Regulating antimicrobial use within hospitals: A qualitative study.

OBJECTIVES: To examine how regulatory structures and processes focused on antimicrobial stewardship and antimicrobial resistance are experienced by hospital managers and clinicians. METHODS: Forty-two hospital managers and clinicians working within accreditation and antimicrobial stewardship teams in three Australian hospitals participated in individual in-depth interviews. Thematic analysis was performed. RESULTS: Thematic analysis revealed participants' experiences of hospital antimicrobial regulation and their perceptions of what would be required for meaningful antimicrobial optimisation. Theme 1: Experience of regulation of antimicrobials within hospitals: Participants described an increased profile of antimicrobial resistance with inclusion in regulatory requirements, but also the risks of bureaucratic manoeuvring to meet standards rather than governance-inducing systemic changes. Theme 2: Growth of accreditation processes and hospitals over time: Both regulatory requirements and hospitals were described as evolving over time, each manoeuvring in response to each other (e.g. development of short notice accreditation). Theme 3: Perceived requirements for change: Participants perceived a need for top-down buy-in, resource prioritisation, complex understanding of power and influence on clinician behaviour, and a critical need for medical engagement. CONCLUSIONS: This study around antimicrobials shows the tension and dynamic relationship between regulatory processes and hospital responses, bringing to light the enduring balance of a system that positions itself to meet regulatory requirements and emerging "demands", without necessarily addressing the key underlying concerns. Antimicrobial resistance-related solutions are perceived as likely to require further resourcing and buy-in across multiple levels, engagement across professional streams and require strategies that consider complex systems change in order for regulatory structures to have potency.

A unique cytotoxic CD4+ T cell-signature defines critical COVID-19.

Objectives: SARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T-cell response to disease resolution or progression is still unclear. As newly emerging variants of concern have the capacity to partially escape NAb responses, defining the contribution of individual T-cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. Methods: Immunophenotyping of T-cell responses in unvaccinated individuals was performed, representing the full spectrum of COVID-19 clinical presentation. Computational and manual analyses were used to identify T-cell populations associated with distinct disease states. Results: Critical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+ lymphocytes (CTL). These CD4+ CTLs were largely absent in asymptomatic to severe disease states. In contrast, non-critical COVID-19 was associated with high frequencies of naïve T cells and lack of activation marker expression. Conclusion: Highly activated and cytotoxic CD4+ T-cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Induction of these potentially detrimental T-cell responses should be considered when developing and implementing effective COVID-19 control strategies.

Comparative Longitudinal Serological Study of Anti-SARS-CoV-2 Antibody Profiles in People with COVID-19.

Serological diagnostic assays are essential tools for determining an individual's protection against viruses like SARS-CoV-2, tracking the spread of the virus in the community, and evaluating population immunity. To assess the diversity and quality of the anti-SARS-CoV-2 antibody response, we have compared the antibody profiles of people with mild, moderate, and severe COVID-19 using a dot blot assay. The test targeted the four major structural proteins of SARS-CoV-2, namely the nucleocapsid (N), spike (S) protein domains S1 and S2, and receptor-binding domain (RBD). Serum samples were collected from 63 participants at various time points for up to 300 days after disease onset. The dot blot assay revealed patient-specific differences in the anti-SARS-CoV-2 antibody profiles. Out of the 63 participants with confirmed SARS-CoV-2 infections and clinical COVID-19, 35/63 participants exhibited diverse and robust responses against the tested antigens, while 14/63 participants displayed either limited responses to a subset of antigens or no detectable antibody response to any of the antigens. Anti-N-specific antibody levels decreased within 300 days after disease onset, whereas anti-S-specific antibodies persisted. The dynamics of the antibody response did not change during the test period, indicating stable antibody profiles. Among the participants, 28/63 patients with restricted anti-S antibody profiles or undetectable anti-S antibody levels in the dot blot assay also exhibited weak neutralization activity, as measured by a surrogate virus neutralization test (sVNT) and a microneutralization test. These results indicate that in some cases, natural infections do not lead to the production of neutralizing antibodies. Furthermore, the study revealed significant serological variability among patients, regardless of the severity of their COVID-19 illness. These differences need to be carefully considered when evaluating the protective antibody status of individuals who have experienced primary SARS-CoV-2 infections.

Clinical variation in the early assessment and management of suspected community-acquired meningitis: a multicentre retrospective study.

