Transportability of bacterial infection prediction models for critically ill patients

OBJECTIVE

Bacterial infections (BIs) are common, costly, and potentially life-threatening in critically ill patients. Patients with suspected BIs may require empiric multidrug antibiotic regimens and therefore potentially be exposed to prolonged and unnecessary antibiotics. We previously developed a BI risk model to augment practices and help shorten the duration of unnecessary antibiotics to improve patient outcomes. Here, we have performed a transportability assessment of this BI risk model in 2 tertiary intensive care unit (ICU) settings and a community ICU setting. We additionally explored how simple multisite learning techniques impacted model transportability.

METHODS

Patients suspected of having a community-acquired BI were identified in 3 datasets: Medical Information Mart for Intensive Care III (MIMIC), Northwestern Medicine Tertiary (NM-T) ICUs, and NM "community-based" ICUs. ICU encounters from MIMIC and NM-T datasets were split into 70/30 train and test sets. Models developed on training data were evaluated against the NM-T and MIMIC test sets, as well as NM community validation data.

RESULTS

During internal validations, models achieved AUROCs of 0.78 (MIMIC) and 0.81 (NM-T) and were well calibrated. In the external community ICU validation, the NM-T model had robust transportability (AUROC 0.81) while the MIMIC model transported less favorably (AUROC 0.74), likely due to case-mix differences. Multisite learning provided no significant discrimination benefit in internal validation studies but offered more stability during transport across all evaluation datasets.

DISCUSSION

These results suggest that our BI risk models maintain predictive utility when transported to external cohorts.

CONCLUSION

Our findings highlight the importance of performing external model validation on myriad clinically relevant populations prior to implementation.

Integrative analysis of functional genomic screening and clinical data identifies a protective role for spironolactone in severe COVID-19

We demonstrate that integrative analysis of CRISPR screening datasets enables network-based prioritization of prescription drugs modulating viral entry in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by developing a network-based approach called Rapid proXimity Guidance for Repurposing Investigational Drugs (RxGRID). We use our results to guide a propensity-score-matched, retrospective cohort study of 64,349 COVID-19 patients, showing that a top candidate drug, spironolactone, is associated with improved clinical prognosis, measured by intensive care unit (ICU) admission and mechanical ventilation rates. Finally, we show that spironolactone exerts a dose-dependent inhibitory effect on viral entry in human lung epithelial cells. Our RxGRID method presents a computational framework, implemented as an open-source software package, enabling genomics researchers to identify drugs likely to modulate a molecular phenotype of interest based on high-throughput screening data. Our results, derived from this method and supported by experimental and clinical analysis, add additional supporting evidence for a potential protective role of the potassium-sparing diuretic spironolactone in severe COVID-19.

First Report of Cowpea Aphid-Borne Mosaic Potyvirus from Cowpeas Grown Commercially in the U.S

Cowpea aphid-borne mosaic potyvirus (CABMV) is one of several seed-borne viruses known to limit cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata) production in Africa, Europe, and Asia, but CABMV has not been reported on commercially grown cowpeas in the United States (1). However, a sesame (Sesamum indicum L.)-infecting isolate of CABMV was recently characterized from plants growing near cowpea introduction plots in Georgia (2). In February 1997, we received samples of three seed lots of cowpea cv. Chinese Red that had been harvested in southern Texas during 1996. Approximately 28% of the plants grown from these seed lots expressed strong mosaic symptoms on primary and trifoliate leaves. Viruslike symptoms were reproduced following mechanical transmission to plants of Chinese Red cowpea, Nicotiana benthamiana, and soybean (Glycine max L.) cv. Lee. When Coronet and Pinkeye Purple Hull-BVR cowpeas were inoculated with sap extracts from symptomatic Chinese Red plants, chlorotic lesions developed on inoculated leaves, but only Coronet plants supported symptomless systemic infections. Similarly inoculated plants of Chenopodium quinoa (L.) and common bean (Phaseolus vulgaris L.) cvs. Pinto and Black Valentine developed localized chlorotic lesions. In Ouchterlony gel diffusion assays, extracts from symptomatic cowpea plants did not react with antisera to blackeye cowpea mosaic potyvirus (BlCMV), cucumber mosaic cucu-movirus (CMV), southern bean mosaic sobemovirus, cowpea mosaic comovirus, cowpea severe mosaic comovirus, or cowpea chlorotic mottle bromovirus. In the indirect enzyme-linked immunosorbent assay, sap extracts from symptomatic plants reacted with antiserum to CABMV, giving OD values at A₄₀₅ of 0.10 to 0.25, and reacted weakly with antiserum to BlCMV, with OD values at A₄₀₅ less than 0.035. Extracts from healthy control plants gave OD values at A₄₀₅ less than 0.010. No positive reactions were obtained with antisera to bean yellow mosaic potyvirus, peanut mottle potyvirus, soybean mosaic potyvirus, or CMV. To our knowledge, this is the first report of CABMV in commercially grown cowpea from the U.S. References: (1) A. G. Gillaspie et al. Plant Dis. 79:388, 1995. (2) H. R. Pappu et al. Arch. Virol. 142:1, 1997.

Occurrence of Cowpea Stunt Disease Causing Viruses on Wild Bean in Arkansas

Cucumber mosaic cucumovirus (CMV) and blackeye cowpea mosaic potyvirus (BlCMV) interact synergistically in dually infected plants to cause cowpea stunt disease (1,2). During a July 1996 survey of cowpea stunt-affected fields in the Arkansas River valley, several wild bean (Strophostyles helvola L. Elliott) plants expressing mosaic symptoms were observed and collected. Sap was extracted from symptomatic leaves and used as inoculum to conduct a host range study. Virus symptoms diagnostic for BlCMV, CMV, or cowpea stunt were observed 6 to 8 days post-inoculation on Vigna unguiculata (L.) Walp. subsp. unguiculata cv. Coronet, while chlorotic lesions and mild systemic mosaic symptoms developed on Nicotiana benthamiana. Enzyme-linked immunosorbent assays (ELISAs) conducted on extracts from symptomatic cowpea and N. benthamiana 14 days after inoculation verified the presence of CMV and BlCMV in single and mixed infections. Additional symptomatic wild bean plants were collected from the same site in October 1996. ELISAs and Ouchterlony gel diffusion assays confirmed the presence of CMV and BlCMV, as well as soybean mosaic potyvirus (SMV), cowpea chlorotic mottle bromovirus, and alfalfa mosaic virus (AlMV) in symptomatic wild bean plants. While some of the collected plants were infected with only one virus, others had combined infections of CMV and BlCMV or these two viruses with AlMV. Interestingly, AlMV isolated from wild bean caused symptoms on greenhouse-grown cowpeas that were as severe or more severe than those caused by the cowpea stunt synergy, often resulting in plant death within 8 to 10 days after inoculation. The SMV from wild bean did not induce symptoms on cowpea and was not detected in extracts from inoculated cowpea plants by Ouchterlony gel diffusion assays, but was able to systemically infect soybean (Glycine max L.) cvs. Bragg and Lee. Another virus known to infect cowpea, southern bean mosaic sobemovirus, was not detected in any of the samples tested. To our knowledge, this is the first report that wild bean can serve as an alternate host for cowpea stunt-causing viruses in single and mixed infections. In addition, these data suggest that AlMV may pose a threat to Arkansas-grown cowpeas. References: (1) E. J. Anderson et al. Ark. Farm Res. 43:14, 1994. (2) G. Pio-Ribeiro et al. Phytopathology 68:1260, 1978.