The APPRISE Virtual Biobank for Infectious Diseases.

The Australian Partnership for Preparedness Research on InfectiouS disease Emergencies (APPRISE) has developed a virtual biobank to support infectious disease research in Australia. The virtual biobank (https://apprise.biogrid.org.au) integrates access to existing distributed infectious disease biospecimen collections comprising multiple specimen types, including plasma, serum, and peripheral blood mononuclear cells. Through the development of a common data model, multiple collections can be searched simultaneously via a secure web portal. The portal enhances the visibility and searchability of existing collections within their current governance and custodianship arrangements. The portal is easily scalable for integration of additional collections.

Robust and prototypical immune responses toward COVID-19 vaccine in First Nations peoples are impacted by comorbidities.

High-risk groups, including Indigenous people, are at risk of severe COVID-19. Here we found that Australian First Nations peoples elicit effective immune responses to COVID-19 BNT162b2 vaccination, including neutralizing antibodies, receptor-binding domain (RBD) antibodies, SARS-CoV-2 spike-specific B cells, and CD4+ and CD8+ T cells. In First Nations participants, RBD IgG antibody titers were correlated with body mass index and negatively correlated with age. Reduced RBD antibodies, spike-specific B cells and follicular helper T cells were found in vaccinated participants with chronic conditions (diabetes, renal disease) and were strongly associated with altered glycosylation of IgG and increased interleukin-18 levels in the plasma. These immune perturbations were also found in non-Indigenous people with comorbidities, indicating that they were related to comorbidities rather than ethnicity. However, our study is of a great importance to First Nations peoples who have disproportionate rates of chronic comorbidities and provides evidence of robust immune responses after COVID-19 vaccination in Indigenous people.

Immune profiling of SARS-CoV-2 infection during pregnancy reveals NK cell and γδ T cell perturbations.

Pregnancy poses a greater risk for severe COVID-19; however, underlying immunological changes associated with SARS-CoV-2 during pregnancy are poorly understood. We defined immune responses to SARS-CoV-2 in unvaccinated pregnant and nonpregnant women with acute and convalescent COVID-19, quantifying 217 immunological parameters. Humoral responses to SARS-CoV-2 were similar in pregnant and nonpregnant women, although our systems serology approach revealed distinct antibody and FcγR profiles between pregnant and nonpregnant women. Cellular analyses demonstrated marked differences in NK cell and unconventional T cell activation dynamics in pregnant women. Healthy pregnant women displayed preactivated NK cells and γδ T cells when compared with healthy nonpregnant women, which remained unchanged during acute and convalescent COVID-19. Conversely, nonpregnant women had prototypical activation of NK and γδ T cells. Activation of CD4+ and CD8+ T cells and T follicular helper cells was similar in SARS-CoV-2-infected pregnant and nonpregnant women, while antibody-secreting B cells were increased in pregnant women during acute COVID-19. Elevated levels of IL-8, IL-10, and IL-18 were found in pregnant women in their healthy state, and these cytokine levels remained elevated during acute and convalescent COVID-19. Collectively, we demonstrate perturbations in NK cell and γδ T cell activation in unvaccinated pregnant women with COVID-19, which may impact disease progression and severity during pregnancy.

Pathway and Network Analyses Identify Growth Factor Signaling and MMP9 as Potential Mediators of Mitochondrial Dysfunction in Severe COVID-19.