BACKGROUND: Bacterial meningitis is a medical emergency and timely management has been shown to improve outcomes. The aim of this study was to compare the early assessment and management of adults with suspected community-onset meningitis between hospitals and identify opportunities for clinical practice improvement. METHODS: This retrospective cohort study was conducted at three principal referral hospitals in Sydney, Australia. Adult patients with suspected meningitis undergoing cerebrospinal fluid sampling between 1 July 2018 and 31 June 2019 were included. Relevant clinical and laboratory data were extracted from the medical record. Differences between sites were analysed and factors associated with time to antimicrobial therapy were assessed by Cox regression. RESULTS: In 260 patients, the median time from triage to antibiotic administration was 332 min with a difference of up to 147 min between hospitals. Median time from triage to lumbar puncture (LP) was 366 min with an inter-hospital difference of up to 198 min. Seventy per cent of patients had neuroimaging prior to LP, and this group had a significantly longer median time to antibiotic administration (367 vs 231 min; P = 0.001). Guideline concordant antibiotics were administered in 84% of patients, with only 39% of those administered adjunctive corticosteroids. Seven (3%) patients had confirmed bacterial meningitis. Modifiable factors associated with earlier antimicrobial administration included infectious diseases involvement (adjusted hazard ratio [aHR], 1.50 [95% confidence interval (CI), 1.01-2.24]) and computed tomography (CT) scanning (aHR, 0.67 [95% CI, 0.46-0.98]). CONCLUSION: Opportunities for improvement include reducing the time to LP and antibiotic administration, improving coadministration of corticosteroids and avoiding potentially unnecessary CT scanning.

Mineralogical characterization of biosilicas versus geological analogs.

Non-crystalline silica mineraloids are essential to life on Earth as they provide architectural structure to dominant primary producers, such as plants and phytoplankton, as well as to protists and sponges. Due to the difficulty in characterizing and quantifying the structure of highly disordered X-ray amorphous silica, relatively little has been done to understand the mineralogy of biogenic silica and how this may impact the material properties of biogenic silica, such as hardness and strength, or how biosilica might be identified and differentiated from its inorganic geological counterparts. Typically, geologically formed opal-A and hyalite opal-AN are regarded as analogs to biogenic silica, however, some spectroscopic and imaging studies suggest that this might not be a reasonable assumption. In this study, we use a variety of techniques (X-ray diffraction, Raman spectroscopy, and scanning electron microscopy) to compare differences in structural disorder and bonding environments of geologically formed hydrous silicas (Opal-A, hyalite, geyserite) and silica glass versus biogenic silicas from an array of organisms. Our results indicate differences in the levels of structural disorder and the Raman-observed bonding environments of the SiO2 network modes (D1 mode) and the Q-species modes (~1015 cm-1 ) between varieties of biogenic silicas and geologically formed silicas, which aligns with previous studies that suggest fundamental differences between biogenic and geologically formed silica. Biosilicas also differ structurally from one another by species of organism. Our mineralogical approach to characterizing biosilicas and differentiating them from other silicas may be expanded to future diagenesis studies, and potentially applied to astrobiology studies of Earth and other planets.

Multidisciplinary team meetings in prosthetic joint infection management: A qualitative study.

BACKGROUND: Prosthetic joint infections (PJIs) cause substantial morbidity to patients and are extremely challenging for clinicians. Their management can include multiple operations, antibiotics, and prolonged hospital admissions. Multidisciplinary team meetings (MDTM) are increasingly used for collaborative decision-making around the management of PJIs, but thus far there has been no examination of the role of MDTM in decisions and management. This study aimed to examine interactions in a PJI MDTM to identify the dynamics in decision-making, and inter-specialty relationships more broadly. METHODS: Twelve MDTMs over 7 months at an Australian tertiary referral hospital were video recorded, transcribed, and thematic analysis was performed. RESULTS: Thematic analysis revealed four key areas of collaborative discussion 1. Achieving Inter-specialty Balance: The role of the multidisciplinary team discussion in providing balance between specialty views, and traversing the barriers between specialty interactions. 2. Negotiating Grey zones: there was frequent discussion of the limits of tests, interpretation of symptoms, and the limits of proposed operative strategies, and the resultant tensions of balancing ideal care vs pragmatic decision-making, and divergent goals of care. 3. Tailoring Treatment: identification of individual patient factors (both physiological and behavioural) and risks into collaborative decision-making. 4. Affording Failure: creating affordances in communication to openly discuss 'failure' to eliminate infection and likely negative outcomes. CONCLUSIONS: MDTM in the management of prosthetic joint infections serve multiple functions including: achieving interdisciplinary balance; effective grey zone management, tailoring reconfigured care; and most critically, recognition of 'failure' to eliminate infection, a communicative affordance most likely leading to better care.

Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.

Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.

The impact of cerebrospinal fluid viral polymerase chain reaction testing on the management of adults with viral meningitis: A multi-center retrospective study.

The aim of this study was to evaluate the role of viral polymerase chain reaction (PCR) testing in patients with aseptic meningitis and identify opportunities for improvement in clinical management. All cerebrospinal fluid samples collected in 1 year from four teaching hospitals in Sydney, Australia, were reviewed. Patients with aseptic meningitis were selected, and clinical and diagnostic features, hospital length of stay (LOS), and treatment were analyzed. Identifying a cause by viral PCR did not reduce hospital LOS (median 3 days) or antibiotic use (median 2 days), but the turnaround time of the PCR test correlated with LOS (Rs = 0.3822, p = 0.0003). Forty-one percent of patients received intravenous acyclovir treatment, which was more frequent in patients admitted under neurologists than infectious diseases physicians (56% vs. 24%; p = 0.013). The majority of patients did not have investigations for alternative causes of aseptic meningitis such as human immunodeficiency virus and syphilis if the viral PCR panel was negative. The benefit of PCR testing in aseptic meningitis in adults in reducing LOS and antibiotic use is unclear. The reasons for unnecessary aciclovir use in meningitis syndromes require further assessment.

High activation levels maintained in receptor-binding domain-specific memory B cells in people with severe coronavirus disease 2019.

The long-term health consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are still being understood. The molecular and phenotypic properties of SARS-CoV-2 antigen-specific T cells suggest a dysfunctional profile that persists in convalescence in those who were severely ill. By contrast, the antigen-specific memory B-cell (MBC) population has not yet been analyzed to the same degree, but phenotypic analysis suggests differences following recovery from mild or severe coronavirus disease 2019 (COVID-19). Here, we performed single-cell molecular analysis of the SARS-CoV-2 receptor-binding domain (RBD)-specific MBC population in three patients after severe COVID-19 and four patients after mild/moderate COVID-19. We analyzed the transcriptomic and B-cell receptor repertoire profiles at ~2 months and ~4 months after symptom onset. Transcriptomic analysis revealed a higher level of tumor necrosis factor-alpha (TNF-α) signaling via nuclear factor-kappa B in the severe group, involving CD80, FOS, CD83 and TNFAIP3 genes that was maintained over time. We demonstrated the presence of two distinct activated MBCs subsets based on expression of CD80hi TNFAIP3hi and CD11chi CD95hi at the transcriptome level. Both groups revealed an increase in somatic hypermutation over time, indicating progressive evolution of humoral memory. This study revealed distinct molecular signatures of long-term RBD-specific MBCs in convalescence, indicating that the longevity of these cells may differ depending on acute COVID-19 severity.

A subacute presentation of Mycoplasma hominis prosthetic valve endocarditis.

Mycoplasma hominis is a rare but important cause of prosthetic valve endocarditis. It is usually associated with acute progression of symptoms and can be difficult to diagnose as it does not grow in standard culture media. We report a case of an immunocompetent man in his 70s who presented with 14-month subacute decline with shortness of breath and evidence of a splenic infarct. Following a redo aortic valve replacement and diagnosis of M. hominis through 16S ribosomal ribonucleic acid PCR, he improved clinically with oral doxycycline therapy. He remained well at follow-up 2 years post-cessation of antibiotics. We present a literature review highlighting the role of PCR testing in the microbiological identification of M. hominis.

Longitudinal Characterization of Phagocytic and Neutralization Functions of Anti-Spike Antibodies in Plasma of Patients after Severe Acute Respiratory Syndrome Coronavirus 2 Infection.

Phagocytic responses by effector cells to opsonized viruses have been recognized to play a key role in antiviral immunity. Limited data on coronavirus disease 2019 suggest that the role of Ab-dependent and -independent phagocytosis may contribute to the observed immunological and inflammatory responses; however, their development, duration, and role remain to be fully elucidated. In this study of 62 acute and convalescent patients, we found that patients with acute coronavirus disease 2019 can mount a phagocytic response to autologous plasma-opsonized Spike protein-coated microbeads as early as 10 d after symptom onset, while heat inactivation of this plasma caused 77-95% abrogation of the phagocytic response and preblocking of Fc receptors showed variable 18-60% inhibition. In convalescent patients, phagocytic response significantly correlated with anti-Spike IgG titers and older patients, while patients with severe disease had significantly higher phagocytosis and neutralization functions compared with patients with asymptomatic, mild, or moderate disease. A longitudinal subset of the convalescent patients over 12 mo showed an increase in plasma Ab affinity toward Spike Ag and preservation of phagocytic and neutralization functions, despite a decline in the anti-Spike IgG titers by >90%. Our data suggest that early phagocytosis is primarily driven by heat-liable components of the plasma, such as activated complements, while anti-Spike IgG titers account for the majority of observed phagocytosis at convalescence. Longitudinally, a significant increase in the affinity of the anti-Spike Abs was observed that correlated with the maintenance of both the phagocytic and neutralization functions, suggesting an improvement in the quality of the Abs.

