Siobhon Egan

Mosquitoes (Culicidae) are the most important vectors of human and animal diseases globally, making them valuable tools for the molecular surveillance of blood-borne pathogens. By screening mosquito populations, we can evaluate local disease prevalence and ascertain which vector species are involved in local transmission cycles. This study presents the first targeted mosquito-based surveillance of blood parasites in Western Australia. Over a 2-year surveillance program in Perth, Western Australia, 3,288 mosquitoes from 12 species across 5 genera were collected and screened in 461 pools. Parasite prevalence and diversity were evaluated using polymerase chain reaction screening of the Haemosporida cytochrome b gene region, and the Dirofilaria 12S rDNA gene region. Haemosporida were detected in 3.9% of mosquito pools, with 72.2% of positives found in Culex species pools. Avian Haemosporida comprised 83.3% of the total detections. Known avian Haemosporida lineages detected included 1 Haemoproteus (H. zosteropis) and 2 Plasmodium (BELL01 and MYNA02). Three novel lineages, Plasmodium CULPER01-03, were identified. Plasmodium falciparum was identified in 2 pools, and no Dirofilaria were detected. These findings indicate that Perth harbors a diverse range of avian Haemosporida, which may be regionally specific, as all lineages detected have only been identified in the Oceania region. The predominance of positive detections in the Culex pipiens species complex supports their role as the primary vectors of avian Plasmodium. This study highlights the utility of mosquito surveillance for monitoring blood-borne parasites and contributes new insight into parasite diversity and vector associations in Australia.

COVID-19 vaccines are crucial in reducing SARS-CoV-2 transmission and severe health outcomes. Despite widespread administration, their long-term systemic effects on human metabolism remain inadequately understood. This longitudinal study aims to evaluate IgG responses, 34 cytokines, 112 lipoproteins, and 21 low-molecular-weight metabolites in 33 individuals receiving two to four COVID-19 vaccine doses. Changes in metabolic profiles for the first 16 days post each dose of vaccine, and up to 480 days post-initial dose, were compared to baseline (before vaccination). Additionally, metabolic profiles of vaccinated participants were compared to a reference cohort of unvaccinated individuals without prior exposure to SARS-CoV-2 infection (controls) and SARS-CoV-2 cases. Positive IgG responses were observed in 78.8% (N = 26) of participants after the first dose, reaching 100% with subsequent doses. The most common side effects were localized pain at the injection site and "flu-like" symptoms, reported by > 50% of participants. Systemic side effects, e.g., sore lymph nodes, fatigue, and brain fog, were reported but showed no significant correlations to IgG responses. Transient temporal changes were observed for cytokine IP10 (CXCL10) and glutamic acid around the third vaccine dose. Compared to the reference cohort, 497 vaccinated samples (95.0%) had profiles similar to the controls, while the remaining 26 samples with prior infection exposures were similar to mild cases of SARS-CooV-2 infection. In conclusion, COVID-19 vaccination did not induce lasting changes in inflammatory and metabolic responses, nor did it induce changes similar to mild cases of SARS-CoV-2 infection. This supports the metabolic safety of the vaccine and contributes to increased vaccine confidence. KEY MESSAGES: Minimal changes in inflammatory/metabolic markers up to 480 days post-vaccination. Transient increase in IP10 (CXCL10) and glutamic acid around the third dose. Post-vaccination IgG response did not alter metabolic profiles like SARS-CoV-2 cases. Our findings provide insights into the safety of repeated COVID-19 vaccinations.

Key messages
• Minimal changes in inflammatory/metabolic markers up to 480 days post-vaccination.
• Transient increase in IP10 (CXCL10) and glutamic acid around the third dose.
• Post-vaccination IgG response did not alter metabolic profiles like SARS-CoV-2 cases.
• Our findings provide insights into the safety of repeated COVID-19 vaccinations.

