IDentif.AI-Omicron: Harnessing an AI-Derived and Disease-Agnostic Platform to Pinpoint Combinatorial Therapies for Clinically Actionable Anti-SARS-CoV-2 Intervention.

Nanomedicine-based and unmodified drug interventions to address COVID-19 have evolved over the course of the pandemic as more information is gleaned and virus variants continue to emerge. For example, some early therapies (e.g., antibodies) have experienced markedly decreased efficacy. Due to a growing concern of future drug resistant variants, current drug development strategies are seeking to find effective drug combinations. In this study, we used IDentif.AI, an artificial intelligence-derived platform, to investigate the drug-drug and drug-dose interaction space of six promising experimental or currently deployed therapies at various concentrations: EIDD-1931, YH-53, nirmatrelvir, AT-511, favipiravir, and auranofin. The drugs were tested in vitro against a live B.1.1.529 (Omicron) virus first in monotherapy and then in 50 strategic combinations designed to interrogate the interaction space of 729 possible combinations. Key findings and interactions were then further explored and validated in an additional experimental round using an expanded concentration range. Overall, we found that few of the tested drugs showed moderate efficacy as monotherapies in the actionable concentration range, but combinatorial drug testing revealed significant dose-dependent drug-drug interactions, specifically between EIDD-1931 and YH-53, as well as nirmatrelvir and YH-53. Checkerboard validation analysis confirmed these synergistic interactions and also identified an interaction between EIDD-1931 and favipiravir in an expanded range. Based on the platform nature of IDentif.AI, these findings may support further explorations of the dose-dependent drug interactions between different drug classes in further pre-clinical and clinical trials as possible combinatorial therapies consisting of unmodified and nanomedicine-enabled drugs, to combat current and future COVID-19 strains and other emerging pathogens.

The IDentif.AI-x pandemic readiness platform: Rapid prioritization of optimized COVID-19 combination therapy regimens.

IDentif.AI-x, a clinically actionable artificial intelligence platform, was used to rapidly pinpoint and prioritize optimal combination therapies against COVID-19 by pairing a prospective, experimental validation of multi-drug efficacy on a SARS-CoV-2 live virus and Vero E6 assay with a quadratic optimization workflow. A starting pool of 12 candidate drugs developed in collaboration with a community of infectious disease clinicians was first narrowed down to a six-drug pool and then interrogated in 50 combination regimens at three dosing levels per drug, representing 729 possible combinations. IDentif.AI-x revealed EIDD-1931 to be a strong candidate upon which multiple drug combinations can be derived, and pinpointed a number of clinically actionable drug interactions, which were further reconfirmed in SARS-CoV-2 variants B.1.351 (Beta) and B.1.617.2 (Delta). IDentif.AI-x prioritized promising drug combinations for clinical translation and can be immediately adjusted and re-executed with a new pool of promising therapies in an actionable path towards rapidly optimizing combination therapy following pandemic emergence.

Remdesivir for 5 or 10 Days in Patients with Severe Covid-19.

BACKGROUND: Remdesivir is an RNA polymerase inhibitor with potent antiviral activity in vitro and efficacy in animal models of coronavirus disease 2019 (Covid-19). METHODS: We conducted a randomized, open-label, phase 3 trial involving hospitalized patients with confirmed SARS-CoV-2 infection, oxygen saturation of 94% or less while they were breathing ambient air, and radiologic evidence of pneumonia. Patients were randomly assigned in a 1:1 ratio to receive intravenous remdesivir for either 5 days or 10 days. All patients received 200 mg of remdesivir on day 1 and 100 mg once daily on subsequent days. The primary end point was clinical status on day 14, assessed on a 7-point ordinal scale. RESULTS: In total, 397 patients underwent randomization and began treatment (200 patients for 5 days and 197 for 10 days). The median duration of treatment was 5 days (interquartile range, 5 to 5) in the 5-day group and 9 days (interquartile range, 5 to 10) in the 10-day group. At baseline, patients randomly assigned to the 10-day group had significantly worse clinical status than those assigned to the 5-day group (P = 0.02). By day 14, a clinical improvement of 2 points or more on the ordinal scale occurred in 64% of patients in the 5-day group and in 54% in the 10-day group. After adjustment for baseline clinical status, patients in the 10-day group had a distribution in clinical status at day 14 that was similar to that among patients in the 5-day group (P = 0.14). The most common adverse events were nausea (9% of patients), worsening respiratory failure (8%), elevated alanine aminotransferase level (7%), and constipation (7%). CONCLUSIONS: In patients with severe Covid-19 not requiring mechanical ventilation, our trial did not show a significant difference between a 5-day course and a 10-day course of remdesivir. With no placebo control, however, the magnitude of benefit cannot be determined. (Funded by Gilead Sciences; GS-US-540-5773 ClinicalTrials.gov number, NCT04292899.).