Patients with preexisting metabolic disorders such as diabetes are at a higher risk of developing severe coronavirus disease 2019 (COVID-19). Mitochondrion, the very organelle that controls cellular metabolism, holds the key to understanding disease progression at the cellular level. Our current study aimed to understand how cellular metabolism contributes to COVID-19 outcomes. Metacore pathway enrichment analyses on differentially expressed genes (encoded by both mitochondrial and nuclear deoxyribonucleic acid (DNA)) involved in cellular metabolism, regulation of mitochondrial respiration and organization, and apoptosis, was performed on RNA sequencing (RNASeq) data from blood samples collected from healthy controls and patients with mild/moderate or severe COVID-19. Genes from the enriched pathways were analyzed by network analysis to uncover interactions among them and up- or downstream genes within each pathway. Compared to the mild/moderate COVID-19, the upregulation of a myriad of growth factor and cell cycle signaling pathways, with concomitant downregulation of interferon signaling pathways, were observed in the severe group. Matrix metallopeptidase 9 (MMP9) was found in five of the top 10 upregulated pathways, indicating its potential as therapeutic target against COVID-19. In summary, our data demonstrates aberrant activation of endocrine signaling in severe COVID-19, and its implication in immune and metabolic dysfunction.

Deconstructing the Dogma: Systematic Literature Review and Meta-analysis of Adjunctive Gentamicin and Rifampin in Staphylococcal Prosthetic Valve Endocarditis.

Background: Based primarily on in vitro and animal models, with little data directly addressing patient outcomes, current guidelines recommend treating staphylococcal prosthetic valve endocarditis (PVE) with antibiotic combinations including gentamicin and rifampin. Here, we synthesize the clinical data on adjunctive rifampin and gentamicin in staphylococcal PVE. Methods: We conducted a systematic review and meta-analysis of PubMed- and Cochrane-indexed studies reporting outcomes of staphylococcal PVE treated with adjunctive rifampin, gentamicin, both agents, or neither (ie, glycopeptide or ß-lactam monotherapy). We recorded outcomes including mortality, relapsed infection, length of stay, nephrotoxicity, hepatotoxicity, and important drug-drug interactions (DDIs). Results: Four relevant studies were identified. Two studies (n = 117) suggested that adding gentamicin to rifampin-containing regimens did not reduce clinical failure (odds ratio [OR], 0.98 [95% confidence interval {CI}, .39-2.46]), and 2 studies (n = 201) suggested that adding rifampin to gentamicin-containing regimens did not reduce clinical failure (OR, 1.29 [95% CI, .71-2.33]). Neither gentamicin nor rifampin was associated with reduced infection relapse; 1 study found that rifampin treatment was associated with longer hospitalizations (mean, 31.3 vs 42.3 days; P < .001). Comparative safety outcomes were rarely reported, but 1 study found rifampin to be associated with hepatoxicity, nephrotoxicity, and DDIs, leading to treatment discontinuation in 31% of patients. Conclusions: The existing clinical data do not suggest a benefit of either adjunctive gentamicin or rifampin in staphylococcal PVE. Given that other studies also suggest these agents add nephrotoxicity, hepatoxicity, and risk of DDIs without benefit in staphylococcal endovascular infections, we suggest that recommendations for gentamicin and rifampin in PVE be downgraded and primarily be used within the context of clinical trials.

Surveillance testing using salivary RT-PCR for SARS-CoV-2 in managed quarantine facilities in Australia: A laboratory validation and implementation study.

