Effect of pooled tracheal sample testing on the probability of Mycoplasma hyopneumoniae detection.

Tracheal pooling for Mycoplasma hyopneumoniae (M. hyopneumoniae) DNA detection allows for decreased diagnostic cost, one of the main constraints in surveillance programs. The objectives of this study were to estimate the sensitivity of pooled-sample testing for the detection of M. hyopneumoniae in tracheal samples and to develop probability of M. hyopneumoniae detection estimates for tracheal samples pooled by 3, 5, and 10. A total of 48 M. hyopneumoniae PCR-positive field samples were pooled 3-, 5-, and 10-times using field M. hyopneumoniae DNA-negative samples and tested in triplicate. The sensitivity was estimated at 0.96 (95% credible interval [Cred. Int.]: 0.93, 0.98) for pools of 3, 0.95 (95% Cred. Int: 0.92, 0.98) for pools of 5, and 0.93 (95% Cred. Int.: 0.89, 0.96) for pools of 10. All pool sizes resulted in PCR-positive if the individual tracheal sample Ct value was < 33. Additionally, there was no significant decrease in the probability of detecting at least one M. hyopneumoniae-infected pig given any pool size (3, 5, or 10) of tracheal swabs. Furthermore, this manuscript applies the probability of detection estimates to various real-life diagnostic testing scenarios. Combining increased total animals sampled with pooling can be a cost-effective tool to maximize the performance of M. hyopneumoniae surveillance programs.

Infection prediction in swine populations with machine learning.

The pork industry is an essential part of the global food system, providing a significant source of protein for people around the world. A major factor restraining productivity and compromising animal wellbeing in the pork industry is disease outbreaks in pigs throughout the production process: widespread outbreaks can lead to losses as high as 10% of the U.S. pig population in extreme years. In this study, we present a machine learning model to predict the emergence of infection in swine production systems throughout the production process on a daily basis, a potential precursor to outbreaks whose detection is vital for disease prevention and mitigation. We determine features that provide the most value in predicting infection, which include nearby farm density, historical test rates, piglet inventory, feed consumption during the gestation period, and wind speed and direction. We utilize these features to produce a generalizable machine learning model, evaluate the model's ability to predict outbreaks both seven and 30 days in advance, allowing for early warning of disease infection, and evaluate our model on two swine production systems and analyze the effects of data availability and data granularity in the context of our two swine systems with different volumes of data. Our results demonstrate good ability to predict infection in both systems with a balanced accuracy of [Formula: see text] on any disease in the first system and balanced accuracies (average prediction accuracy on positive and negative samples) of [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] on porcine reproductive and respiratory syndrome, porcine epidemic diarrhea virus, influenza A virus, and Mycoplasma hyopneumoniae in the second system, respectively, using the six most important predictors in all cases. These models provide daily infection probabilities that can be used by veterinarians and other stakeholders as a benchmark to more timely support preventive and control strategies on farms.

Association of Reported Candidate Monogenic Genes With Lung Cancer Risk.

INTRODUCTION/BACKGROUND: Published studies on association of germline monogenic genes and lung cancer risk were inconsistent. Our objective is to assess the validity of reported candidate monogenic genes for their association with lung cancer. MATERIALS AND METHODS: A systematic review of published papers prior to August 2022 was performed first to identify all genes where germline mutations were associated with lung cancer risk. We then performed a confirmation study in 2,050 lung cancer cases and 198,553 controls in the UK Biobank (UKB). Germline mutations of these genes were identified from sequencing data and annotated using The American College of Medical Genetics criteria. The robust SKAT-O, a gene-based analysis that properly controls for false positives due to unbalanced case-control ratio, was used for association tests adjusting for age at recruitment, gender, and genetic background. RESULTS: The systematic review identified 12 genes that were statistically significantly associated with lung cancer risk in at least one study (P < .05), including ATM, BLM, BRCA2, BRIP1, CHEK2, FANCA, FANCD2, MSH6, PMS1, RAD51C, RAD51D, and TP53. When pathogenic/likely pathogenic mutations were aggregated within each gene, the association was confirmed for ATM (P = 4.47E-4) at the study-wise significance level (P < .0042, Bonferroni correction for 12 tests). Suggestive evidence of association was found for 2 other genes, BRCA2 (P = .007) and TP53 (P = .03). Among these 3 genes, the lung cancer risks range from 1.95 (BRCA2) to 5.28 (TP53). CONCLUSION: This study provides statistical evidence for association of previously reported genes and lung cancer risk and has clinical utility for risk assessment and genetic counseling.