Longitudinal Study of Cellular and Systemic Cytokine Signatures to Define the Dynamics of a Balanced Immune Environment During Disease Manifestation in Zika Virus-Infected Patients.

Background: Since its unexpected reemergence, Zika virus (ZIKV) has caused numerous outbreaks globally. This study characterized the host immune responses during ZIKV infection. Methods: Patient samples were collected longitudinally during the acute, convalescence and recovery phases of ZIKV infection over 6 months during the Singapore outbreak in late 2016. Plasma immune mediators were profiled via multiplex microbead assay, while changes in blood cell numbers were determined with immunophenotyping. Results: Data showed the involvement of various immune mediators during acute ZIKV infection accompanied by a general reduction in blood cell numbers for all immune subsets except CD14+ monocytes. Importantly, viremic patients experiencing moderate symptoms had significantly higher quantities of interferon γ-induced protein 10, monocyte chemotactic protein 1, interleukin 1 receptor antagonist, interleukin 8, and placental growth factor 1, accompanied by reduced numbers of peripheral CD8+ T cells, CD4+ T cells, and double-negative T cells. Levels of T-cell associated mediators, including interferon γ-induced protein 10, interferon γ, and interleukin 10, were high in recovery phases of ZIKV infection, suggesting a functional role for T cells. The identification of different markers at specific disease phases emphasizes the dynamics of a balanced cytokine environment in disease progression. Conclusions: This is the first comprehensive study that highlights specific cellular changes and immune signatures during ZIKV disease progression, and it provides valuable insights into ZIKV immunopathogenesis.

A Sensitive Method for Detecting Zika Virus Antigen in Patients' Whole-Blood Specimens as an Alternative Diagnostic Approach.

Background: Epidemics caused by the reemergence of Zika virus (ZIKV) warrant the need to develop new diagnostic measures to complement currently used detection methods. In this study, we explored the detection of ZIKV antigen in a defined leukocyte subset from patients' whole-blood specimens. Methods: Whole-blood samples were obtained at the acute and early convalescent phases from ZIKV-infected patients during the Singapore outbreak in August-September 2016. Presence of ZIKV antigen was determined by flow cytometry staining for intracellular ZIKV NS3, using a ZIKV-specific polyclonal antibody. The presence of ZIKV antigen was determined in CD45+CD14+ monocytes. Results: Data showed that ZIKV NS3 antigen could be detected in CD45+CD14+ monocytes. The levels of detection were further categorized into 3 groups: high (positivity among >40% of monocytes), moderate (positivity among 10%-40%), and low (positivity among <10%). While a majority of patients showed a decrease in the amount of ZIKV antigen detected at later time points, some patients displayed higher levels as the disease progressed. Conclusions: Our data highlights an alternative approach in using flow cytometry as a sensitive method for detecting ZIKV antigen in whole blood. Importantly, it further confirms the role of CD14+ monocytes as an important cellular target for ZIKV infection during the viremic phase.

MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and long-term care facilities (ILTCFs), the transmission dynamics of MRSA between healthcare settings is not well understood. METHODS: We conducted a cross-sectional study in a network comprising an ACH and 5 closely affiliated ILTCFs in Singapore. A total of 1700 inpatients were screened for MRSA over a 6-week period in 2014. MRSA isolates underwent whole-genome sequencing, with a pairwise single-nucleotide polymorphism (Hamming distance) cutoff of 60 core genome single-nucleotide polymorphisms used to define recent transmission clusters (clades) for the 3 major clones. RESULTS: MRSA prevalence was significantly higher in intermediate-term (29.9%) and long-term (20.4%) care facilities than in the ACH (11.8%) (P < .001). The predominant clones were sequence type [ST] 22 (n = 183; 47.8%), ST45 (n = 129; 33.7%), and ST239 (n = 26; 6.8%), with greater diversity of STs in ILTCFs relative to the ACH. A large proportion of the clades in ST22 (14 of 21 clades; 67%) and ST45 (7 of 13; 54%) included inpatients from the ACH and ILTCFs. The most frequent source of the interfacility transmissions was the ACH (n = 28 transmission events; 36.4%). CONCLUSIONS: MRSA transmission dynamics between the ACH and ILTCFs were complex. The greater diversity of STs in ILTCFs suggests that the ecosystem in such settings might be more conducive for intrafacility transmission events. ST22 and ST45 have successfully established themselves in ILTCFs. The importance of interconnected infection prevention and control measures and strategies cannot be overemphasized.

Local transmission and global dissemination of New Delhi Metallo-Beta-Lactamase (NDM): a whole genome analysis.

BACKGROUND: New Delhi metallo-ß-lactamase (bla NDM), a plasmid-borne carbapenemase gene associated with significant mortality and severely limited treatment options, is of global public health concern as it is found in extremely diverse Gram-negative bacterial strains. This study thus aims to genetically characterize local and global spread of bla NDM. METHODS: To investigate local transmission patterns in the context of a single hospital, whole genome sequencing data of the first 11 bla NDM-positive bacteria isolated in a local hospital were analyzed to: (1) identify and compare bla NDM-positive plasmids; and (2) study the phylogenetic relationship of the bacteria chromosomes. The global analysis was conducted by analyzing 2749 complete plasmid sequences (including 39 bla NDM-positive plasmids) in the NCBI database, where: (1) the plasmids were clustered based on their gene composition similarity; (2) phylogenetic study was conducted for each bla NDM-positive plasmid cluster to infer the phylogenetic relationship within each cluster; (3) gene transposition events introducing bla NDM into different plasmid backbones were identified; and (4) clustering pattern was correlated with the plasmids' incompatibility group and geographical distribution. RESULTS: Analysis of the first 11 bla NDM-positive isolates from a single hospital revealed very low bla NDM-positive plasmid diversity. Local transmission was characterized by clonal spread of a predominant plasmid with 2 sporadic instances of plasmid introduction. In contrast to the low diversity locally, global bla NDM spread involved marked plasmid diversity with no predominant bacterial clone. Thirty-nine (1.4 %) out of the 2749 complete plasmid sequences were bla NDM-positive, and could be resolved into 7 clusters, which were associated with plasmid incompatibility group and geographical distribution. The bla NDM gene module was witnessed to mobilize between different plasmid backbones on at least 6 independent occasions. CONCLUSIONS: Our analysis revealed the complex genetic pathways of bla NDM spread, with global dissemination characterized mainly by transposition of the bla NDM gene cassette into varied plasmids. Early local transmission following plasmid introduction is characterized by plasmid conjugation and bacterial spread. Our findings emphasize the importance of plasmid molecular epidemiology in understanding bla NDM spread.

Psychosocial determinants of physicians' acceptance of recommendations by antibiotic computerised decision support systems: A mixed methods study.

