Predictors of postpandemic preparedness for special pathogens.

In this survey of 31 hospitals, large metropolitan facilities had a 9.5-fold odds of reporting preparedness for special pathogens; hospitals with special pathogens teams had a 14.3-fold odds of reporting preparedness for special pathogens. In the postpandemic world, healthcare institutions must invest in special pathogen responses to maximize patient safety.

The heat is on: Thermoregulatory and evaporative cooling patterns of desert-dwelling bats.

For small endotherms inhabiting desert ecosystems, defending body temperatures (Tb) is challenging as they contend with extremely high ambient temperatures (Ta) and limited standing water. In the arid zone, bats may thermoconform whereby Tb varies with Ta, or may evaporatively cool themselves to maintain Tb < Ta. We used an integrative approach that combined both temperature telemetry and flow through respirometry to investigate the ecological and physiological strategies of lesser long-eared bats (Nyctophilus geoffroyi) in Australia's arid zone. We predicted individuals would exhibit desert-adapted thermoregulatory patterns (i.e., thermoconform to prioritise water conservation), and that females would be more conservative with their water reserves for evaporative cooling compared to males. Temperature telemetry data indicated that free-ranging N. geoffroyi were heterothermic (Tskin = 18.9-44.9 °C) during summer and thermoconformed over a wide range of temperatures, likely to conserve water and energy during the day. Experimentally, at high Tas, females maintained significantly lower Tb and resting metabolic rates, despite lower evaporative water loss (EWL) rates compared to males. Females only increased EWL at experimental Ta = 42.5 °C, significantly higher than males (40.7 °C), and higher than any bat species yet recorded. During the hottest day of this study, our estimates suggest the water required for evaporative cooling ranged from 18.3% (females) and 25.5% (males) of body mass. However, if we extrapolate these results to a recent heatwave these values increase to 36.5% and 47.3%, which are likely beyond lethal limits. It appears this population is under selective pressures to conserve water reserves and that these pressures are more pronounced in females than males. Bats in arid ecosystems are threatened by both current and future heatwaves and we recommend future conservation efforts focus on protecting current roost trees and creating artificial standing water sites near vulnerable populations.

Variation in spatial population structure in the Anopheles gambiae species complex.

Anopheles gambiae, Anopheles coluzzii, and Anopheles arabiensis are three of the most widespread vectors of malaria parasites, with geographical ranges stretching across wide swaths of Africa. Understanding the population structure of these closely related species, including the extent to which populations are connected by gene flow, is essential for understanding how vector control implemented in one location might indirectly affect vector populations in other locations. Here, we assessed the population structure of each species based on a combined data set of publicly available and newly processed whole-genome sequences. The data set included single nucleotide polymorphisms from whole genomes of 2,410 individual mosquitoes sampled from 128 locations across 19 African countries. We found that A. gambiae sampled from several countries in West and Central Africa showed low genetic differentiation from each other according to principal components analysis (PCA) and ADMIXTURE modeling. Using Estimated Effective Migration Surfaces (EEMS), we showed that this low genetic differentiation indicates high effective migration rates for A. gambiae across this region. Outside of this region, we found eight groups of sampling locations from Central, East, and Southern Africa for which A. gambiae showed higher genetic differentiation, and lower effective migration rates, between each other and the West/Central Africa group. These results indicate that the barriers to and corridors for migration between populations of A. gambiae differ across the geographical range of this malaria vector species. Using the same methods, we found higher genetic differentiation and lower migration rates between populations of A. coluzzii in West and Central Africa than for A. gambiae in the same region. In contrast, we found lower genetic differentiation and higher migration rates between populations of A. arabiensis in Tanzania, compared to A. gambiae in the same region. These differences between A. gambiae, A. coluzzii, and A. arabiensis indicate that migration barriers and corridors may vary, even between very closely related species. Overall, our results demonstrate that migration rates vary both within and between species of Anopheles mosquitoes, presumably based on species-specific responses to the ecological or environmental conditions that may impede or facilitate migration, and the geographical patterns of these conditions across the landscape. Together with previous findings, this study provides robust evidence that migration rates between populations of malaria vectors depend on the ecological context, which should be considered when planning surveillance of vector populations, monitoring for insecticide resistance, and evaluating interventions.

