A COMPARISON OF CAVE MICROBIAL COMMUNITIES TO CAVE ROOSTING BAT MICROBIOTA IN EL MALPAIS NATIONAL MONUMENT, USA

The arrival of white-nose syndrome (WNS), a devastating fungal disease, has highlighted the need to better understand bat microbiota and how bats acquire their microbiota. To address this need, we investigated how bat microbiota compare to microbiota from the cave walls in two El Malpais National Monument caves. The external surfaces of six roosting bats from each cave, representing four different bat species, and their associated microbial mats were sampled. One to three air samples were taken in each cave. Samples were sequenced using Illumina MiSeq sequencing of the 16S rRNA gene for bacterial diversity and the ITS region for fungal diversity. Many bacterial and fungal operational taxonomic units (OTUs) were shared among the sample types. Within the bacterial OTUs, Actinobactria were highest overall in all samples, but were higher in bats than mats. The most prevalent actinobacterial genera recovered were Rhodococcus, Streptomyces, Arthrobacter, and Rubrobacter. SourceTracker suggested bat bacterial communities may originate from mat and air samples. Within the fungal OTUs, Ascomycota were highest overall in all samples, but higher in bats than mats. Prevalent fungal families included Cladosporiaceae, Pleosporaceae, Pseudeurotiaceae, Microascaceae, Leucosporidiaceae, and Mortierellaceae. A top fungal OTU recovered was a close relative of Pseudogymnoascus destructans, the cause of WNS. Our results shed light on a relatively understudied area that could have implications for understanding the source of potential natural defenses of bats, which could be important in predicting which western bats species are most vulnerable to WNS

Are microclimate conditions in El Malpais National Monument caves in New Mexico, USA suitable for Pseudogymnoascus growth?

White-nose syndrome (WNS) is a bat disease caused by the fungal pathogen Pseudogymnoascus destructans, which thrives in cold and very humid environments where bats frequently hibernate. Conidia of Pseudogymnoascus species are often documented on bats prior to the onset of WNS, but characterization of high-risk areas defined by microclimate cave conditions have been lacking. Investigating the occurrence of this fungal genus and appropriate environmental conditions to support P. destructans in southwestern U.S. caves is key to understanding the sites most likely to be impacted by WNS. Microclimate conditions in ten caves at El Malpais (ELMA) National Monument in New Mexico, USA were recorded using i-Button data loggers during the winters of 2011–2014 to assess appropriate environmental conditions (temperature and relative humidity) for P. destructans and other Pseudogymnoascus species. Optimal microclimate conditions for P. destructans and other psychrophilic fungi were found in all the caves with at least 50% of the caves identified as high-risk areas. Pseudogymnoascus species were detected in 70% of the caves using culturing methods and PCR, but no soil samples were positive for P. destructans using real-time PCR in soil and guano samples. Pseudogymnoascus destructans has a recognized range of appropriate temperatures and relative humidity for growth and cave microclimate can help define high-risk areas. This study offers resource managers guidance for establishing priority monitoring areas in their bat caves to determine which bat species are at higher risk

Are microclimate conditions in El Malpais National Monument caves in New Mexico, USA suitable for Pseudogymnoascus growth?

White-nose syndrome (WNS) is a bat disease caused by the fungal pathogen Pseudogymnoascus destructans, which thrives in cold and very humid environments where bats frequently hibernate. Conidia of Pseudogymnoascus species are often documented on bats prior to the onset of WNS, but characterization of high-risk areas defined by microclimate cave conditions have been lacking. Investigating the occurrence of this fungal genus and appropriate environmental conditions to support P. destructans in southwestern U.S. caves is key to understanding the sites most likely to be impacted by WNS. Microclimate conditions in ten caves at El Malpais (ELMA) National Monument in New Mexico, USA were recorded using i-Button data loggers during the winters of 2011–2014 to assess appropriate environmental conditions (temperature and relative humidity) for P. destructans and other Pseudogymnoascus species. Optimal microclimate conditions for P. destructans and other psychrophilic fungi were found in all the caves with at least 50% of the caves identified as high-risk areas. Pseudogymnoascus species were detected in 70% of the caves using culturing methods and PCR, but no soil samples were positive for P. destructans using real-time PCR in soil and guano samples. Pseudogymnoascus destructans has a recognized range of appropriate temperatures and relative humidity for growth and cave microclimate can help define high-risk areas. This study offers resource managers guidance for establishing priority monitoring areas in their bat caves to determine which bat species are at higher risk

Comparison of Fungal and Bacterial Microbiomes of Bats and Their Cave Roosting Environments at El Malpais National Monument, New Mexico, USA

The arrival in North America of white-nose syndrome (WNS), a devastating fungal disease in bats, has emphasized the necessity of a comprehensive understanding of the bats’ external skin microbiota. Here, we investigated the composition of the natural bat microbiota pre-WNS and how they are acquired. The fur surfaces of 12 roosting bats, adjacent cave walls, and cave chamber air were sampled in two New Mexican lava caves. Bacterial and fungal diversity were assessed using Illumina MiSeq sequencing. Although many taxa were shared among the sample types, there were significant differences in alpha and beta diversity within and among communities. Bacterial phyla Actinobacteriota (39.1%) and Proteobacteria (27.9%) comprised two-thirds of the sequences. Fungal communities were dominated by Ascomycota (78.9%), followed by Basidiomycota (14.7%), and Mucoromycota (4.3%). Results for bacterial communities suggested that cave walls and cave air influence the bat microbiome and that the bat microbiome can have a reciprocal influence on the microbiome of cave walls. Fungal microbiomes of cave walls, air, and bats appear to have very low impact on each other. Our results begin to elucidate how cave environments may provide natural microbial defenses for bats, one facet in predicting the effect of WNS on western bats.</p

Are microclimate conditions in El Malpais National Monument caves in New Mexico, USA suitable for \u3cem\u3ePseudogymnoascus\u3c/em\u3e growth?

