Bronchiectasis-associated infections and outcomes in a large, geographically diverse electronic health record cohort in the United States.

BACKGROUND: Bronchiectasis is a pulmonary disease characterized by irreversible dilation of the bronchi and recurring respiratory infections. Few studies have described the microbiology and prevalence of infections in large patient populations outside of specialized tertiary care centers. METHODS: We used the Cerner HealthFacts Electronic Health Record database to characterize the nature, burden, and frequency of pulmonary infections among persons with bronchiectasis. Chronic infections were defined based on organism-specific guidelines. RESULTS: We identified 7,749 patients who met our incident bronchiectasis case definition. In this study population, the organisms with the highest rates of isolate prevalence were Pseudomonas aeruginosa with 937 (12%) individuals, Staphylococcus aureus with 502 (6%), Mycobacterium avium complex (MAC) with 336 (4%), and Aspergillus sp. with 288 (4%). Among persons with at least one isolate of each respective pathogen, 219 (23%) met criteria for chronic P. aeruginosa colonization, 74 (15%) met criteria for S. aureus chronic colonization, 101 (30%) met criteria for MAC chronic infection, and 50 (17%) met criteria for Aspergillus sp. chronic infection. Of 5,795 persons with at least two years of observation, 1,860 (32%) had a bronchiectasis exacerbation and 3,462 (60%) were hospitalized within two years of bronchiectasis diagnoses. Among patients with chronic respiratory infections, the two-year occurrence of exacerbations was 53% and for hospitalizations was 82%. CONCLUSIONS: Patients with bronchiectasis experiencing chronic respiratory infections have high rates of hospitalization.

Incidence of Nontuberculous Mycobacterial Pulmonary Infection, by Ethnic Group, Hawaii, USA, 2005-2019.

To further clarify differences in the risk for nontuberculous mycobacterial pulmonary infection (NTM-PI) among ethnic populations in Hawaii, USA, we conducted a retrospective cohort study among beneficiaries of Kaiser Permanente Hawaii (KPH). We abstracted demographic, socioeconomic, clinical, and microbiological data from KPH electronic health records for 2005-2019. An NTM-PI case-patient was defined as a person from whom >1 NTM pulmonary isolate was obtained. We performed Cox proportional hazards regression to estimate incidence of NTM-PI while controlling for confounders. Across ethnic groups, risk for NTM-PI was higher among persons who were underweight (body mass index [BMI] <18.5 kg/m2). Among beneficiaries who self-identified as any Asian ethnicity, risk for incident NTM-PI was increased by 30%. Low BMI may increase susceptibility to NTM-PI, and risk may be higher for persons who self-identify as Asian, independent of BMI.

A missense variant in FTCD is associated with arsenic metabolism and toxicity phenotypes in Bangladesh.

Inorganic arsenic (iAs) is a carcinogen, and exposure to iAs via food and water is a global public health problem. iAs-contaminated drinking water alone affects >100 million people worldwide, including ~50 million in Bangladesh. Once absorbed into the blood stream, most iAs is converted to mono-methylated (MMA) and then di-methylated (DMA) forms, facilitating excretion in urine. Arsenic metabolism efficiency varies among individuals, in part due to genetic variation near AS3MT (arsenite methyltransferase; 10q24.32). To identify additional arsenic metabolism loci, we measured protein-coding variants across the human exome for 1,660 Bangladeshi individuals participating in the Health Effects of Arsenic Longitudinal Study (HEALS). Among the 19,992 coding variants analyzed exome-wide, the minor allele (A) of rs61735836 (p.Val101Met) in exon 3 of FTCD (formiminotransferase cyclodeaminase) was associated with increased urinary iAs% (P = 8x10-13), increased MMA% (P = 2x10-16) and decreased DMA% (P = 6x10-23). Among 2,401 individuals with arsenic-induced skin lesions (an indicator of arsenic toxicity and cancer risk) and 2,472 controls, carrying the low-efficiency A allele (frequency = 7%) was associated with increased skin lesion risk (odds ratio = 1.35; P = 1x10-5). rs61735836 is in weak linkage disequilibrium with all nearby variants. The high-efficiency/major allele (G/Valine) is human-specific and eliminates a start codon at the first 5´-proximal Kozak sequence in FTCD, suggesting selection against an alternative translation start site. FTCD is critical for catabolism of histidine, a process that generates one-carbon units that can enter the one-carbon/folate cycle, which provides methyl groups for arsenic metabolism. In our study population, FTCD and AS3MT SNPs together explain ~10% of the variation in DMA% and support a causal effect of arsenic metabolism efficiency on arsenic toxicity (i.e., skin lesions). In summary, this work identifies a coding variant in FTCD associated with arsenic metabolism efficiency, providing new evidence supporting the established link between one-carbon/folate metabolism and arsenic toxicity.

Correction: A missense variant in FTCD is associated with arsenic metabolism and toxicity phenotypes in Bangladesh.