Background: Regular repeat surveillance testing is a strategy to identify asymptomatic individuals with SARS-CoV-2 infections in high-risk work settings to prevent onward community transmission. Saliva sampling is less invasive compared to nasal/oropharyngeal sampling, thus making it suitable for regular testing. In this multi-centre evaluation, we aimed to validate RT-PCR using salivary swab testing of SARS-CoV-2 for large-scale surveillance testing and assess implementation amongst staff working in the hotel quarantine system in Victoria, Australia. Methods: A multi-centre laboratory evaluation study was conducted to systematically validate the in vitro and clinical performance of salivary swab RT-PCR for implementation of SARS-CoV-2 surveillance testing. Analytical sensitivity for multiple RT-PCR platforms was assessed using a dilution series of known SARS-CoV-2 viral loads, and assay specificity was examined using a panel of viral pathogens other than SARS-CoV-2. In addition, we tested capacity for large-scale saliva testing using a four-sample pooling approach, where positive pools were subsequently decoupled and retested. Regular, frequent self-collected saliva swab RT-PCR testing was implemented for staff across fourteen quarantine hotels. Samples were tested at three diagnostic laboratories validated in this study, and results were provided back to staff in real-time. Findings: The agreement of self-collected saliva swabs for RT-PCR was 84.5% (95% CI 68.6 to 93.8) compared to RT-PCR using nasal/oropharyngeal swab samples collected by a healthcare practitioner, when saliva samples were collected within seven days of symptom onset. Between 7th December 2020 and 17th December 2021, almost 500,000 RT-PCR tests were performed on saliva swabs self-collected by 102 staff working in quarantine hotels in Melbourne. Of these, 20 positive saliva swabs were produced by 13 staff (0.004%). The majority of staff that tested positive occurred during periods of community transmission of the SARS-CoV-2 Delta variant. Interpretation: Salivary RT-PCR had an acceptable level of agreement compared to standard nasal/oropharyngeal swab RT-PCR within early symptom onset. The scalability, tolerability and ease of self-collection highlights utility for frequent or repeated testing in high-risk settings, such as quarantine or healthcare environments where regular monitoring of staff is critical for public health, and protection of vulnerable populations. Funding: This work was funded by the Victorian Department of Health.

SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity.

Respiratory tract infection with SARS-CoV-2 results in varying immunopathology underlying COVID-19. We examine cellular, humoral and cytokine responses covering 382 immune components in longitudinal blood and respiratory samples from hospitalized COVID-19 patients. SARS-CoV-2-specific IgM, IgG, IgA are detected in respiratory tract and blood, however, receptor-binding domain (RBD)-specific IgM and IgG seroconversion is enhanced in respiratory specimens. SARS-CoV-2 neutralization activity in respiratory samples correlates with RBD-specific IgM and IgG levels. Cytokines/chemokines vary between respiratory samples and plasma, indicating that inflammation should be assessed in respiratory specimens to understand immunopathology. IFN-α2 and IL-12p70 in endotracheal aspirate and neutralization in sputum negatively correlate with duration of hospital stay. Diverse immune subsets are detected in respiratory samples, dominated by neutrophils. Importantly, dexamethasone treatment does not affect humoral responses in blood of COVID-19 patients. Our study unveils differential immune responses between respiratory samples and blood, and shows how drug therapy affects immune responses during COVID-19.

Blood transcriptome responses in patients correlate with severity of COVID-19 disease.

Background: Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infected individuals display a wide spectrum of disease severity, as defined by the World Health Organization (WHO). One of the main factors underlying this heterogeneity is the host immune response, with severe COVID-19 often associated with a hyperinflammatory state. Aim: Our current study aimed to pinpoint the specific genes and pathways underlying differences in the disease spectrum and outcomes observed, through in-depth analyses of whole blood transcriptomics in a large cohort of COVID-19 participants. Results: All WHO severity levels were well represented and mild and severe disease displaying distinct gene expression profiles. WHO severity levels 1-4 were grouped as mild disease, and signatures from these participants were different from those with WHO severity levels 6-9 classified as severe disease. Severity level 5 (moderate cases) presented a unique transitional gene signature between severity levels 2-4 (mild/moderate) and 6-9 (severe) and hence might represent the turning point for better or worse disease outcome. Gene expression changes are very distinct when comparing mild/moderate or severe cases to healthy controls. In particular, we demonstrated the hallmark down-regulation of adaptive immune response pathways and activation of neutrophil pathways in severe compared to mild/moderate cases, as well as activation of blood coagulation pathways. Conclusions: Our data revealed discrete gene signatures associated with mild, moderate, and severe COVID-19 identifying valuable candidates for future biomarker discovery.

