ColV/ColBM and ColIa/senB F virulence plasmids feature prominently in Escherichia coli associated with urinary tract and bloodstream infections globally. Australian-sourced E. coli that carry these plasmids were examined among 5,471 isolates (3,316 sequenced by the APG and AusGEM programmes; 2,155 from public databases) spanning years 1986-2020 from humans (n=2,996/5,471; 54.8%), wild animals (n=870/5,471; 15.9%), livestock (n=649/5,471; 11.9%), companion animals (n=375/5,471; 6.9%), environmental sources (n=292/5,471; 5.3%) and food (n=289/5,471; 5.3%). Putative plasmid reconstruction, assisted by a plasmid database comprising 23,700 complete plasmid sequences, identified 22,534 putative plasmids of which 21,814 (96.8%) represented 547 known plasmid clusters. E. coli harbouring ColV-associated putative plasmids, particularly plasmid cluster AA176 [F replicon sequence type (RST): F18:A-:B1 (repFII-18:repFIA-null:repFIB-1)] was identified among phylogenetically diverse strains from humans, livestock, particularly poultry, and food. Closely related isolates, defined as ≤10 core-genome multilocus sequence type allelic distance, that carried either ColV or ColIa/senB-associated putative (F) plasmids were identified across multiple sources and diverse phylogenetic backgrounds. ColIa/senB-associated putative (F) plasmid clusters AA337 (RST: F29:A-:B10) and AA171 (RST: F2:A1:B20) were associated with phylogenetically closely related isolates from humans, wild animals and companion animals, but their absence in E. coli sourced from food and livestock was notable. E. coli carrying ColV and ColIa/senB plasmids frequently exhibit genotypic multidrug resistance, many with critically important antimicrobial resistance genes, highlighting their role in the evolution of clinically problematic lineages. Our study has important epidemiological considerations for understanding the spread of extraintestinal pathogenic and hybrid E. coli lineages across the One Health spectrum.

Human astroviruses (HAstVs) account for 2% to 9% of gastroenteritis cases in children and are occasionally associated with central nervous system complications. We report six draft HAstV genomes from Malawian children <5 years old with gastroenteritis, providing baseline information for the understanding of HAstV diversity and disease burden in sub-Saharan Africa.

The segmented genome of Rotavirus alphagastroenteritidis facilitates the emergence of unusual reassortants, increasingly documented in the post-vaccine era. However, their long-term evolutionary dynamics and population-level persistence remain poorly understood. We investigated G1P[8] strains detected through hospital-based surveillance in northern and central Vietnam from 2012 to 2016. Electropherotyping, whole-genome sequencing, and phylogenetic analyses were performed to define genomic constellations and reconstruct evolutionary dynamics of DS-1-like reassortants. We documented four-year circulation patterns of DS-1-like G1P[8] strains, emerging in 2012/2013, peaking in mid-2014, and declining by 2016. Among 44 strains exhibiting short electropherotypes, at least three sequential genotype constellations (A-C) were identified: Constellation A likely arose in northern Vietnam through inter-genogroup reassortment between Wa-like G1P[8] (VP7/VP4) and DS-1-like G2P[4] strains; A related variant in central Vietnam suggested regional transmission from contemporaneous strains reported in Thailand and Japan; Constellation B involved acquisition of a Wa-like NSP2 gene; Constellation C included additional reassortment with bovine-like NSP2 and NSP4 genes from a co-circulating G8P[8] strain. No significant differences in clinical severity were observed between DS-1-like and Wa-like infections, and no cases of either genotype were detected among fully vaccinated children. Overall, this study describes a stepwise reassortment process involving intergenogroup, intragenogroup, and potential zoonotic events. Genomic diversification in this setting was not associated with increased virulence or evidence of immune escape. These findings highlight the need for continued genomic surveillance and broader sampling to better resolve the evolutionary dynamics of rotavirus reassortants.