Antibiotic computerised decision support systems (CDSSs) were developed to facilitate optimal prescribing, but acceptance of their recommendations has remained low. We aimed to evaluate physicians' perceptions and attitudes toward antibiotic CDSSs and determine psychosocial factors associated with acceptance of CDSS recommendations for empirical therapy. A mixed methods study was conducted in an adult tertiary-care hospital in Singapore, with its in-house antibiotic CDSS that integrates antimicrobial stewardship with electronic prescribing. Focus group discussions were conducted among purposively sampled physicians and data were analysed using the framework approach. Emerging themes were included in the questionnaire with newly developed scales for the subsequent cross-sectional survey involving all physicians. Principal components analysis was performed to derive the latent factor structure that was later applied in multivariate analyses. Physicians expressed confidence in the credibility of CDSS recommendations. Junior physicians accepted CDSS recommendations most of the time, whilst senior physicians acknowledged overriding recommendations in complex patients with multiple infections or allergies. Willingness to consult the CDSS for common and complex infections (OR=1.68, 95% CI 1.16-2.44) and preference for personal or team decision (OR=0.61, 95% CI 0.43-0.85) were associated with acceptance of CDSS recommendations. Cronbach's α for scales measuring physicians' attitudes and perceptions towards acceptance of CDSS recommendations ranged from 0.64 to 0.88. Physicians' willingness to consult an antibiotic CDSS determined acceptance of its recommendations. Physicians would choose to exercise their own or clinical team's decision over CDSS recommendations in complex patient situations when the antibiotic prescribing needs were not met.

Antibiotic therapy and clinical outcomes of Pseudomonas aeruginosa (PA) bacteraemia.

INTRODUCTION: Pseudomonas aeruginosa (PA) bacteraemia is associated with high morbidity and mortality. We assessed clinical outcomes in patients with PA bacteraemia treated with piperacillin-tazobactam (TZP) versus other antibiotics, and monotherapy versus combination, all with proven activity by disc testing without minimum inhibitory concentration (MIC) data. MATERIALS AND METHODS: All patients with PA bacteraemia in 2007 to 2008 were reviewed for demographic, comorbidity, clinical, laboratory, treatment and outcome data. Primary outcome was 30-day mortality. Secondary outcomes included microbiological clearance, clinical response and length of stay (LOS). RESULTS: Median age for 91 patients was 65 years. Median Simplified Acute Physiology Score (SAPS) II score was 30. Monotherapy was used in 77 cases: 42 on ceftazidime, 17 on TZP, 10 on carbapenems, and 8 on other antipseudomonal antibiotics. The 30-day mortality was 20.9%, and similar between ceftazidime and TZP versus other antibiotics respectively. More patients in combination versus monotherapy group had cardiovascular diseases, diabetes mellitus and vascular access as source of bacteraemia. Patients on monotherapy had higher 30-day mortality (24.7% vs 0%, P = 0.037). Multivariate analysis identified SAPS II score (OR = 1.097, 95% CI, 1.032 to 1.166, P = 0.003) and cancer (OR = 4.873, 95% CI, 1.235 to 19.223, P = 0.024) as independent predictors of 30-day mortality. CONCLUSION: TZP appeared to be an effective culture-guided antibiotic for PA bacteraemia. High 30-day mortality in monotherapy might be confounded by comorbidity, illness severity and sample size. Cancer patients and a high SAPS II score were independent predictors of 30-day mortality.

Severe community-acquired Acinetobacter baumannii pneumonia: an emerging highly lethal infectious disease in the Asia-Pacific.

BACKGROUND AND OBJECTIVE: Patients with community-acquired Acinetobacter baumannii (AB) pneumonia have been reported from subtropical countries. We investigated the epidemiology, clinical and microbiological characteristics of community-acquired pneumonia (CAP) due to AB in Singapore. METHOD: A retrospective case series was performed over a 21-month period at two institutions. RESULTS: From 1 January 2007 to 30 September 2008, eight patients were diagnosed with CAP due to AB. Seven had bacteraemia and five were sputum culture-positive. The median age at presentation was 58.5 years (range 45-76 years). Five patients (71.4%) acquired the pneumonia in the warmer months of June to September. Presentation was acute, with a median duration of 2.5 days (range 1-7 days). The median Acute Physiology and Chronic Health Evaluation II score was 28.5 (range 6-36). Six patients presented with septic shock, lactic acidosis, acute kidney injury and respiratory failure, necessitating ICU care; five of these patients eventually died. All patients received empirical antibiotics, including third-generation cephalosporins, which were inactive against the organism. All isolates were susceptible to ampicillin/sulbactam, ciprofloxacin, co-trimoxazole, aminoglycosides and imipenem. CONCLUSIONS: Community-acquired AB pneumonia have a fulminant course. In a region endemic for melioidosis and severe community-acquired Klebsiella pneumoniae, the challenge lies in rapid identification and initiation of appropriate empirical antibiotics to improve the survival of patients with AB CAP.