The Effect of Retained Hardware on Failure Among Prosthetic Joint Infections of the Knee in the Presence and Absence of Staphylococcus aureus.

Background: The risk of failure associated with different surgical strategies for prosthetic joint infections (PJIs) among patients with and without Staphylococcus aureus is uncertain. The purpose of this study was to assess whether S. aureus modifies the association between retained hardware and failure following revision surgery for PJI of the knee. Methods: This was a single-center retrospective cohort study of 106 first PJIs of the knee between 2016 and 2020 at a rural academic medical center. The exposure was retained hardware following revision surgery for PJI, and the outcomes were recurrent infection, any infection, and a composite outcome including any infection, unplanned revision, failure to undergo reimplantation, amputation, or death within 2 years of revision. We used negative binomial regression to quantify the association between the exposure and outcome and to assess the presence of S. aureus as an effect modifier. Results: Retained hardware was significantly associated with failure when defined as recurrent infection among S. aureus PJI (adjusted risk difference [aRD], 0.38; 95% CI, 0.12-0.64) but not in the absence of S. aureus (aRD, -0.02; 95% CI, -0.17 to 0.13), and S. aureus was an effect modifier (P interaction = .01). Conclusions: We report a significant association between the presence of retained hardware and recurrent infection among S. aureus PJI of the knee, but not for non-S. aureus PJI. This could help inform the surgical management of PJI of the knee in cases where the microbiology is known before surgery.

Vascular endothelial-derived SPARCL1 exacerbates viral pneumonia through pro-inflammatory macrophage activation.

Inflammation induced by lung infection is a double-edged sword, moderating both anti-viral and immune pathogenesis effects; the mechanism of the latter is not fully understood. Previous studies suggest the vasculature is involved in tissue injury. Here, we report that expression of Sparcl1, a secreted matricellular protein, is upregulated in pulmonary capillary endothelial cells (EC) during influenza-induced lung injury. Endothelial overexpression of SPARCL1 promotes detrimental lung inflammation, with SPARCL1 inducing 'M1-like' macrophages and related pro-inflammatory cytokines, while SPARCL1 deletion alleviates these effects. Mechanistically, SPARCL1 functions through TLR4 on macrophages in vitro, while TLR4 inhibition in vivo ameliorates excessive inflammation caused by endothelial Sparcl1 overexpression. Finally, SPARCL1 expression is increased in lung ECs from COVID-19 patients when compared with healthy donors, while fatal COVID-19 correlates with higher circulating SPARCL1 protein levels in the plasma. Our results thus implicate SPARCL1 as a potential prognosis biomarker for deadly COVID-19 pneumonia and as a therapeutic target for taming hyperinflammation in pneumonia.

A nurse-driven penicillin allergy risk score in the preoperative setting was associated with increased cefazolin use perioperatively.