Archival specimens held in biorepositories (e.g. natural history collections) offer rare temporal snapshots of global biodiversity. These collections not only preserve species morphology and aspects of ecology, but increasingly provide access to historical molecular data, including insights into wildlife disease. As several pandemics have originated from animal viruses spilling over into the human population (i.e. SARS-CoV-2/COVID-19, 2009 H1N1 influenza, and HIV/AIDS), characterizing the diversity of viruses circulating in wildlife populations is essential for proactive pandemic preparedness. Yet, current surveillance remains biased toward contemporary viruses of economic importance. One solution to bridging spatiotemporal gaps in wildlife virus knowledge is retrospective screening of vouchered wildlife specimens. However, molecular analysis of specimens has been hindered by formalin fixation, which degrades and cross-links nucleic acids. Here, we demonstrate that formalin-fixed vouchered wildlife specimens retain both host and viral RNA fragments after being stored for up to 60 years. We recovered fragments of divergent strains of Rotavirus alphagastroenteritidis from two Australian species of order Chiroptera; Nyctophilus geoffroyi (lesser long-eared bat) and Rhinolophus megaphyllus (smaller horseshoe bat), representing the first characterization of R. alphagastroenteritidis (RVA) in Australian bats, and the oldest identification of the virus to date worldwide. Concurrently, we sequenced endogenous host RNA, providing a proof-of-concept for dual host-virus transcript recovery from vouchered specimens. This study highlights the role biorepositories can play in reconstructing unbiased historical viral landscapes from specimens, irrespective of the host disease status, and enabling spatiotemporal host-virus insight to advance both biodiversity science and global pandemic preparedness.

BACKGROUND:In low and middle-income countries (LMICs), understanding the burden of typhoid disease has been challenging as clinical surveillance based on blood culture data alone often poorly represents the community burden. Underreported cases, unclear case definitions, the presence of a chronic carrier state and emerging antimicrobial resistance necessitate alternative approaches to assess disease prevalence and target public health interventions, such as vaccine introduction. This study aimed to assess the feasibility of wastewater and environmental surveillance (WES) in measuring the prevalence of typhoid infection in Indonesia. METHODS:Between October 11, 2022, and August 31, 2023, WES was conducted in 18 locations across 3 districts in Yogyakarta province, Indonesia. Samples were collected fortnightly from wastewater treatment plants (WWTPs), manholes, a river, and public spaces, using grab and passive sampling methods. Salmonella Typhi (S. Typhi) detection was conducted using quantitative PCR for S. Typhi genes (ttr, tviB, and staG - all positive). RESULTS:Of the 406 samples collected, 13 % (51/406) tested positive for S. Typhi, with monthly positivity rates ranging from 2 % (1/51) in March 2023 to 47 % (16/34) in October 2022. Mean concentrations (in log10) in ttr, tviB, and staG in grab samples were 0.67 (SD ± 0.99), 0.23 (SD ± 1.14), and -0.11 (SD ± 1.05). The highest detection rates were observed in samples from the river compared to central WWTPs (OR 12.68; 95 % CI 2.03-79.20, P = 0.007). No correlation was observed between rainfall and S. Typhi gene detection (P > 0.05 for all genes). CONCLUSION:WES is feasible in Indonesia and can be used to monitor typhoid disease burden in an endemic region. High positivity rates from the river and septic tanks in traditional markets support a broad approach to sampling in LMICs where formal wastewater management systems may not accurately represent community disease prevalence due to its low population coverage. WES can be a valuable tool to inform public health responses, including vaccine introduction.