High levels of psychosocial distress among Australian frontline healthcare workers during the COVID-19 pandemic: a cross-sectional survey.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has had a profound and prolonged impact on healthcare services and healthcare workers. AIMS: The Australian COVID-19 Frontline Healthcare Workers Study aimed to investigate the severity and prevalence of mental health issues, as well as the social, workplace and financial disruptions experienced by Australian healthcare workers during the COVID-19 pandemic. METHODS: A nationwide, voluntary, anonymous, single timepoint, online survey was conducted between 27 August and 23 October 2020. Individuals self-identifying as frontline healthcare workers in secondary or primary care were invited to participate. Participants were recruited through health organisations, professional associations or colleges, universities, government contacts and national media. Demographics, home and work situation, health and psychological well-being data were collected. RESULTS: A total of 9518 survey responses were received; of the 9518 participants, 7846 (82.4%) participants reported complete data. With regard to age, 4110 (52.4%) participants were younger than 40 years; 6344 (80.9%) participants were women. Participants were nurses (n=3088, 39.4%), doctors (n=2436, 31.1%), allied health staff (n=1314, 16.7%) or in other roles (n=523, 6.7%). In addition, 1250 (15.9%) participants worked in primary care. Objectively measured mental health symptoms were common: mild to severe anxiety (n=4694, 59.8%), moderate to severe burnout (n=5458, 70.9%) and mild to severe depression (n=4495, 57.3%). Participants were highly resilient (mean (SD)=3.2 (0.66)). Predictors for worse outcomes on all scales included female gender; younger age; pre-existing psychiatric condition; experiencing relationship problems; nursing, allied health or other roles; frontline area; being worried about being blamed by colleagues and working with patients with COVID-19. CONCLUSIONS: The COVID-19 pandemic is associated with significant mental health symptoms in frontline healthcare workers. Crisis preparedness together with policies and practices addressing psychological well-being are needed.

Coping strategies adopted by Australian frontline health workers to address psychological distress during the COVID-19 pandemic.

OBJECTIVES: The Australian COVID-19 Frontline Healthcare Workers Study investigated coping strategies and help-seeking behaviours, and their relationship to mental health symptoms experienced by Australian healthcare workers (HCWs) during the COVID-19 pandemic. METHODS: Australian HCWs were invited to participate a nationwide, voluntary, anonymous, single time-point, online survey between 27th August and 23rd October 2020. Complete responses on demographics, home and work situation, and measures of health and psychological wellbeing were received from 7846 participants. RESULTS: The most commonly reported adaptive coping strategies were maintaining exercise (44.9%) and social connections (31.7%). Over a quarter of HCWs (26.3%) reported increased alcohol use which was associated with a history of poor mental health and worse personal relationships. Few used psychological wellbeing apps or sought professional help; those who did were more likely to be suffering from moderate to severe symptoms of mental illness. People living in Victoria, in regional areas, and those with children at home were significantly less likely to report adaptive coping strategies. CONCLUSIONS: Personal, social, and workplace predictors of coping strategies and help-seeking behaviour during the pandemic were identified. Use of maladaptive coping strategies and low rates of professional help-seeking indicate an urgent need to understand the effectiveness of, and the barriers and enablers of accessing, different coping strategies.

Integrated immune dynamics define correlates of COVID-19 severity and antibody responses.

SARS-CoV-2 causes a spectrum of COVID-19 disease, the immunological basis of which remains ill defined. We analyzed 85 SARS-CoV-2-infected individuals at acute and/or convalescent time points, up to 102 days after symptom onset, quantifying 184 immunological parameters. Acute COVID-19 presented with high levels of IL-6, IL-18, and IL-10 and broad activation marked by the upregulation of CD38 on innate and adaptive lymphocytes and myeloid cells. Importantly, activated CXCR3+cTFH1 cells in acute COVID-19 significantly correlate with and predict antibody levels and their avidity at convalescence as well as acute neutralization activity. Strikingly, intensive care unit (ICU) patients with severe COVID-19 display higher levels of soluble IL-6, IL-6R, and IL-18, and hyperactivation of innate, adaptive, and myeloid compartments than patients with moderate disease. Our analyses provide a comprehensive map of longitudinal immunological responses in COVID-19 patients and integrate key cellular pathways of complex immune networks underpinning severe COVID-19, providing important insights into potential biomarkers and immunotherapies.