Esophageal Perforation Due to a Calcium Supplement Tablet.

Pill-induced esophagitis due to calcium supplements is extremely uncommon. We present a 60-year-old female patient with pill-induced esophageal perforation complicated by mediastinal abscess and esophago-pleural fistula following ingestion of a single over-the-counter "bone supplement" tablet containing mainly calcium.

National guideline concordance and outcomes for pathologic N2 disease in non-small cell lung cancer.

Background: Real-world treatment practices for positive mediastinal nodal disease in non-small cell lung cancer (NSCLC) continues to vary despite guidelines. We aim to assess national trends in the treatment of pathologic-N2 disease, and evaluate the association with clinical nodal staging and timing of systemic therapy. Methods: The National Cancer Database was queried for patients with NSCLC who underwent lobectomy and had pathologic-N2 disease from 2010-2017. National Comprehensive Cancer Network (NCCN) guideline concordance was evaluated. cN2 patients were analyzed based on timing of systemic therapy and response. Multivariable logistic regression evaluated outcomes by type of systemic therapy. Survival analysis utilized Cox proportional hazards regression and Kaplan-Meier methods. Results: 10,225 patients met inclusion criteria. Fifty-four percent of patients were understaged prior to surgery as either cN0 or cN1. Of clinically staged N2 patients, 56% received NCCN recommended neoadjuvant therapy. Annual guideline concordance increased until 2016 to a max of 62.9%. Neoadjuvant and adjuvant systemic therapy showed an overall survival benefit compared with no systemic therapy (HR 0.54 & 0.57), but no difference when compared against each other. Complete response after neoadjuvant therapy was associated with improved survival (5-year OS 56.1%, P<0.001), while partial response, no-response, and adjuvant therapy were similar. All systemic treatment strategies improved survival compared with no systemic therapy (5-year OS 24.5%). Conclusions: Guideline concordance for treatment of cN2 disease has been increasing, but still not followed in over 1/3 of patients. Responsiveness to neoadjuvant therapy appears to be a predictor of survival, and may become a prognostic adjunct for determining which patients would benefit from additional systemic therapy.

Germline mutations in high penetrance genes are associated with worse clinical outcomes in patients with non-small cell lung cancer.

Objective: To determine the frequency of pathogenic mutations in high-penetrance genes (HPGs) in patients with non-small cell lung cancer (NSCLC) and identify whether such mutations are associated with clinicopathologic outcomes. Methods: Patients with NSCLC who had consented to participate in a linked clinical database and biorepository underwent germline DNA sequencing using a next-generation sequencing panel that included cancer-associated HPGs and cancer risk-associated single nucleotide polymorphisms (SNPs). These data were linked to the clinical database to assess for associations between germline variants and clinical phenotype using Fisher's exact test and multivariable logistic and Cox regression. Results: We analyzed 151 patients, among whom 33% carried any pathogenic HPG mutation and 23% had a genetic risk score (GRS) >1.5. Among the patients without any pathogenic mutation, 31% were at cancer stage II or higher, compared with 55% of those with 2 types of HPG mutations (P = .0293); 40% of patients with both types of HPG mutations had cancer recurrence, compared with 21% of patients without both types (P = .0644). In multivariable analysis, the presence of 2 types of HPG mutations was associated with higher cancer stage (odds ratio [OR], 3.32; P = .0228), increased recurrence of primary tumor (OR, 2.93; P = .0527), shorter time to recurrence (hazard ratio [HR], 3.03; P = .0119), and decreased cancer-specific (HR, 3.53; P = .0039) and overall survival (HR, 2.44; P = .0114). Conclusions: The presence of mutations in HPGs is associated with higher cancer stage, increased risk of recurrence, and worse cancer-specific and overall survival in patients with NSCLC. Further large studies are needed to better delineate the role of HPGs in cancer recurrence and the potential benefit of adjuvant treatment in patients harboring such mutations.