Patterns and correlates of hepatitis C virus phylogenetic clustering among people living with HIV in Australia in the direct-acting antiviral era: A molecular epidemiology study among participants in the CEASE cohort.

Background and Aims: In moving towards the elimination of hepatitis C virus (HCV) infection among people living with HIV, understanding HCV transmission patterns may provide insights to guide and evaluate interventions. In this study, we evaluated patterns of, and factors associated with HCV phylogenetic clustering among people living with HIV/HCV co-infection in Australia in the direct-acting antiviral era. Methods: HCV RNA was extracted from dried blood spot (DBS) samples collected between 2014 and 2018 in the CEASE cohort study. The HCV Core-E2 region was amplified by a polymerase chain reaction and Sanger sequenced. Maximum likelihood phylogenetic trees (1000 bootstrap replicates) were used to identify patterns of clustering (3% genetic distance threshold). Mixed-effects logistic regression was used to determine correlates of phylogenetic clustering. Factors assessed were sexual risk behavior, education, injecting drug use, housing, employment, HIV viral load, age, sex, and sexuality. Results: Phylogenetic trees were reconstructed for HCV subtype 1a (n = 139) and 3a (n = 63) sequences, with 29% (58/202) in a pair or cluster. Overall (n = 202), phylogenetic clustering was positively associated with younger age (under 40; adjusted odds ratio [aOR] 2.52, 95% confidence interval [CI] 1.20-5.29), and among gay and bisexual men (n = 168), was positively associated with younger age (aOR 2.61, 95% CI 1.10-6.19), higher education (aOR 2.58, 95% CI 1.09-6.13), and reporting high-risk sexual behavior (aOR 3.94, 95% CI 1.31-11.84). During follow-up, five reinfections were observed, but none were in phylogenetic clusters. Conclusion: This study found a high proportion of phylogenetic relatedness, predominantly among younger people and gay and bisexual men reporting high-risk sexual behavior. Despite this, few reinfections were observed, and reinfections demonstrated little relationship with known clusters. These findings highlight the importance of rapid HCV treatment initiation, together with monitoring of the phylogeny.

Effects of cobalt doping on the reactivity of hausmannite for As(III) oxidation and As(V) adsorption.

Hausmannite is a common low valence Mn oxide mineral, with a distorted spinel structure, in surficial sediments. Although natural Mn oxides often contain various impurities of transitional metals (TMs), few studies have addressed the effect and related mechanism of TM doping on the reactivity of hausmannite with metal pollutants. Here, the reactivity of cobalt (Co) doped hausmannite with aqueous As(III) and As(V) was studied. Co doping decreased the point of zero charge of hausmannite and its adsorption capacity for As(V). Despite a reduction of the initial As(III) oxidation rate, Co-doped hausmannite could effectively oxidize As(III) to As(V), followed by the adsorption and fixation of a large amount of As(V) on the mineral surface. Arsenic K-edge EXAFS analysis of the samples after As(V) adsorption and As(III) oxidation revealed that only As(V) was adsorbed on the mineral surface, with an average As-Mn distance of 3.25-3.30 Å, indicating the formation of bidentate binuclear complexes. These results provide new insights into the interaction mechanism between TMs and low valence Mn oxides and their effect on the geochemical behaviors of metal pollutants.

Super-hydration and reduction of manganese oxide minerals at shallow terrestrial depths.

Manganese oxides are ubiquitous marine minerals which are redox sensitive. As major components of manganese nodules found on the ocean floor, birnessite and buserite have been known to be two distinct water-containing minerals with manganese octahedral interlayer separations of ~7 Å and ~10 Å, respectively. We show here that buserite is a super-hydrated birnessite formed near 5 km depth conditions. As one of the most hydrous minerals containing ca. 34.5 wt. % water, super-hydrated birnessite, i.e., buserite, remains stable up to ca. 70 km depth conditions, where it transforms into manganite by releasing ca. 24.3 wt. % water. Subsequent transformations to hausmannite and pyrochroite occur near 100 km and 120 km depths, respectively, concomitant with a progressive reduction of Mn4+ to Mn2+. Our work forwards an abiotic geochemical cycle of manganese minerals in subduction and/or other aqueous terrestrial environments, with implications for water storage and cycling, and the redox capacity of the region.

