Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data.

New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data.

Target product profile for cell-based and gene-based therapies to achieve a cure for HIV.

This target product profile (TPP) highlights the minimal and optimal characteristics for ex-vivo and in-vivo cell and gene therapy-based products aimed at achieving an HIV cure (ie, durable antiretroviral-free viral control). The need for an effective, safe, scalable, affordable, accessible, and acceptable cure for HIV infection remains a major global priority. The possibilities for cell and gene therapy-based products for an HIV cure are rapidly expanding.

Parameters for one health genomic surveillance of Escherichia coli from Australia.

Genomics 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.

Mucosal vaccination against SARS-CoV-2 using recombinant influenza viruses delivering self-assembling nanoparticles.

Recombinant influenza viruses are promising vectors that can bolster antibody and resident lymphocyte responses within mucosal sites. This study evaluates recombinant influenza viruses with SARS-CoV-2 RBD genes in eliciting mucosal and systemic responses. Using reverse genetics, we generated replication-competent recombinant influenza viruses carrying heterologous RBD genes in monomeric, trimeric, or ferritin-based nanoparticle forms.

Mentorship advances antimicrobial use surveillance systems in low- and middle-income countries.

A shortage of trained personnel poses significant challenges to implementing antimicrobial use (AMU) surveillance systems in low- and middle-income countries (LMICs). Traditional training models, such as workshops, seminars and online courses, often lack the sustained engagement and support necessary for deep learning and skill mastery. This article advocates for mentorship as an effective training method for AMU professionals in LMICs.

Burkholderia cenocepacia outbreak linked to taps in a neonatal intensive care unit.

Background: Burkholderia cenocepacia complex is an important cause of hospital acquired infections. We describe the management of an outbreak in a neonatal intensive care unit (NICU) due to tap colonisation.

Methods: Microbiological testing of touch (n = 26) and non-touch taps (n = 28), sinks and drains, including genomic sequencing of selected isolates.

Exploring cytokine outputs for diagnostics in drug reaction with eosinophilia and systemic symptoms (DRESS).

Background: In an exploratory study to assess the potential to individualize T-cell diagnostics in antibiotic-associated severe T-cell mediated hypersensitivity, we focused on drug reaction with eosinophilia and systemic symptoms (DRESS) and the related cytokine outputs IL-4 and IL-5.

Methods: Patients with well-phenotyped RegiSCAR ≥4 DRESS, positive intradermal skin testing, and a previous negative IFN-γ Enzyme-Linked ImmunoSpot (ELISpot) assay were prospectively recruited. We specifically performed an ELISpot assay with IL-4 and IL-5 cytokine outputs.

Induction of Fc-dependent functional antibodies against different variants of SARS-CoV-2 varies by vaccine type and prior infection.

Background: SARS-CoV-2 transmission and COVID-19 disease severity is influenced by immunity from natural infection and/or vaccination. Population-level immunity is complicated by the emergence of viral variants. Antibody Fc-dependent effector functions are as important mediators in immunity.

Protektem pikinini blong yu trial: protocol for a single arm field trial to assess the effectiveness of treating-all pregnant women with hepatitis B infection with tenofovir prophylaxis to prevent mother-to-child transmission in Vanuatu, 2024-2025.

Background: Hepatitis B infection is a major public health concern in Vanuatu, with approximately 9% of the general population estimated to be living with chronic hepatitis B. Most new infections are due to mother-to-child transmission (MTCT). Hepatitis B vaccination is available in Vanuatu, but coverage rates for first dose within 24 h of birth and third dose are suboptimal.

Characterization of a novel SNP identified in Australian group A isolates derived from the M1 lineage.

Group A (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1 lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections. However, the basis for its evolutionary success is not yet fully understood.

Bovine tracheal organoids for studying Mycoplasma bovis respiratory infections.

In vitro three-dimensional organoid models simulate key aspects of the structure and function of in vivo organs and have been used to study physiology, host-pathogen interactions, pathogenesis and pharmacodynamics. Although most organoid studies have been developed using human or mouse tissues, recent advancements have enabled the establishment of intestinal and respiratory tract organoids from domestic animal samples. Mycoplasma bovis causes chronic respiratory tract infections in cattle with significant health and economic consequences.