Economic Considerations of Lung Volume Reduction Surgery and Bronchoscopic Valves.

Chronic obstructive pulmonary disease is a challenging disease to treat, and at advanced stages of the disease, procedural interventions become some of the only effective methods for improving quality of life. However, these procedures are often very costly. This article reviews the medical literature on cost-effectiveness of lung volume reduction surgery and bronchoscopic valve placement for lung volume reduction. It discusses the anticipated costs and economic impact in the future as technique is perfected and outcomes are improved.

Mycoplasma hyopneumoniae Surveillance in Pig Populations: Establishing Sampling Guidelines for Detection in Growing Pigs.

Antemortem detection of Mycoplasma hyopneumoniae infection in swine production systems has relied on antibody testing, but the availability of tests based on DNA detection and novel diagnostic specimens, e.g., tracheal swabs and oral fluids, has the potential to improve M. hyopneumoniae surveillance. A field study was performed over a 14-week period during which 10 pigs in one pen at the center of a room with 1,250 6-week-old pigs housed in 46 pens were intratracheally inoculated with M. hyopneumoniae Thereafter, one tracheal sample, four serum samples, and one oral fluid sample were collected from every pen at 2-week intervals. Tracheal and oral fluid samples were tested for M. hyopneumoniae DNA and serum samples for M. hyopneumoniae antibody. Test results were modeled using a hierarchical Bayesian model, based on a latent spatial piecewise exponential survival model, to estimate the probability of detection by within-pen prevalence, number of positive pens in the barn, sample allocation, sample size, and sample type over time. Analysis showed that tracheal samples provided the earliest detection, especially at large sample sizes. While serum samples are more commonly collected and are less expensive to test, high probability of detection estimates were only obtained 30 days postexposure at large sample sizes. In all scenarios, probability of detection estimates for oral fluids within 30 days were significantly lower than those for tracheal and serum samples. Ultimately, the choice of specimen type, sample number, and assay will depend on testing objectives and economics, but the estimates provided here will assist in the design of M. hyopneumoniae surveillance and monitoring programs for different situations.

Consensus for Thoracoscopic Left Upper Lobectomy-Essential Components and Targets for Simulation.

BACKGROUND: Simulation-based training is a valuable component of cardiothoracic surgical education. Effective curriculum development requires consensus on procedural components and focused attention on specific learning objectives. Through use of a Delphi process, we established consensus on the steps of video-assisted thoracoscopic surgery (VATS) left upper lobectomy and identified targets for simulation. METHODS: Experienced thoracic surgeons were randomly selected for participation. Surgeons voted and commented on the necessity of individual steps comprising VATS left upper lobectomy. Steps with greater than 80% of participants in agreement of their necessity were determined to have established "consensus." Participants voted on the physical or cognitive complexity of each, or both, and chose steps most amenable to focused simulation. RESULTS: Thirty thoracic surgeons responded and joined in the voting process. Twenty operative steps were identified, with surgeons reaching consensus on the necessity of 19. Components deemed most difficult and amenable to simulation included those related to dissection and division of the bronchus, artery, and vein. CONCLUSIONS: Through a Delphi process, surgeons with a variety of practice patterns can achieve consensus on the operative steps of left upper lobectomy and agreement on those most appropriate for simulation. This information can be implemented in the development of targeted simulation for VATS lobectomy.

COVID-19 guidance for triage of operations for thoracic malignancies: A consensus statement from Thoracic Surgery Outcomes Research Network.

The extraordinary demands of managing the COVID-19 pandemic has disrupted the world's ability to care for patients with thoracic malignancies. As a hospital's COVID-19 population increases and hospital resources are depleted, the ability to provide surgical care is progressively restricted, forcing surgeons to prioritize among their cancer populations. Representatives from multiple cancer, surgical, and research organizations have come together to provide a guide for triaging patients with thoracic malignancies as the impact of COVID-19 evolves as each hospital.