STUDY OBJECTIVE: To characterize and assess the effects of a preoperative, nurse-driven penicillin allergy risk stratification tool on rates of perioperative cefazolin and second-line antibiotic use. DESIGN: Quasi-experimental quality improvement study of penicillin-allergic surgical patients undergoing procedures for which cefazolin is indicated. SETTING: Outpatient Perioperative Care Clinic (PCC) for preoperative surgical patients at a tertiary care center. PATIENTS: 670 and 1371 adult penicillin-allergic PCC attendants and non-attendants, respectively. INTERVENTION: A paper penicillin allergy risk stratification questionnaire was administered during the PCC visit. Nurses were educated on its use. MEASUREMENTS: Antibiotic (cefazolin, clindamycin, vancomycin) use rates in the 24 months before and 17 months after intervention implementation in November 2020 (November 2018 - April 2022) were assessed in penicillin-allergic PCC attendants with statistical process control charts. Multivariable logistic regression assessed antibiotic use rates pre- and post-intervention adjusting for age, sex, surgical specialty and penicillin allergy history severity. Similar analyses were done in penicillin-allergic PCC non-attendants. MAIN RESULTS: Of 670 penicillin-allergic PCC attendants, 451 (median [IQR] age, 66 (Sousa-Pinto et al., 2021 [14])) were analyzed pre-intervention and 219 (median [IQR] age, 66 (Mine et al., 1970 [13])) post-intervention. One month after implementation, process measures demonstrated an upward shift in cefazolin use for PCC attendants versus no shift or other special cause variation for PCC non-attendants. There were increased odds of cefazolin use (aOR 1.67, 95% CI [1.09-2.57], P = 0.019), decreased odds of clindamycin use (aOR 0.61, 95% CI [0.42-0.89], P = 0.010) and decreased odds of vancomycin use (aOR 0.56, 95% CI [0.35-0.88], P = 0.013) in PCC attendants post-intervention. This effect did not occur in PCC non-attendants. There was no increase in perioperative anaphylaxis post-intervention. CONCLUSIONS: A simple penicillin allergy risk stratification tool implemented in the preoperative setting was associated with increased use of cefazolin and decreased rates of second-line agents post implementation.

Guided construction of single cell reference for human and mouse lung.

Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.

Vascular Endothelial-derived SPARCL1 Exacerbates Viral Pneumonia Through Pro-Inflammatory Macrophage Activation.

Inflammation upon infectious lung injury is a double-edged sword: while tissue-infiltrating immune cells and cytokines are necessary to control infection, these same factors often aggravate injury. Full appreciation of both the sources and targets of inflammatory mediators is required to facilitate strategies to maintain antimicrobial effects while minimizing off-target epithelial and endothelial damage. Recognizing that the vasculature is centrally involved in tissue responses to injury and infection, we observed that pulmonary capillary endothelial cells (ECs) exhibit dramatic transcriptomic changes upon influenza injury punctuated by profound upregulation of Sparcl1 . Endothelial deletion and overexpression of SPARCL1 implicated this secreted matricellular protein in driving key pathophysiologic symptoms of pneumonia, which we demonstrate result from its effects on macrophage polarization. SPARCL1 induces a shift to a pro-inflammatory "M1-like" phenotype (CD86 + CD206 - ), thereby increasing associated cytokine levels. Mechanistically, SPARCL1 acts directly on macrophages in vitro to induce the pro-inflammatory phenotype via activation of TLR4, and TLR4 inhibition in vivo ameliorates inflammatory exacerbations caused by endothelial Sparcl1 overexpression. Finally, we confirmed significant elevation of SPARCL1 in COVID-19 lung ECs in comparison with those from healthy donors. Survival analysis demonstrated that patients with fatal COVID-19 had higher levels of circulating SPARCL1 protein compared to those who recovered, indicating the potential of SPARCL1 as a biomarker for prognosis of pneumonia and suggesting that personalized medicine approaches might be harnessed to block SPARCL1 and improve outcomes in high-expressing patients.

A comparison of National Healthcare Safety Network surveillance definitions to physician review for central-line-associated bloodstream infections.

For 147 hospital-onset bloodstream infections, we assessed the sensitivity, specificity, positive predictive value, and negative predictive value of the National Healthcare Safety Network surveillance definitions of central-line-associated bloodstream infections against the gold standard of physician review, examining the drivers of discrepancies and related implications for reporting and infection prevention.

Investigating potential drivers of increased central line...associated bloodstream infections during the coronavirus disease 2019 (COVID-19) Omicron surge.

Central line...associated bloodstream infection rates increased during the Omicron surge at our rural academic medical center. To identify potential drivers of this increase, we investigated period- and patient-specific factors associated with the increase in central line...associated bloodstream infection. Increased central line utilization, decreased central line bundle compliance monitoring, increased proportion of traveling nurses, increased short-term venous catheter use in the internal jugular vein, increased multilumen catheter use, decreased port...associated infection, and increased patient acuity were significantly associated with the surge. Our results helped us target our local infection prevention efforts.