Knowledge, attitudes and practices of healthcare workers within an Australian tertiary hospital to managing high-consequence infectious diseases.

BACKGROUND: Adequate preparation and support for healthcare workers (HCWs) managing high-consequence infectious diseases (HCIDs) is critical to the overall clinical management of HCIDs. Qualitative studies examining how well prepared and supported HCWs feel are lacking despite their key role. This study investigated how prepared and supported front-line HCWs at an Australian tertiary hospital felt about managing HCIDs such as viral haemorrhagic fever (VHF). METHODS: A qualitative research approach was used to undertake interviews with 45 Royal Melbourne Hospital medical and nursing staff from emergency, intensive care and infectious diseases. Interview questions captured data on HCWs' role, familiarity with using protocols, psychological attributes and training for scenarios related to VHF patient management. Interviews were recorded and transcribed. Categorical responses were analysed quantitatively and open-ended responses were analysed thematically. RESULTS: Ninety-eight percent of participants indicated feeling capable of undertaking their role in managing VHF patients; 77% felt supported through personnel/resources. However, 69% indicated barriers to managing these patients effectively; and 68% felt anxious at the prospect of managing VHF patients. Themes emerging from participants' observations included concerns about training frequency, miscommunication, difficulty with uncertainty, feeling underprepared, and fear of transmitting infection to others. CONCLUSION: Although the majority of HCWs feel confident about their ability to care for VHF patients, they also have a moderately-high degree of anxiety. Perceptions of interviewed staff have fed into recommendations to increase HCW preparedness and reduce anxiety, which include investigating support services, and exploring training options that create multi-departmental groups of highly specialised medical officers and nurses.

Clinical presentation and management of COVID-19.

The rapid spread of severe acute respiratory syndrome coronavirus 2 led to the declaration of a global pandemic within 3 months of its emergence. The majority of patients presenting with coronavirus disease 2019 (COVID-19) experience a mild illness that can usually be managed in the community. Patients require careful monitoring and early referral to hospital if any signs of clinical deterioration occur. Increased age and the presence of comorbidities are associated with more severe disease and poorer outcomes. Treatment for COVID-19 is currently predominantly supportive care, focused on appropriate management of respiratory dysfunction. Clinical evidence is emerging for some specific therapies (including antiviral and immune-modulating agents). Investigational therapies for COVID-19 should be used in the context of approved randomised controlled trials. Australian clinicians need to be able to recognise, diagnose, manage and appropriately refer patients affected by COVID-19, with thousands of cases likely to present over the coming years.

The Rise of Imported Dengue Infections in Victoria, Australia, 2010⁻2016.

Dengue notifications have increased dramatically over the past seven years in Victoria, Australia-a trend which has been seen nationally and reflects increased cases internationally. We reviewed the epidemiology of dengue among Victorian travellers, changes in diagnostic methods and describe the burden placed on local health systems resulting from this disease of public health importance. Cases of dengue notified to the Department of Health and Human Services in Victoria, Australia, between 1 January 2010 and 31 December 2016 were included in this review. Demographic, clinical, diagnostic methods, and risk factor data were examined using descriptive epidemiological analyses. Cases of dengue increased on average by 22% per year, with a total of 2187 cases (5.5 cases/100,000 population) notified over the 7-year reporting period. The most frequently reported country of acquisition was Indonesia (45%) followed by Thailand (14%). The use of multiple diagnostic methods, including the non-structural protein 1 antigen (NS1Ag) detection test, increased over time. The median time between onset of illness and diagnosis diminished from 9 days (IQR: 2⁻15) in 2010 to 4 days (IQR: 2⁻7) in 2016. Proportionally more cases were discharged directly from emergency departments in recent years (10% in 2010 to 28% in 2016, p < 0.001).The increasing incidence of dengue in Australia is reflective of its growing prominence as a travel medicine problem in western countries. For travellers with non-severe dengue, the improved timeliness of dengue diagnostics allows for consideration of best practice ambulatory management approaches as used in endemic areas.

