pipeline and the accompanying data available for use by the wider public health community to aid others in implementing similar programs. Consultation with infectious disease clinicians, microbiologists and epidemiologists has allowed us to develop a robust workflow, that encompasses sequencing, analysis, interpretation, reporting, discrepancy resolution and ongoing verification. Implications of all the available evidenceThis study addressed the specific needs of reporting genomic AMR for M. tuberculosis in a clinical and public health laboratory. Furthermore, this work makes available a pipeline and data for laboratories to utilise to implement genomic AMR for M. tuberculosis. Through the use and further development of publicly available and open-source bioinformatics software, we have demonstrated the feasibility of clinical reporting of genomic AMR results for M. tuberculosis in a low-incidence high-income setting. We believe that this work lays the foundation for making reporting of genomic AMR for M. tuberculosis more accessible to public health and reference laboratories in general.

genomics↗

bioRxiv2022

Bridging the gap between bioinformatics and the clinical and public health microbiology laboratory: An ISO-accredited genomics workflow for antimicrobial resistance

Realising the promise of genomics to revolutionise routine AMR diagnosis and surveillance has been a long-standing challenge in clinical and public health microbiology. We have directly addressed this issue by creating and validating abritAMR, an ISO-accredited bioinformatics platform for genomics-based bacterial AMR gene detection. abritAMR utilises the NCBI AMRFinderPlus for detection of AMR genes and mutations, with additional features to classify AMR determinants into an antibiotic class. We validated abritAMR by comparing with multiplex PCR or gold-standard reference genomes, together representing 1500 different bacteria across 29 genera and covering 415 antibiotic resistance alleles. We also assessed inference of phenotypic resistance by comparing genomic predictions with agar dilution results for 864 Salmonella spp. Performance of abritAMR was excellent, detecting AMR genes with 99.9% accuracy (95% CI 99.9-99.9%), 97.9% sensitivity (95% CI 97.5-98.4%) and 100% specificity (100-100%). Phenotypic inference of resistance for Salmonella spp. was equally impressive, with 98.9% accuracy (98.7-99.1%). Validation data were submitted to the governing authority and ISO15189 accreditation was achieved. Implementation of abritAMR resulted in streamlined bioinformatics and reporting pathways, and it was readily updated and re-verified with database revisions or changes in reporting requirements. abritAMR is publicly and freely available to assist clinical and public health microbiology laboratories everywhere harness the power of AMR genomics in their professional practice.

microbiology↗

bioRxiv2020

Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA

2.IntroductionThe SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues. AimTo establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs. MethodologyWe used a commercial RT-LAMP mastermix from OptiGene Ltd in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby as little as 1 L of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65{degrees}C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals. ResultsAssay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87% and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 minutes (SD {+/-}7 minutes). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 mL-1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay. ConclusionWith a simplified workflow, N1-STOP-LAMP is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19. 3. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2017

Real-time genomic and epidemiological investigation of a multi-institution outbreak of KPC-producing Enterobacteriaceae: a translational study

BackgroundUntil recently, KPC-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.\n\nMethods and FindingsAll KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing (WGS) was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Initial investigations indicated the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012-2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.\n\nConclusionsA real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase producing Enterobacteriaceae management.

genomics↗