Association between in situ steroids and spine surgical site infections among instrumented procedures.

OBJECTIVE: To estimate the association between in situ steroids and spine surgical-site infections (SSIs), assessing spinal instrumentation as an effect modifier and adjusting for confounders. DESIGN: Case-control study. SETTING: Rural academic medical center. PARTICIPANTS: We identified 1,058 adults undergoing posterior fusion and laminectomy procedures as defined by the National Healthcare Safety Network without a pre-existing SSI between January 2020 and December 2021. We identified 26 SSI as cases and randomly selected 104 controls from the remaining patients without SSI. METHODS: The primary exposure was the intraoperative administration of methylprednisolone in situ (ie, either in the wound bed or as an epidural injection). The primary outcome was a clinical diagnosis of SSI within 6 months of a patient's first spine surgery at our facility. We quantified the association between the exposure and outcome using logistic regression, using a product term to assess for effect modification by spinal instrumentation and the change-in-estimate approach to select significant confounders. RESULTS: Adjusting for Charlson comorbidity index and malignancy, in situ steroids were significantly associated with spine SSI relative to no in situ steroids for instrumented procedures (adjusted odds ratio [aOR], 9.93; 95% confidence interval [CI], 1.54-64.0), but they were not associated with spine SSIs among noninstrumented procedures (aOR, 0.86; 95% CI, 0.15-4.93). CONCLUSIONS: In situ steroids were significantly associated with spine SSI among instrumented procedures. The benefits of in situ steroids for pain management following spine surgery should be weighed against the risk of SSI, especially for instrumented procedures.

Spatiotemporal patterns of drug use disorder in Sweden assessed using population-based registries.

BACKGROUND: Drug Use Disorder (DUD) is a major contributor to world-wide morbidity and mortality. The extensive national registers in Sweden provide the basis for a study of spatial and temporal patterns of DUD onset and recurrence in Sweden from 2001-2015. METHODS: To identify patterns of DUD over space, time and gender for Swedish individuals aged 15-35, space-time clustering using SaTScan was applied. We used yearly information on residential locations in Demographic Statistical Areas (DeSO) for all of Sweden. The clustering analysis used a Poisson probability model and a null hypothesis that the expected number of cases in each DeSO was proportional to the population size of DeSOs. As SaTScan results can be unstable, steps were taken to determine stable clusters and to refine and optimize cluster size. Results for each gender-register combination were compared to the results of spatial clustering using Gi* statistics. The space-time scanning model was also run with an adjustment for neighborhood socioeconomic status to determine DUD prevalence as it relates to education, income, unemployment and receipt of social welfare. RESULTS: DUD prevalence increased over time. Males yielded more significant clusters than females for both criminal and medical registers. Female DUD prevalence rates increased over time, especially after 2012. Higher correlations in DUD rates existed across the two registers than across gender. Male clusters were present from 2004 onwards while female-criminal clusters appeared after 2007, and female-medical clusters not until 2010. By 2013, clusters existed for all gender-register combinations. Male-criminal clusters were concentrated in Stockholm, Göteborg and Malmö as were male and female-medical clusters. Neighborhood SES was more highly related to the distribution of criminal than medical DUD clusters. A persistent gap in core clusters was identified in Stockholm in an area with notably high SES. CONCLUSIONS: Persistent hotspots of DUD in Sweden were confirmed as well as new and emerging hotspots, especially in Stockholm, Göteborg and Malmö. Higher correlations existed in DUD rates across registers than across gender. The findings are useful for monitoring the current drug problem and for identifying drivers underlying patterns of spread and important causal pathways to DUD.

Understanding work-related travel and its relation to malaria occurrence in Thailand using geospatial maximum entropy modelling.