Clinical variation in the use of echocardiography in Staphylococcus aureus bacteraemia: a multi-centre cohort study.

The objective of this investigation was to assess whether between-hospital variation in echocardiography usage for patients with Staphylococcus aureus bacteraemia (SAB) is explained by differences in patients' pre-test probability of endocarditis. This was a retrospective cohort study at three neighbouring hospitals in Australia. Consecutive episodes of SAB were reviewed for the presence of three endocarditis risk factors (community onset, prolonged bacteraemia and the presence of an intracardiac prosthetic device) and the performance and results of all echocardiography studies within 30 days. Multivariate logistic regression was used to examine the effect of hospital site on the performance of (i) transoesophageal and (ii) transthoracic echocardiography controlling for major endocarditis risk factors. Significant variation in echocardiography usage was demonstrated between sites in a total cohort of 1167 episodes of SAB. None of the three sites were found to exhibit echocardiography usage that could be considered consistent with current guidelines, and each differed from the guidelines in different ways. Hospital site, rather than endocarditis risk factors, was the strongest predictor of transthoracic echocardiography use; however, the use of transoesophageal echocardiography was strongly predicted by endocarditis risk factors. Variation in echocardiography use between these hospitals is not adequately explained by differences in the risk factor profile of their SAB cohorts.

Prolonged Detection of Japanese Encephalitis Virus in Urine and Whole Blood in a Returned Short-term Traveler.

We describe a fatal case of Japanese encephalitis virus infection following short-term travel to Thailand. Viral RNA was detected in urine and whole blood out to 26 and 28 days, respectively, after the onset of symptoms. Live virus was isolated from a urine specimen from day 14.

Influence of changing endotracheal tube cuff management on antibiotic use for ventilator-associated pneumonia in a tertiary intensive care unit.

BACKGROUND: Routine deflation of the endotracheal tube (ETT) cuff of critically ill patients receiving MV is common in Australia and New Zealand. Literature about ventilatorassociated pneumonia (VAP) and antibiotic use rates with different ETT cuff maintenance practices is lacking. OBJECTIVE: To determine the impact of a change in ETT cuff maintenance from a minimal leak technique to pressure manometry on the administration of antibiotics for VAP. DESIGN, SETTING AND PARTICIPANTS: A prospective, pre- post observational study conducted in a metropolitan tertiary referral intensive care unit. We analysed data from 178 patients receiving MV for > 48 hours during 13 weeks of minimal leak test ETT cuff technique (pre-intervention, n = 92) or 13 weeks of cuff pressure manometry (postintervention, n = 86), separated by 3 weeks' "wash-out". MAIN OUTCOME MEASURES: Primary outcome was the number of patients receiving antibiotics for the indication of VAP. Secondary outcomes were incidence of ventilatorassociated surveillance events, lengths of stay (LOSs) and mortality. RESULTS: Antibiotics were administered for VAP in 24 patients (26.1%) in the pre-intervention period compared with 11 post-intervention patients (12.8%). The univariate antibiotic administraion rate per 100 ventilation days was 15.3% (95% CI, 12.6%-18.4%) v 6.8% (95% CI, 4.9%- 9.3%), and the incident rate ratio (IRR) was 0.45 (95% CI, 0.31-0.64); P < 0.001). After adjustment for ventilation duration, IRR was 0.55 (95% CI, 0.24-1.27); P = 0.160. The ventilator-associated complication incidence rate was lower in the post-intervention group (11.4% v 16.3%; IRR, 0.70 [95% CI, 0.51-0.95]; P = 0.018). After adjustment for duration of MV, IRR was 0.66 (95% CI, 0.25-1.70); P = 0.387. Antibiotic administration for VAP was associated with increased ICU and hospital LOSs, but not with mortality. CONCLUSIONS: ETT cuff pressure manometry is associated with a reduced rate of antibiotic administration for a diagnosis of VAP compared with a minimal leak test technique.