Maintenance of broad neutralizing antibodies and memory B cells 1 year post-infection is predicted by SARS-CoV-2-specific CD4+ T cell responses.

Understanding the long-term maintenance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity is critical for predicting protection against reinfection. In an age- and gender-matched cohort of 24 participants, the association of disease severity and early immune responses on the maintenance of humoral immunity 12 months post-infection is examined. All severely affected participants maintain a stable subset of SARS-CoV-2 receptor-binding domain (RBD)-specific memory B cells (MBCs) and good neutralizing antibody breadth against the majority of the variants of concern, including the Delta variant. Modeling these immune responses against vaccine efficacy data indicate a 45%-76% protection against symptomatic infection (variant dependent). Overall, these findings indicate durable humoral responses in most participants after infection, reasonable protection against reinfection, and implicate baseline antigen-specific CD4+ T cell responses as a predictor of maintenance of antibody neutralization breadth and RBD-specific MBC levels at 12 months post-infection.

Standardized testing and written communication improve patient understanding of beta-lactam allergy testing outcomes: A multicenter, prospective study.

Background: Historical penicillin allergy is commonly reported, but the lack of standardized allergy clinic practices may diminish the ability to delabel beta-lactam allergy appropriately. Objective: We sought to improve beta-lactam allergy testing and patient understanding of their antibiotic allergy status by standardizing testing and communication practices between 7 adult and pediatric hospital centers. Methods: Phase 1 prospectively described the beta-lactam allergy testing practices at each center. Following this, practice was standardized to achieve a defined panel of skin testing reagents, pro forma result letters for patients and referring doctors, and provision of medical alert jewelry to those with confirmed allergy. Testing outcomes and patient perception regarding allergy status 8 weeks postassessment were compared before (phase 1) and after standardization (phase 2). Primary outcomes were the percentage of participants delabeled after testing, and concordance rates between participant perception of their allergy status and their status as determined by the treating physician at 8-week follow-up. Results: Of 195 adult and pediatric participants (median age, 50 years; 21.5% <18 years; 36.9% males), 75% were delabeled of their beta-lactam allergy. No patient experienced anaphylaxis related to any beta-lactam delabeling testing. In phase 1, 75% of participants received written results, 52% were informed verbally, and 48% received results in more than 1 form. All phase 2 participants received written results (P < .01), 61% received verbal results from a physician as well (P > .05). At 8-week follow-up, 54% of phase 1 participants had concordant perceptions of their allergy status as the testing team versus 91.6% in phase2 (P < .001). Of the 17 participants who were delabeled and treated with a beta-lactam antibiotic during the 8-week follow-up period, there were no reported allergic reactions, although 1 participant experienced anaphylaxis following exposure to amoxicillin-clavulanic acid 1 year after delabeling. Conclusions: Standardization of testing and written patient information improved short-term patient perception of beta-lactam allergy status.

The impact of re-opening the international border on COVID-19 hospitalisations in Australia: a modelling study.

OBJECTIVE: To estimate the numbers of COVID-19-related hospitalisations in Australia after re-opening the international border. DESIGN: Population-level deterministic compartmental epidemic modelling of eight scenarios applying various assumptions regarding SARS-CoV-2 transmissibility (baseline R0 = 3.5 or 7.0), vaccine rollout speed (slow or fast), and scale of border re-opening (mean of 2500 or 13 000 overseas arrivals per day). SETTING: Simulation population size, age structure, and age-based contact rates based on recent estimates for the Australian population. We assumed that 80% vaccination coverage of people aged 16 years or more was reached in mid-October 2021 (fast rollout) or early January 2022 (slow rollout). MAIN OUTCOME MEASURES: Numbers of people admitted to hospital with COVID-19, December 2021 - December 2022. RESULTS: In scenarios assuming a highly transmissible SARS-CoV-2 variant (R0  = 7.0), opening the international border on either scale was followed by surges in both infections and hospitalisations that would require public health measures beyond mask wearing and social distancing to avoid overwhelming the health system. Reducing the number of hospitalisations to manageable levels required several cycles of additional social and mobility restrictions. CONCLUSIONS: If highly transmissible SARS-CoV-2 variants are circulating locally or overseas, large and disruptive COVID-19 outbreaks will still be possible in Australia after 80% of people aged 16 years or more have been vaccinated. Continuing public health measures to restrict the spread of disease are likely to be necessary throughout 2022.