BACKGROUND: Estimating malaria risk associated with work locations and travel across a region provides local health officials with information useful to mitigate possible transmission paths of malaria as well as understand the risk of exposure for local populations. This study investigates malaria exposure risk by analysing the spatial pattern of malaria cases (primarily Plasmodium vivax) in Ubon Ratchathani and Sisaket provinces of Thailand, using an ecological niche model and machine learning to estimate the species distribution of P. vivax malaria and compare the resulting niche areas with occupation type, work locations, and work-related travel routes. METHODS: A maximum entropy model was trained to estimate the distribution of P. vivax malaria for a period between January 2019 and April 2020, capturing estimated malaria occurrence for these provinces. A random simulation workflow was developed to make region-based case data usable for the machine learning approach. This workflow was used to generate a probability surface for the ecological niche regions. The resulting niche regions were analysed by occupation type, home and work locations, and work-related travel routes to determine the relationship between these variables and malaria occurrence. A one-way analysis of variance (ANOVA) test was used to understand the relationship between predicted malaria occurrence and occupation type. RESULTS: The MaxEnt (full name) model indicated a higher occurrence of P. vivax malaria in forested areas especially along the Thailand-Cambodia border. The ANOVA results showed a statistically significant difference between average malaria risk values predicted from the ecological niche model for rubber plantation workers and farmers, the two main occupation groups in the study. The rubber plantation workers were found to be at higher risk of exposure to malaria than farmers in Ubon Ratchathani and Sisaket provinces of Thailand. CONCLUSION: The results from this study point to occupation-related factors such as work location and the routes travelled to work, being risk factors in malaria occurrence and possible contributors to transmission among local populations.

A counterfactual analysis of opioid-involved deaths during the COVID-19 pandemic using a spatiotemporal random forest modeling approach.

The global pandemic of SARS-CoV-2 (COVID-19) has been linked to adversely impacting individuals with opioid use disorder in the United States. This study focuses on analyzing opioid-involved mortality in the context of COVID-19 in the U.S. from a geospatial perspective. We investigated spatiotemporal patterns of opioid-involved deaths during 2020 and compared the spatiotemporal pattern of these deaths with patterns for the previous three years (2017-2019) to understand changes in the context of the COVID-19 pandemic. A counterfactual analysis framework together with a space-time random forest (STRF) model were used to estimate the increase in opioid-involved deaths related to the pandemic. To gain further insight into the relationship between opioid deaths and COVID-19-related factors, we built a space-time random forest model for the City of Chicago, that experienced a steep increase in opioid-related deaths during 2020. High ranking indicators identified by the model such as the number of positive COVID-19 cases adjusted by population and the change in stay-at-home dwell time during the pandemic were used to generate a vulnerability index for opioid overdoses during the COVID-19 pandemic in Chicago.

Geographic information science and the United States opioid overdose crisis: A scoping review of methods, scales, and application areas.

BACKGROUND: The Opioid Overdose Crisis (OOC) continues to generate morbidity and mortality in the United States, outpacing other prominent accident-related reasons. Multiple disciplines have applied geographic information science (GIScience) to understand geographical patterns in opioid-related health measures. However, there are limited reviews that assess how GIScience has been used. OBJECTIVES: This scoping review investigates how GIScience has been used to conduct research on the OOC. Specific sub-objectives involve identifying bibliometric trends, the location and scale of studies, the frequency of use of various GIScience methodologies, and what direction future research can take to address existing gaps. METHODS: The review was pre-registered with the Open Science Framework ((https://osf.io/h3mfx/) and followed the PRISMA-ScR guidelines. Scholarly research was gathered from the Web of Science Core Collection, PubMed, IEEE Xplore, ACM Digital Library. Inclusion criteria was defined as having a publication date between January 1999 and August 2021, using GIScience as a central part of the research, and investigating an opioid-related health measure. RESULTS: 231 studies met the inclusion criteria. Most studies were published from 2017 onward. While many (41.6%) of studies were conducted using nationwide data, the majority (58.4%) occurred at the sub-national level. California, New York, Ohio, and Appalachia were most frequently studied, while the Midwest, north Rocky Mountains, Alaska, and Hawaii lacked studies. The most common GIScience methodology used was descriptive mapping, and county-level data was the most common unit of analysis across methodologies. CONCLUSIONS: Future research of GIScience on the OOC can address gaps by developing use cases for machine learning, conducting analyses at the sub-county level, and applying GIScience to questions involving illicit fentanyl. Research using GIScience is expected to continue to increase, and multidisciplinary research efforts amongst GIScientists, epidemiologists, and other medical professionals can improve the rigor of research.