In forensic science, detecting transfers of physical and biological material is critical for establishing evidence of criminal involvement. Unique bacterial signatures from the reproductive system transfer during unprotected penetrative intercourse offer a novel tool for criminal investigation. Here, we demonstrate this transfer using full-length 16S rRNA gene sequencing and discuss the impact of barrier contraceptives. These microbial signatures can potentially aid in sexual assault casework for perpetrator identification when human male DNA is absent.
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•Transfer of unique and non-unique bacterial taxa during intercourse was observed•Lactobacillus spp. contributed to the most female to male sexome transfer•Despite the use of a condom during intercourse, transfer of the sexome was still observed•Condom/lube use, oral intercourse, circumcision/pubic hair: no impact on microbial diversity
Biological sciences; Microbiome

Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases’ pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.

Methods: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.

Results: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.

Conclusion: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.

Marsupials, inhabiting diverse ecosystems, including urban and peri-urban regions in Australasia and the Americas, intersect with human activities, leading to zoonotic spill-over and anthroponotic spill-back of pathogens, including Cryptosporidium and Giardia. This review assesses the current knowledge on the diversity of Cryptosporidium and Giardia species in marsupials, focusing on the potential zoonotic risks. Cryptosporidium fayeri and C. macropodum are the dominant species in marsupials, while in possums, the host-specific possum genotype dominates. Of these three species/genotypes, only C. fayeri has been identified in two humans and the zoonotic risk is considered low. Generally, oocyst shedding in marsupials is low, further supporting a low transmission risk. However, there is some evidence of spill-back of C. hominis into kangaroo populations, which requires continued monitoring. Although C. hominis does not appear to be established in small marsupials like possums, comprehensive screening and analysis are essential for a better understanding of the prevalence and potential establishment of zoonotic Cryptosporidium species in small marsupials. Both host-specific and zoonotic Giardia species have been identified in marsupials. The dominance of zoonotic G. duodenalis assemblages A and B in marsupials may result from spill-back from livestock and humans and it is not yet understood if these are transient or established infections. Future studies using multilocus typing tools and whole-genome sequencing are required for a better understanding of the zoonotic risk from Giardia infections in marsupials. Moreover, much more extensive screening of a wider range of marsupial species, particularly in peri-urban areas, is required to provide a clearer understanding of the zoonotic risk of Cryptosporidium and Giardia in marsupials.

Rodents represent the single largest group within mammals and host a diverse array of zoonotic pathogens. Urbanisation impacts wild mammals, including rodents, leading to habitat loss but also providing new resources. Urban-adapted (synanthropic) rodents, such as the brown rat (R. norvegicus), black rat (R. rattus), and house mouse (Mus musculus), have long successfully adapted to living close to humans and are known carriers of zoonotic pathogens. Two important enteric, zoonotic protozoan parasites, carried by rodents, include Cryptosporidium and Giardia. Their environmental stages (oocysts/cysts), released in faeces, can contaminate surface and wastewaters, are resistant to common drinking water disinfectants and can cause water-borne related gastritis outbreaks. At least 48 species of Cryptosporidium have been described, with C. hominis and C. parvum responsible for the majority of human infections, while Giardia duodenalis assemblages A and B are the main human-infectious assemblages. Molecular characterisation is crucial to assess the public health risk linked to rodent-related water contamination due to morphological overlap between species. This review explores the global molecular diversity of these parasites in rodents, with a focus on evaluating the zoonotic risk from contamination of water and wasterwater with Cryptosporidium and Giardia oocysts/cysts from synanthropic rodents. Analysis indicates that while zoonotic Cryptosporidium and Giardia are prevalent in farmed and pet rodents, host-specific Cryptosporidium and Giardia species dominate in urban adapted rodents, and therefore the risks posed by these rodents in the transmission of zoonotic Cryptosporidium and Giardia are relatively low. Many knowledge gaps remain however, and therefore understanding the intricate dynamics of these parasites in rodent populations is essential for managing their impact on human health and water quality. This knowledge can inform strategies to reduce disease transmission and ensure safe drinking water in urban and peri‑urban areas.

Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter".