This report from the Australian Rotavirus Surveillance Program describes the circulating rotavirus genotypes identified in children and adults during the period 1 January to 31 December 2023. During this period, 1,942 faecal samples were referred for rotavirus G- and P- genotype analysis; of these samples, 1,781 were confirmed as rotavirus positive. This is the highest number of rotavirus-positive confirmed samples by the Australian Rotavirus Surveillance Program in the past > 20 years of operation of the program. Of these confirmed rotavirus positive samples, 1,554 of 1,781 (87.3%) were identified as wildtype rotavirus, and 226 of 1,781 (12.7%) were identified as the Rotarix vaccine-like strain. G3P[8] was the dominant genotype nationally (n = 1,117/1,554; 71.9%), comprised of both human G3P[8] (n = 662/1,554; 42.6%) and the equine-like G3P[8] variant (455/1,554; 29.3%). Other frequently identified genotypes included G2P[4] (n = 146/1,554; 9.4%), G12P[8] (n = 100/1,554; 6.4%), G1P[8] (n = 40/1,554; 2.6%), G9P[4] (n = 32/1,554; 2.1%) and G8P[8] (n = 21/1,554; 1.4%). Genotype distribution was consistent amongst most jurisdictions, with human G3P[8] and equine-like G3P[8] the two dominant genotypes in all jurisdictions, with the exception of the Northern Territory and Western Australia where G2P[4] (7/103; 6.8%) and G12P[8] (54/241; 22.4%) were the second most dominant genotypes respectively. Consistent with observations in 2022, a small number of unusual genotypes were identified (n = 42/1,554; 2.7%), including G2P[8] (n = 18/1,554; 1.2%), and G3P[4] (n = 6/1,554; 0.4%). The high number of rotavirus positive samples received by the program reflected the notifications for rotavirus disease reported to the National Notifiable Disease Surveillance Service. The ability to monitor the genotypes of rotavirus strains causing disease across ages and across jurisdictions provides important data on assessing the performance of the national rotavirus vaccine program and to inform public health interventions during outbreaks. This Australian Rotavirus Surveillance Program also provides important data to monitor annual variations in genotypic patterns and to provide diagnostic laboratories with quality assurance by reporting incidences of wildtype, vaccine-like, or false positive rotavirus results.

Rotavirus vaccines are less effective in high mortality regions. A rotavirus vaccine administered at birth may overcome challenges to vaccine uptake posed by a complex gut microbiome. We investigated the association between the microbiome and vaccine responses following RV3-BB vaccine (G3P[6]) administered in a neonatal schedule (dose 1: 0-5 days), or infant schedule (dose 1: 6-8 weeks) in Indonesia (Phase 2b efficacy study) ( n = 478 samples/193 infants) (ACTRN12612001282875) and in Malawi (Immunigenicity study) (n = 355 samples/186 infants) (NCT03483116). Vaccine responses assessed using anti-rotavirus IgA seroconversion (IgA), stool shedding of vaccine virus and vaccine take (IgA seroconversion and/or shedding). Here we report, high alpha diversity, beta diversity differences and high abundance of Bacteroides is associated with positive vaccine take and shedding following RV3-BB administered in the neonatal schedule, but not with IgA seroconversion, or in the infant schedule. Higher alpha diversity was associated with shedding after three doses of RV3-BB in the neonatal schedule compared to non-shedders, or the placebo group. High abundance of Streptococcus and Staphylococcus is associated with no shedding in the neonatal schedule group. RV3-BB vaccine administered in a neonatal schedule modulates the early microbiome environment and presents a window of opportunity to optimise protection from rotavirus disease.

Human adenovirus F (HAdV-F), genotype 40/41, ranks as the second leading cause of pediatric viral gastroenteritis globally. Here, we report four draft genomes of HAdV-F from Malawi, obtained from children with acute gastroenteritis at Queen Elizabeth Central Hospital and Bangwe Health Centre, Blantyre, between 2012 and 2024.

AbstractGenomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in a One Health context is challenging, as strains circulate and evolve within and between diverse hosts and environments. To identify phylogenetic linkages and better define relevant measures of genomic relatedness in a One Health context, we collated 5471 Escherichia coli genome sequences from Australia originating from humans (n = 2996), wild animals (n = 870), livestock (n = 649), companion animals (n = 375), environmental sources (n = 292) and food (n = 289) spanning over 36 years. Of the 827 multi-locus sequence types (STs) identified, 10 STs were commonly associated with cross-source genomic clusters, including the highly clonal ST131, pandemic zoonotic lineages such as ST95, and emerging human ExPEC ST1193. Here, we show that assessing genomic relationships at ≤ 100 SNP threshold enabled detection of cross-source linkage otherwise obscured when applying typical outbreak-oriented relatedness thresholds ( ≤ 20 SNPs) and should be considered in interrogation of One Health genomic datasets.