[This corrects the article DOI: 10.1371/journal.pgen.1007984.].

Prostate cancer survival in South West Victoria.

OBJECTIVE: To explore reasons for survival disparities for patients with prostate cancer in the Barwon South West area of Victoria. DESIGN, SETTING AND PARTICIPANTS: We have described incidence, diagnostics, treatment pathways, and survival for four regions of the Barwon South Western Victoria. Analysis included all newly diagnosed prostate cancer patients from 2009 to 2015 in the Evaluation of Cancer Outcomes Barwon South West Registry. Regions included 1: Queenscliffe 2: Geelong, Colac Otway and Corangamite 3: Moyne, Warrnambool and Southern Grampians and 4: Glenelg. Across the four regions, variables were compared using a chi square statistic or analysis of variance and survival data was assessed with the Kaplan-Meier curves. MAIN OUTCOME MEASURES: Incidence, treatment pathways and survival for prostate cancer patients. RESULTS: A total of 1776 patients were diagnosed with prostate cancer from 2009 to 2015 in the Barwon South West area. In regions 1-4, there were 298 (1.04%), 1085 (0.92%), 273 (0.97%) and 120 (1.2%) cases, respectively. There was no significant difference in Gleason score and treatment. The 5-year survival rate was 85%, 76%, 71% and 80%, respectively, as compared with the national average of 95%. PSA scores >20 ng/ml at diagnosis, as a surrogate for high-risk disease, occurred in 23%, 29%, 22% and 21%, respectively (p < 0.01). The proportions presenting with stage IV disease were 17%, 26%, 21% and 6%, respectively (p = 0.10). CONCLUSION: Men diagnosed with prostate cancer in South West Victoria have a considerably lower 5-year survival compared with the national average with later disease at presentation in some areas.

Mycobacterial Testing Trends, United States, 2009-20151.

We studied 31 US healthcare facilities to characterize trends in mycobacterial testing. During 2009-2015, testing for acid-fast bacilli increased 3.2% annually, and prevalence of pathogenic nontuberculous mycobacteria increased 4.5% annually. These increases were highest for subpopulations at high risk of infection, including older women, Asians, and patients with concurrent conditions.

Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise.

Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut-fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine-scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal-associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.

Thymic Carcinoid in a Patient with Concurrent Manifestations of Multiple Endocrine Neoplasia Type 1.

Thymic carcinoid tumours, especially in the context of multiple endocrine neoplasia type 1 (MEN 1), present significant clinical challenges due to their rarity and aggressive nature. This case report describes a complex patient with MEN 1, who suffered from multiple manifestations of the disease, including thymic carcinoid. The tumour was initially resected and treated with adjuvant radiotherapy. Due to slow progression over the years, the tumour was treated with two lines of chemotherapy before the patient succumbed to progressive disease. There is currently limited evidence favoring any specific medical treatment for thymic carcinoid.

Pain Management After Cesarean Delivery Among Women with Opioid Use Disorder: Results from a Retrospective Pregnancy Cohort in a Rural Region of the Midwest.

Background: Increasing numbers of pregnant women are being treated with buprenorphine for opioid use disorder (OUD), which can interfere with effectiveness of other opioids used for pain relief, making perioperative guidance for patients requiring cesarean delivery unclear. Methods: Using a retrospective cohort design, we abstracted 8 years of medical records (2013-2020) from a hospital in rural Michigan. We compared analgesic use (as a proxy for pain) and hospital length of stay (LOS) between groups of women with OUD whose buprenorphine treatment was (1) discontinued before cesarean delivery (discontinuation) versus (2) continued throughout the perioperative period (maintenance). We used t-tests and Fisher's Exact tests for comparison of continuous and categorical variables, respectively. Results: Maternal characteristics reflected the local population (87% non-Hispanic White; 9% American Indian). Of 12,179 mothers giving birth during the study timeframe, 87 met all inclusion criteria (2.4% with diagnosed OUD; 38% of those delivered by cesarean; 76% of those received prenatal buprenorphine treatment). Using the first 2 days of the hospital stay as the standard time window for comparison, there were no differences in perioperative opioid analgesic use (mean ± standard deviation [SD] = 141.6 ± 205.4 vs. 134.0 ± 136.3 morphine milligram equivalents, p = 0.89) or LOS (mean ± SD = 2.9 ± 0.9 vs. 3.3 ± 1.0 days, p = 0.14) between discontinuation (n = 17) versus maintenance (n = 70). There was a lower use of acetaminophen in the discontinuation group (mean ± SD = 3,842.6 ± 2,108.1 vs. 4,938.2 ± 2,008.4 mg, p = 0.0489). Conclusion: This study provides empirical evidence supporting continued buprenorphine treatment for women with OUD throughout the perioperative period of a cesarean delivery in a rural setting, although replication with larger sample sizes would provide more confidence in the results.