Predictive value of simple clinical and laboratory variables for dengue hemorrhagic fever in adults.

BACKGROUND: Singapore experienced its worst dengue outbreak in 30 years in 2004, with 9459 notified cases, of which 83% were hospitalized. OBJECTIVES: To determine predictors of dengue hemorrhagic fever (DHF) upon first presentation to hospital to aid clinicians in determining need for admission. STUDY DESIGN: We conducted a retrospective cohort study on dengue patients in Tan Tock Seng Hospital, Singapore in 2004, with patients categorized into dengue fever (DF) and DHF. Demographic, clinical, and laboratory variables upon first presentation were compared to determine the likelihood of developing DHF. RESULTS: There were 1973 dengue patients-118 (6.0%) were DHF, of which 82 (4.2%) developed DHF during hospitalization. From the multivariate analysis, patients with bleeding had an odds of developing DHF 237.6 times that of DF, a unit decrease in total protein (g/L) had an odds of 1.28 times, a unit increase in blood urea (mmol/L) had an odds of 1.31 times, and a unit decrease in lymphocyte proportion had an odds of 1.08 times. The model had a sensitivity of 97.6%, specificity of 60.2%, and may reduce 1118 (56.7%) dengue admissions. CONCLUSIONS: A few easily available clinical and laboratory results may assist clinicians in determining dengue admissions.

Cluster of Staphylococcus aureus and dengue co-infection in Singapore.

INTRODUCTION: Singapore saw a resurgence of dengue infections in 2005. Concurrent bacterial co-infections in dengue is rare. CLINICAL PICTURE: We report a cluster of serious methicillin-susceptible Staphylococcus aureus (MSSA) bacteraemia or severe soft tissue infection in 5 epidemiologically linked construction workers presenting with dengue and non-resolving fever. TREATMENT: Surgical intervention was indicated in 4 of the 5 patients despite appropriate antistaphylococcal therapy. OUTCOME: All but 1 patient were eventually discharged. Clonality and Panton-Valentine leucocidin genes were not demonstrated. Epidemiological investigations suggested that occupational contact dermatitis could have predisposed the patients to this opportunistic co-infection. CONCLUSION: Clinicians need to be vigilant to unusual manifestations of dengue which may signal a concomitant aetiology.

Review of human infections with avian influenza H5N1 and proposed local clinical management guideline.

INTRODUCTION: The current avian and human H5N1 influenza epidemic has been in resurgence since 2004. We decided to evaluate published evidence in relation to epidemiology, clinical features and course, laboratory diagnosis, treatment and outcome of human H5N1 influenza, and develop institutional clinical management guidelines. METHODS: A search of PubMed was conducted for all English language articles with search terms "avian", "influenza" and "H5N1". The bibliography of articles was searched for other references of interest. RESULTS: Published case series from Hong Kong in 1997, and Thailand and Vietnam since 2004 have indicated a rapidly progressive primary viral pneumonia resulting in acute respiratory distress syndrome. The majority of human H5N1 infections can be linked to poultry exposure. Hitherto there has been no evidence of efficient human-to-human transmission. Case fatality rates have varied from 71% in Thailand to 100% in Cambodia. Oseltamivir appears to be the only potentially effective antiviral therapy. H5N1 isolates in Vietnam have become resistant to oseltamivir, resulting in persistent viral replication and death. There is as yet no effective human H5N1 vaccine. CONCLUSIONS: National and international preparedness plans are well advised. Clinical trials to evaluate higher dose oseltamivir therapy and immunomodulatory treatment are urgently needed.