We report a bacteriophage from Malawi recovered during rotavirus RNA sequencing. It shares 84.3% nucleotide identity with MH400309, a Kayfunavirus bacteriophage. This incidental finding shows RNA virus sequencing can also detect bacteriophages, offering insights into the broader viral diversity in clinical and environmental samples.

Human sapoviruses are increasingly recognized as a cause of acute gastroenteritis in children worldwide but remain poorly studied, particularly in African settings. Here, we report the four draft genome sequences of human sapovirus from Malawi, Southern Africa, collected from children with acute gastroenteritis.

The sub-Saharan African region bears the highest burden of rotavirus-associated morbidity and mortality, with substantial genetic diversity observed in circulating strains despite vaccine introduction. The G8 genotype, originally predominant in bovine strains, has increasingly become prevalent in humans, suggesting a possible interface of animal-to-human transmission and highlighting its role in African strain diversity. In this study, we performed whole genome sequencing and evolutionary analysis of 21 archival G8P[4] strains collected through gastroenteritis surveillance in South Africa between 2009 and 2021 from children under five years of age. All strains exhibited DS-1-like genome constellations and phylogenetically clustered closely with sub-Saharan African G8P[4] strains across all 11 genome segments. A time-resolved phylogeny indicated the co-circulation of multiple G8 sub-lineages, with specific variants persisting for nearly a decade. The mean evolutionary rate for the G8 lineage V sequences was estimated at 1.49 × 10-3 substitutions per site per year, with a time to most common recent ancestor of 1981.8, suggesting long-term endemic divergence. Radical amino acid substitutions were identified in neutralising epitopes of VP4 (11 variations) and VP7 (18 variations) relative to the Rotarix® vaccine strain. These changes may impact antigenicity and immune recognition. These findings within the key antigenic sites of G8P[4] strains may reflect ongoing viral adaptation with potential implications for infectivity and sustained circulation in African regions. Taken together, the findings underscore the significance of continued genomic surveillance to monitor evolution and guide the reassessment, optimisation of current vaccines and the development of future vaccines with broader protective efficacy.

Mozambique introduced the Rotarix® vaccine into the National Immunization Program in September 2015. Following vaccine introduction, rotavirus A (RVA) genotypes, G9P[4] and G9P[6], were detected for the first time since rotavirus surveillance programs were implemented in the country. To understand the emergence of these strains, the whole genomes of 47 ELISA RVA positive strains detected between 2015 and 2018 were characterized using an Illumina MiSeq-based sequencing pipeline. Of the 29 G9 strains characterized, 14 exhibited a typical Wa-like genome constellation and 15 a DS-1-like genome constellation. Mostly, the G9P[4] and G9P[6] strains clustered consistently for most of the genome segments, except the G- and P-genotypes. For the G9 genotype, the strains formed three different conserved clades, separated by the P type (P[4], P[6] and P[8]), suggesting different origins for this genotype. Analysis of the VP6-encoding gene revealed that seven G9P[6] strains clustered close to antelope and bovine strains. A rare E6 NSP4 genotype was detected for strain RVA/Human-wt/MOZ/HCN1595/2017/G9P[4] and a genetically distinct lineage IV or OP354-like P[8] was identified for RVA/Human-wt/MOZ/HGJM0644/2015/G9P[8] strain. These results highlight the need for genomic surveillance of RVA strains detected in Mozambique and the importance of following a One Health approach to identify and characterize potential zoonotic strains causing acute gastroenteritis in Mozambican children.

In the face of an escalating antimicrobial resistance (AMR) crisis, genomic technologies have emerged as indispensable allies, providing innovative tools for a nuanced understanding of the abundance, persistence and mobilisation of antimicrobial resistance genes within microbial populations. This article explores advancements in genomic surveillance, including the integration with advanced computational tools to enhance our ability to predict AMR trends, detect outbreaks, and inform mitigation strategies. It highlights the critical role of a One Health approach, emphasising the importance of cross-sectoral collaboration among scientists, health care professionals, industry and policymakers to leverage genomic data for AMR management. The article showcases pioneering initiatives in Australia, such as the Melbourne Genomics Alliance’s Controlling Superbugs Clinical Flagship, the Australian Centre for Genomic Epidemiological Microbiology and AusTrakka, and discusses the need to both build global genomic databases that promote equitable analytics, and secure data-sharing platforms that support comprehensive surveillance networks. Through national and international collaborative efforts, One Health genomic surveillance represents a key strategy in enhancing our understanding and control of AMR and should be integrated into public health frameworks to safeguard against ever emerging AMR threats.