Impact of close interpersonal contact on COVID-19 incidence: Evidence from 1 year of mobile device data.

Close contact between people is the primary route for transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). We quantified interpersonal contact at the population level using mobile device geolocation data. We computed the frequency of contact (within 6 feet) between people in Connecticut during February 2020 to January 2021 and aggregated counts of contact events by area of residence. When incorporated into a SEIR-type model of COVID-19 transmission, the contact rate accurately predicted COVID-19 cases in Connecticut towns. Contact in Connecticut explains the initial wave of infections during March to April, the drop in cases during June to August, local outbreaks during August to September, broad statewide resurgence during September to December, and decline in January 2021. The transmission model fits COVID-19 transmission dynamics better using the contact rate than other mobility metrics. Contact rate data can help guide social distancing and testing resource allocation.

A Multi-Center Real-World Experience of IMpower150 in Oncogene Driven Tumors and CNS Metastases.

BACKGROUND: There are limited real world data on the IMpower150 regimen in oncogene driven tumors and central nervous system metastases; this study aims to address this gap. MATERIALS AND METHODS: Retrospective analysis of patients with advanced non-small cell lung cancer treated with the IMpower150 regimen across 12 Australian sites between July 2018 and April 2021. Clinicopathologic and treatment parameters were correlated with efficacy and toxicity. RESULTS: A total of 106 patients identified with median follow up of 8 months (range 0-72). Median age was 61 years (range 33-83), 34% Asian and 58% never-smokers. An oncogene was reported in 94 (89%) patients, EGFR in 72 (68%). At treatment commencement, 50 (47%) patients had brain metastases, 21 (20%) leptomeningeal disease (LMD) and 47 (44%) liver metastases. 27% were treatment-naïve and pemetrexed was substituted for paclitaxel in 44 (42%). The overall response rate was 51% for all patients; 52% in patients with EGFR mutations. Patients with untreated brain metastases prior to commencing IMpower150 had a similar intracranial response as those with treated brain metastases (55% vs. 53%). The median time to treatment failure and overall survival from commencement of IMpower150 was 5.7 and 11.4 months respectively for the entire cohort and 5.2 and 10.5 months in those with an EGFR sensitizing mutation. Overall survival in patients with liver, brain metastases and LMD was 11.0, 11.4, and 7.1 months respectively. No new safety signals seen. CONCLUSION: In this largely oncogene positive, pre-treated population the IMpower150 regimen demonstrated clinically-meaningful responses, including in patients with CNS disease.

Impact of close interpersonal contact on COVID-19 incidence: evidence from one year of mobile device data.

Close contact between people is the primary route for transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). We sought to quantify interpersonal contact at the population-level by using anonymized mobile device geolocation data. We computed the frequency of contact (within six feet) between people in Connecticut during February 2020 - January 2021. Then we aggregated counts of contact events by area of residence to obtain an estimate of the total intensity of interpersonal contact experienced by residents of each town for each day. When incorporated into a susceptible-exposed-infective-removed (SEIR) model of COVID-19 transmission, the contact rate accurately predicted COVID-19 cases in Connecticut towns during the timespan. The pattern of contact rate in Connecticut explains the large initial wave of infections during March-April, the subsequent drop in cases during June-August, local outbreaks during August-September, broad statewide resurgence during September-December, and decline in January 2021. Contact rate data can help guide public health messaging campaigns to encourage social distancing and in the allocation of testing resources to detect or prevent emerging local outbreaks more quickly than traditional case investigation. ONE SENTENCE SUMMARY: Close interpersonal contact measured using mobile device location data explains dynamics of COVID-19 transmission in Connecticut during the first year of the pandemic.

The association between telomere length and mortality in Bangladesh.

Telomeres are tandem repeat sequences at the end of chromosomes that bind proteins to protect chromosome ends. Telomeres shorten with age, and shorter leukocyte telomere length (TL) has been associated with overall mortality in numerous studies. However, this association has not been tested in populations outside of Europe and the U.S. We assessed the association between TL and subsequent mortality using data on 744 mortality cases and 761 age-/sex-matched controls sampled from >27,000 participants from three longitudinal Bangladeshi cohorts: Health Effects of Arsenic Longitudinal Study (HEALS), HEALS Expansion (HEALS-E), and Bangladesh Vitamin E and Selenium Trial (BEST). We used conditional logistic regression to estimate odds ratios (ORs) for the association between a standardized TL variable and overall mortality, as well as mortality from chronic diseases, respiratory diseases, circulatory diseases, and cancer. In HEALS and BEST, we observed an association between shorter TL and increased overall mortality (P=0.03 and P=0.03), mortality from chronic disease (P=0.01 and P=0.03) and mortality from circulatory disease (P=0.03 and P=0.04). Results from pooled analyses of all cohorts were consistent with HEALS and BEST. This is the first study demonstrating an association between short TL and increased mortality in a population of non-European ancestry.