Understanding Spatiotemporal Human Mobility Patterns for Malaria Control Using a Multiagent Mobility Simulation Model.

BACKGROUND: More details about human movement patterns are needed to evaluate relationships between daily travel and malaria risk at finer scales. A multiagent mobility simulation model was built to simulate the movements of villagers between home and their workplaces in 2 townships in Myanmar. METHODS: An agent-based model (ABM) was built to simulate daily travel to and from work based on responses to a travel survey. Key elements for the ABM were land cover, travel time, travel mode, occupation, malaria prevalence, and a detailed road network. Most visited network segments for different occupations and for malaria-positive cases were extracted and compared. Data from a separate survey were used to validate the simulation. RESULTS: Mobility characteristics for different occupation groups showed that while certain patterns were shared among some groups, there were also patterns that were unique to an occupation group. Forest workers were estimated to be the most mobile occupation group, and also had the highest potential malaria exposure associated with their daily travel in Ann Township. In Singu Township, forest workers were not the most mobile group; however, they were estimated to visit regions that had higher prevalence of malaria infection over other occupation groups. CONCLUSIONS: Using an ABM to simulate daily travel generated mobility patterns for different occupation groups. These spatial patterns varied by occupation. Our simulation identified occupations at a higher risk of being exposed to malaria and where these exposures were more likely to occur.

A survey study of the association between active utilization of National Healthcare Safety Network resources and central-line-associated bloodstream infection reporting.

In this survey of 41 hospitals, 18 (72%) of 25 respondents reporting utilization of National Healthcare Safety Network resources demonstrated accurate central-line-associated bloodstream infection reporting compared to 6 (38%) of 16 without utilization (adjusted odds ratio, 5.37; 95% confidence interval, 1.16-24.8). Adherence to standard definitions is essential for consistent reporting across healthcare facilities.

Making Space in Geographical Analysis.

In this commentary we reflect on the potential and power of geographical analysis, as a set of methods, theoretical approaches, and perspectives, to increase our understanding of how space and place matter for all. We emphasize key aspects of the field, including accessibility, urban change, and spatial interaction and behavior, providing a high-level research agenda that indicates a variety of gaps and routes for future research that will not only lead to more equitable and aware solutions to local and global challenges, but also innovative and novel research methods, concepts, and data. We close with a set of representation and inclusion challenges to our discipline, researchers, and publication outlets.

Human distal airways contain a multipotent secretory cell that can regenerate alveoli.

The human lung differs substantially from its mouse counterpart, resulting in a distinct distal airway architecture affected by disease pathology in chronic obstructive pulmonary disease. In humans, the distal branches of the airway interweave with the alveolar gas-exchange niche, forming an anatomical structure known as the respiratory bronchioles. Owing to the lack of a counterpart in mouse, the cellular and molecular mechanisms that govern respiratory bronchioles in the human lung remain uncharacterized. Here we show that human respiratory bronchioles contain a unique secretory cell population that is distinct from cells in larger proximal airways. Organoid modelling reveals that these respiratory airway secretory (RAS) cells act as unidirectional progenitors for alveolar type 2 cells, which are essential for maintaining and regenerating the alveolar niche. RAS cell lineage differentiation into alveolar type 2 cells is regulated by Notch and Wnt signalling. In chronic obstructive pulmonary disease, RAS cells are altered transcriptionally, corresponding to abnormal alveolar type 2 cell states, which are associated with smoking exposure in both humans and ferrets. These data identify a distinct progenitor in a region of the human lung that is not found in mouse that has a critical role in maintaining the gas-exchange compartment and is altered in chronic lung disease.