BACKGROUND:Wastewater-based epidemiology (WBE) surveillance has been proposed as an early warning system (EWS) for community SARS-CoV-2 transmission. However, there is limited data from low-and middle-income countries (LMICs). This study aimed to assess the ability of WBE surveillance to detect SARS-CoV-2 in formal and informal environments in Indonesia using different methods of sample collection, to compare WBE data with patterns of clinical cases of COVID-19 within the relevant communities, and to assess the WBE potential to be used as an EWS for SARS-CoV-2 outbreaks within a community. MATERIALS AND METHODS:We conducted WBE surveillance in three districts in Yogyakarta province, Indonesia, over eleven months (27 July 2021 to 7 January 2022 [Delta wave]; 18 January to 3 June 2022 [Omicron wave]). Water samples using grab, and/or passive sampling methods and soil samples were collected either weekly or fortnightly. RNA was extracted from membrane filters from processed water samples and directly from soil. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the SARS-CoV-2 N and ORF1ab genes. RESULTS:A total of 1,582 samples were collected. Detection rates of SARS-CoV-2 in wastewater reflected the incidence of community cases, with rates of 85% at the peak to 2% at the end of the Delta wave and from 94% to 11% during the Omicron wave. A 2-week lag time was observed between the detection of SARS-CoV-2 in wastewater and increasing cases in the corresponding community. CONCLUSION:WBE surveillance for SARS-CoV-2 in Indonesia was effective in monitoring patterns of cases of COVID-19 and served as an early warning system, predicting the increasing incidence of COVID-19 cases in the community.

Delivering large-scale routine pathogen genomics surveillance for public health is of considerable interest, although translational research models that promote national-level implementation are not well defined. We describe the development and deployment of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national partnership between academia, public health laboratories, and public health agencies that commenced in January, 2021. Successfully establishing and delivering a national programme requires inclusive and transparent collaboration between stakeholders, defined and clear focus on public health priorities, and support for strengthening national genomics capacity. Major enablers for delivering such a programme include technical solutions for data integration and analysis, such as the genomics surveillance platform AusTrakka, standard bioinformatic analysis methods, and national ethics and data sharing agreements that promote nationally integrated surveillance systems. Training of public health officials to interpret and act on genomic data is crucial, and evaluation and cost-effectiveness programmes will provide a benchmark and evidence for sustainable investment in genomics nationally and globally.

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The coronavirus disease 2019 (COVID-19) pandemic and resulting non-pharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed.Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

High titres of rotavirus-specific maternal antibodies may contribute to lower rotavirus vaccine efficacy in low- and middle-income countries (LMICs). RV3-BB vaccine (G3P[6]) is based on a neonatal rotavirus strain that replicates well in the newborn gut in the presence of breast milk. This study investigated the association between maternal serum antibodies and vaccine response in infants administered the RV3-BB vaccine. Serum was collected antenatally from mothers of 561 infants enrolled in the RV3-BB Phase II study conducted in Blantyre, Malawi, and analysed for rotavirus-specific serum IgA and IgG antibodies using enzyme-linked immunosorbent assay. Infant vaccine take was defined as cumulative IgA seroconversion (≥3 fold increase) and/or stool vaccine shedding. Maternal IgA or IgG antibody titres did not have a negative impact on vaccine-like stool shedding at any timepoint. Maternal IgG (but not IgA) titres were associated with reduced take post dose 1 (p < 0.005) and 3 (p < 0.05) in the neonatal vaccine schedule group but not at study completion (week 18). In LMICs where high maternal antibodies are associated with low rotavirus vaccine efficacy, RV3-BB in a neonatal or infant vaccine schedule has the potential to provide protection against severe rotavirus disease.

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.