Evaluation of a Powered Vascular Stapler in Video-Assisted Thoracic Surgery Lobectomy.

BACKGROUND: A narrow-profile powered vascular stapler (PVS) was developed to provide superior access and precise staple placement in thoracic procedures. The objective of this study was to determine if the PVS would yield an equivalent rate of hemostatic interventions compared with standard of care (SOC) staplers in video-assisted thoracoscopic surgery lobectomy. MATERIALS AND METHODS: A randomized, controlled, multicenter study was conducted comparing PVS with SOC staplers in lobectomies performed for non-small cell lung cancer. The primary performance endpoint was the incidence of intraoperative hemostatic interventions, and the primary safety endpoint was the frequency of postoperative bleeding-related interventions. RESULTS: A total of 98 subjects participated in the SOC group and 103 in the PVS group. Rates of intraoperative hemostatic interventions were 5.3% and 8.3% for the SOC and PVS groups, respectively. These rates were not statistically different (P = 0.137), although the upper bound of the 95% confidence interval for the difference in intervention rates between PVC and SOC exceeded a predefined 3% criterion for equivalence. Simple compressions were performed more frequently in the PVS subjects, which accounted for the higher intervention rate in this group. Postoperative interventions for bleeding were required in one SOC subject (1.0%) and one subject from the PVS group (0.9%). Procedure-related adverse events occurred in 21 (21.9%) SOC subjects and 23 (21.9%) PVS subjects, with no adverse events related to use of the study devices. CONCLUSIONS: The PVS exhibited similar overall safety and effectiveness to SOC staplers in video-assisted thoracoscopic surgery lobectomy.

COVID-19 Guidance for Triage of Operations for Thoracic Malignancies: A Consensus Statement From Thoracic Surgery Outcomes Research Network.

The extraordinary demands of managing the COVID-19 pandemic has disrupted the world's ability to care for patients with thoracic malignancies. As a hospital's COVID-19 population increases and hospital resources are depleted, the ability to provide surgical care is progressively restricted, forcing surgeons to prioritize among their cancer populations. Representatives from multiple cancer, surgical, and research organizations have come together to provide a guide for triaging patients with thoracic malignancies as the impact of COVID-19 evolves as each hospital.

Invasive Mediastinal Staging for Lung Cancer by The Society of Thoracic Surgeons Database Participants.

BACKGROUND: Prior studies suggest underutilization of invasive mediastinal staging for lung cancer. We hypothesized that The Society of Thoracic Surgeons General Thoracic Surgery Database (STS-GTSD) participants would have higher rates of invasive staging compared with previous reports. METHODS: We conducted a retrospective cohort study (2012 to 2016) of lung cancer patients staged by computed tomography and positron-emission tomography and first treated with an anatomic resection. We defined invasive staging by the use of mediastinoscopy, endosonography, or thoracoscopy. Standardized incidence ratios were used to compare participant-level rates of invasive staging, and Poisson regression was used to identify factors associated with invasive staging. RESULTS: Among 29,015 patients across 256 participating STS-GTSD sites, 34% (95% confidence interval: 33% to 34%) underwent invasive staging. The overall rate of invasive staging did not change between 2012 and 2016 (p trend = 0.16). Increasing clinical stage and features suggestive of a central tumor were associated with invasive staging (p < 0.001). Rates of invasive staging among patients with clinical stage IB or greater or features suggestive of a central tumor were 43% (95% confidence interval: 42% to 44%) and 52% (95% confidence interval: 50% to 54%), respectively. There was a more than 40-fold variation in rates of invasive staging across 251 centers contributing at least 10 cases (standardized incidence ratio: lowest = 0.08; highest = 3.26); 66 sites (26%) performed invasive mediastinal staging less often than average and 77 sites (31%) performed invasive staging more often than average. CONCLUSIONS: The STS-GTSD participants performed invasive mediastinal staging more frequently than prior reports, and yet only in a minority of patients. Rates of invasive mediastinal staging vary widely across STS-GTSD participants.