White-nose syndrome (WNS) is a bat disease caused by the fungal pathogen Pseudogymnoascus destructans, which thrives in cold and very humid environments where bats frequently hibernate. Conidia of Pseudogymnoascus species are often documented on bats prior to the onset of WNS, but characterization of high-risk areas defined by microclimate cave conditions have been lacking. Investigating the occurrence of this fungal genus and appropriate environmental conditions to support P. destructans in southwestern U.S. caves is key to understanding the sites most likely to be impacted by WNS. Microclimate conditions in ten caves at El Malpais (ELMA) National Monument in New Mexico, USA were recorded using i-Button data loggers during the winters of 2011–2014 to assess appropriate environmental conditions (temperature and relative humidity) for P. destructans and other Pseudogymnoascus species. Optimal microclimate conditions for P. destructans and other psychrophilic fungi were found in all the caves with at least 50% of the caves identified as high-risk areas. Pseudogymnoascus species were detected in 70% of the caves using culturing methods and PCR, but no soil samples were positive for P. destructans using real-time PCR in soil and guano samples. Pseudogymnoascus destructans has a recognized range of appropriate temperatures and relative humidity for growth and cave microclimate can help define high-risk areas. This study offers resource managers guidance for establishing priority monitoring areas in their bat caves to determine which bat species are at higher risk

Clinical impact of COVID-19 on patients with cancer (CCC19): a cohort study

BackgroundData on patients with COVID-19 who have cancer are lacking. Here we characterise the outcomes of a cohort of patients with cancer and COVID-19 and identify potential prognostic factors for mortality and severe illness.MethodsIn this cohort study, we collected de-identified data on patients with active or previous malignancy, aged 18 years and older, with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from the USA, Canada, and Spain from the COVID-19 and Cancer Consortium (CCC19) database for whom baseline data were added between March 17 and April 16, 2020. We collected data on baseline clinical conditions, medications, cancer diagnosis and treatment, and COVID-19 disease course. The primary endpoint was all-cause mortality within 30 days of diagnosis of COVID-19. We assessed the association between the outcome and potential prognostic variables using logistic regression analyses, partially adjusted for age, sex, smoking status, and obesity. This study is registered with ClinicalTrials.gov, NCT04354701, and is ongoing.FindingsOf 1035 records entered into the CCC19 database during the study period, 928 patients met inclusion criteria for our analysis. Median age was 66 years (IQR 57-76), 279 (30%) were aged 75 years or older, and 468 (50%) patients were male. The most prevalent malignancies were breast (191 [21%]) and prostate (152 [16%]). 366 (39%) patients were on active anticancer treatment, and 396 (43%) had active (measurable) cancer. At analysis (May 7, 2020), 121 (13%) patients had died. In logistic regression analysis, independent factors associated with increased 30-day mortality, after partial adjustment, were: increased age (per 10 years; partially adjusted odds ratio 1·84, 95% CI 1·53-2·21), male sex (1·63, 1·07-2·48), smoking status (former smoker vs never smoked: 1·60, 1·03-2·47), number of comorbidities (two vs none: 4·50, 1·33-15·28), Eastern Cooperative Oncology Group performance status of 2 or higher (status of 2 vs 0 or 1: 3·89, 2·11-7·18), active cancer (progressing vs remission: 5·20, 2·77-9·77), and receipt of azithromycin plus hydroxychloroquine (vs treatment with neither: 2·93, 1·79-4·79; confounding by indication cannot be excluded). Compared with residence in the US-Northeast, residence in Canada (0·24, 0·07-0·84) or the US-Midwest (0·50, 0·28-0·90) were associated with decreased 30-day all-cause mortality. Race and ethnicity, obesity status, cancer type, type of anticancer therapy, and recent surgery were not associated with mortality.InterpretationAmong patients with cancer and COVID-19, 30-day all-cause mortality was high and associated with general risk factors and risk factors unique to patients with cancer. Longer follow-up is needed to better understand the effect of COVID-19 on outcomes in patients with cancer, including the ability to continue specific cancer treatments.FundingAmerican Cancer Society, National Institutes of Health, and Hope Foundation for Cancer Research

A Systematic Framework to Rapidly Obtain Data on Patients with Cancer and COVID-19: CCC19 Governance, Protocol, and Quality Assurance

When the COVID-19 pandemic began, formal frameworks to collect data about affected patients were lacking. The COVID-19 and Cancer Consortium (CCC19) was formed to collect granular data on patients with cancer and COVID-19 at scale and as rapidly as possible. CCC19 has grown from five initial institutions to 125 institutions with >400 collaborators. More than 5,000 cases with complete baseline data have been accrued. Future directions include increased electronic health record integration for direct data ingestion, expansion to additional domestic and international sites, more intentional patient involvement, and granular analyses of still-unanswered questions related to cancer subtypes and treatments. When the COVID-19 pandemic began, formal frameworks to collect data about affected patients were lacking. The COVID-19 and Cancer Consortium (CCC19) was formed to collect granular data on patients with cancer and COVID-19 at scale and as rapidly as possible. CCC19 has grown from five initial institutions to 125 institutions with >400 collaborators. More than 5,000 cases with complete baseline data have been accrued. Future directions include increased electronic health record integration for direct data ingestion, expansion to additional domestic and international sites, more intentional patient involvement, and granular analyses of still-unanswered questions related to cancer subtypes and treatments