Is Respiratory Viral Infection an Inciting Event in the Development of Melioidosis? A Systematic Evaluation of Co-infection With and SARS-CoV-2 or Influenza.

Respiratory viral infection may increase infection with progressing to clinical disease (melioidosis). This data linkage study evaluated associations between melioidosis and SARS-CoV-2 or influenza. Among 160 melioidosis cases, there was no difference in risk factors, vaccine status, or disease severity between 17 with viral co-infection and 143 without.

A longitudinal study of alcohol consumption among adults in Victoria, Australia during the COVID-19 pandemic.

Objectives: Whilst public health measures were effective in reducing COVID-19 transmission, unintended negative consequences may have occurred. This study aims to assess changes alcohol consumption and the heavy episodic drinking (HED) during the pandemic.

Methods: Data were from the Optimise Study, a longitudinal cohort of Australian adults September 2020-August 2022 that over-sampled priority populations at higher risk of contracting COVID-19, developing severe COVID-19 or experiencing adverse consequences of lockdowns.

Multi-methods process evaluation of the SToP (See, Treat, Prevent) trial: a cluster randomised, stepped wedge trial to support healthy skin.

Background: Healthy skin is important for maintaining overall physical and cultural health and wellbeing. However, remote-living Australian Aboriginal children contend with disproportionally high rates of (Strep A) infected impetigo. The SToP Trial was a large stepped-wedge cluster randomised trial of See, Treat, and Prevent (SToP) skin health activities implemented between 2019 and 2022 in the Kimberley region of Western Australia, during which a decrease in impetigo was observed.

MAIT cell plasticity enables functional adaptation that drives antibacterial immune protection.

Mucosal-associated invariant T (MAIT) cells are known for their rapid effector functions and antibacterial immune protection. Here, we define the plasticity of interferon-γ (IFN-γ)-producing MAIT1 and interleukin-17A (IL-17A)-producing MAIT17 cell subsets in vivo. Whereas T-bet MAIT1 cells remained stable in all experimental settings, after adoptive transfer or acute or infection, RORγt MAIT17 cells could undergo phenotypic and functional conversion into both RORγtT-bet MAIT1/17 and RORγtT-bet MAIT1 cells.

Successful management of a multi-species outbreak of carbapenem-resistant organisms in Fiji: a prospective genomics-enhanced investigation and response.

Background: Fiji is a Pacific Island nation grappling with the increasing threat of antimicrobial resistance (AMR). While genomic technologies are increasingly utilised to understand the emergence and spread of AMR globally, its application to inform outbreak responses in low- and middle-income settings has not been reported.

Methods: Through an established capacity building program, suspected carbapenem-resistant organisms (CRO) identified at Colonial War Memorial Hospital in Fiji (Jan 2022-Oct 2023) underwent whole genome sequencing and analysis.

A call to innovate Antarctic avian influenza surveillance.

Highly pathogenic avian influenza (HPAI) viruses are increasingly spreading between birds and mammals globally, with sporadic transmission to humans. With recent emergence in Antarctica, traditional animal capture and influenza testing approaches have proven challenging and logistically impractical. Without reference laboratories in the region, responses are slow and few samples will ever be collected or tested from local outbreaks due to lack of infrastructure.

Identifying gaps in infection prevention and control practice in Australian residential aged care using scenarios.

Background: Older people living in residential aged care are vulnerable to infections. High quality infection prevention and control (IPC) practice is therefore vital in this setting. It is important to assess current IPC practice to identify areas where best practice is lacking, and where improvement efforts could most effectively be targeted.

Nosocomial Transmission of Necrotizing Fasciitis: A Molecular Characterization of Group A Streptococcal DNases in Clinical Virulence.

, or Group A (GAS), is responsible for over 500,000 deaths per year. Approximately 15% of these deaths are caused by necrotizing soft-tissue infections. In 2008, we isolated an M5 GAS, named the LO1 strain, responsible for the nosocomial transmission of necrotizing fasciitis between a baby and a nurse in Belgium.