Rabbits are highly abundant in many countries and can serve as reservoirs of diseases for a diversity of pathogens including the enteric protozoan parasites, Cryptosporidium and Giardia. Both parasites shed environmentally robust environmental stages (oo/cysts) and have been responsible for numerous waterborne outbreaks of diseases. Cryptosporidium hominis and C. parvum are responsible for most infections in humans, while Giardia duodenalis assemblages A and B, cause most human cases of giardiasis. Cryptosporidium cuniculus, the dominant species infecting rabbits, is the only spceies other than C. hominis and C. parvum to have caused a waterborne outbreak of gastritis, which occurred in the United Kingdom in 2008. This review examines the prevalence of Cryptosporidium and Giardia species in rabbits to better understand the public health risks of contamination of water sources with Cryptosporidium and Giardia oo/cysts from rabbits. Despite the abundance of C. cuniculus in rabbits, reports in humans are relatively rare, with the exception of the United Kingdom and New Zealand, and reports of C. cuniculus in humans from the United Kingdom have declined substantially since the 2008 outbreak. Subtyping of C. cuniculus has supported the potential for zoonotic transmission. Relatively few studies have been conducted on Giardia, but assemblage B dominates. However, improved typing methods are required to better understand the transmission dynamics of Giardia assemblages in rabbits. Similarly, it is not well understood if pet rabbits or contaminated water are the main source of C. cuniculus infections in humans. Well-planned studies using high-resolution typing tools are required to understand the transmission dynamics better and quantify the public health risk of Cryptosporidium and Giardia from rabbits.

The zoonotic potential of the protist parasites Cryptosporidium spp. and Giardia duodenalis in amphibians and reptiles raises public health concerns due to their growing popularity as pets. This review examines the prevalence and diversity of these parasites in wild and captive amphibians and reptiles to better understand the zoonotic risk. Research on Giardia in both groups is limited, and zoonotic forms of Cryptosporidium or Giardia have not been reported in amphibians. Host-adapted Cryptosporidium species dominate in reptiles, albeit some reptiles have been found to carry zoonotic (C. hominis and C. parvum) and rodent-associated (C. tyzzeri, C. muris and C. andersoni) species, primarily through mechanical carriage. Similarly, the limited reports of Giardia duodenalis (assemblages A, B and E) in reptiles may also be due to mechanical carriage. Thus, the available evidence indicates minimal zoonotic risk associated with these organisms in wild and captive frogs and reptiles. The exact transmission routes for these infections within reptile populations remain poorly understood, particularly regarding the importance of mechanical carriage. Although the risk appears minimal, continued research and surveillance efforts are necessary to gain a more comprehensive understanding of the transmission dynamics and ultimately improve our ability to safeguard human and animal health.

Introduction/Aim: To gain an insight into the ancient lung virome possibly associated to Tuberculosis (TB), we reanalysed metagenomics data from lung tissue samples of mummified remains found in a crypt in Hungary (DOI:10.1038/ncomms7717). These 18th Century crypts contained remains from individuals who died from TB and underwent shotgun metagenomic sequencing to identify TB strains. Therefore, this study aimed to assess the virome associated with TB by characterising and taxonomically classifying the viral contigs (vContigs) associated with the TB-infected mummified remains.

Methods: Two lung virome studies utilising shotgun metagenomics on mummified lung tissue were collated from the public database Sequence Read Archive (SRA) public database. The bioproject data was then run through the EVEREST pipeline (https://agudeloromero.github.io/EVEREST/). Additionally phylogenetic analyses were performed on both viral contigs to confirm their taxonomic classification.

Results: vContig-Cressdnaviridae and vContig-Caudovirales captured 87 vContigs, of which two were scored with medium and high-quality genomes and were found to belong to the orders Cressdnaviridae and Caudovirales. The length of the vContigs were 7180 base pairs (bp) and 98030 bp, respectively. Genomic annotation showed GC contents of 58.23% and 67.55% for vContig-Cressdnaviridae and vContig-Caudovirales, respectively. Gene coding densities of 87.16% (12 CDS, 25% known function) and 95.77% (162 CDS, 20.37% known function), including genes related to host takeover and tail proteins.

Conclusion: Two complete vContigs were identified from publicly available mummified lung tissue metagenomic samples through the EVEREST pipeline. This has given a historic insight into the lung virome from Eastern Europe related to TB, and the lineage of historic bacteriophages.

Keywords: Virome, tuberculosis, viral genomics

Grant Support: Pawsey Supercomputing Research Centre, and Australian Government Research Training Program Scholarship.