Biology subjects

Mercoulia, K.

Publications and source records attributed to Mercoulia, K..

5 recordsLinked to original sources

bioRxiv2026

Incremental AMR acquisition driving successive genotype replacements and the rise of extensively drug resistant (XDR) Shigella sonnei in Australia over 20 years.

BackgroundIn Australia, the burden of shigellosis is predominantly in returning travellers or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and international travel to explore population dynamics of Shigella sonnei and the expansion of multi-drug resistant (MDR) and extensively drug-resistant (XDR) sub-lineages. MethodsA population-level study of all cultured Shigella sonnei isolates in the state of Victoria, Australia, was undertaken between January 2002 and December 2024. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 1,305 Shigella sonnei isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Enhanced metadata on source attribution including travel and sexual exposure were collected through surveillance forms or by interviews. ResultsThis study highlights significant shifts in Shigella sonnei cases in Victoria from sensitive strains to MDR and then XDR, particularly in the MSM-associated groups but also associated with a large point source outbreak. We describe an historical pattern of shifting genotype prevalence, and replacement to more varied and higher proportions of antimicrobial resistance over the last decade, resulting in the establishment of two distinct but highly concerning XDR sub-lineages within Victoria. ConclusionsOur genomic-epidemiological analyses highlight that drug-resistant Shigella sonnei remains an ongoing public health threat, and the importance of ongoing surveillance. We determined local evolutionary trajectories and identified expanding sub-lineages that informed shifts in clinical management and antimicrobial recommendations over time, including the use of azithromycin and carbapenems. Placing these local dynamics within the broader global epidemiology, we link how regional evolution interconnects with international dissemination, proving valuable context for guiding local, national and global strategies for prevent outbreaks and antimicrobial resistance.

microbiology↗

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

Exploring use of ozone nanobubbles for removal of cyanobacteria and co-occurring antimicrobial resistance genes in water supply and reuse systems

Harmful cyanobacterial blooms present persistent risks to both drinking water security and wastewater reuse, driving the need for advanced treatment strategies. Treatment barrier(s) need to be capable of simultaneously controlling cyanobacteria, cyanotoxins, and co-occurring contaminants like bloom-associated antimicrobial resistance genes (ARGs) particularly in the case of recycling treated wastewater. Ozone nanobubble technology has emerged as a promising innovation, offering extended oxidative stability and enhanced interfacial reactivity compared to conventional ozonation. Hence this research objectives were to (a) assess the removal performance of ozone nanobubbles in eliminating cyanobacteria and their co-occurring contaminants in comparison to conventional ozone systems, and (b) investigate the repeatability of the results in varying background water qualities, ozone decay and the potential for by-products formation Ozonation using nanobubbles enhanced oxidation performance by 19%-34% in the drinking water reservoir compared to conventional ozonation while keeping the ozone concentration below 2mg/l. Lower oxidation efficiencies were observed in treated wastewater compared to drinking water sources, reflecting the higher content of organic matter and suspended solids, and oxidant demand characteristic of recycled water systems. Despite these challenges, ozone nanobubbles consistently outperformed conventional ozonation in reducing both cyanobacterial biomass and cell viability, underscoring their potential as an advanced "polishing" step for algal management in wastewater reuse applications. By exploring fate of ARGs alongside cyanobacteria and toxin removal, this work extends beyond traditional ozonation trials. It provides valuable field-based evidence that bridges the divide between laboratory efficacy and full-scale operational performance. Future studies should build on this by exploring combined or sequential treatment barriers that enhance DNA degradation, thereby addressing both cellular and genetic risks in water supply and reuse systems. Observing the action of nanobubbles under dynamic, real-world water quality conditions is currently challenging; however, this studys novel field trials demonstrate potential nanobubble applications and provide valuable insights to guide future investigations. The results reinforce the broader applicability of ozone nanobubble technology for multi-target contaminant control in water reservoirs.

microbiology↗

bioRxiv2023

High performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks

Hepatitis A virus (HAV) infections are an increasing public health concern in low-endemicity regions due to outbreaks from foodborne infections and sustained transmission among vulnerable groups, including persons experiencing homelessness, those who inject drugs, and men who have sex with men (MSM), which is further compounded by aging, unvaccinated populations. DNA sequence characterisation of HAV for source tracking is performed by comparing small subgenomic regions of the virus. While this approach has been successful when robust epidemiological data are available, poor genetic resolution can lead to conflation of outbreaks with sporadic cases. HAV outbreak investigations would greatly benefit from the additional phylogenetic resolution obtained by whole virus genome sequence comparisons. However, HAV genomic approaches can be difficult because of challenges in isolating the virus, low sensitivity of direct metagenomic sequencing in complex sample matrices like various foods such as fruits, vegetables and molluscs, and difficulty designing highly multiplexed PCR primers across diverse HAV genotypes. Here, we introduce a proof-of-concept pan-HAV oligonucleotide hybrid capture enrichment assay from serum and frozen berry specimens that yields complete and near-complete HAV genomes from as few as four input HAV genome copies. We used this method to recover HAV genomes from human serum specimens with high C{tau} values (34{middle dot}7--42{middle dot}7), with high assay performance for all six human HAV sub-genotypes, both contemporary and historical. Our approach provides a highly sensitive and streamlined workflow for HAV WGS from diverse sample types, that can be the basis for harmonised and high-resolution molecular epidemiology during HAV outbreak surveillance. ImportanceThis proof-of-concept study introduces a hybrid capture oligo panel for whole genome sequencing (WGS) of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows for a single, streamlined workflow, thus facilitating the potential harmonization of molecular surveillance of HAV with other enteric viruses. Even challenging sample matrices can be accommodated, making it suitable for broad implementation in clinical and public health laboratories. The ability to capture small amounts of virus from complex samples is promising for passive surveillance application to environmental substrates, such as wastewater. This innovative approach has significant implications for enhancing multijurisdictional outbreak investigations, as well as our understanding of the global diversity and transmission dynamics of HAV.

genomics↗

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↗