Differentiating nontuberculous mycobacterium pulmonary disease from pulmonary tuberculosis through the analysis of the cavity features in CT images using radiomics

Objective To differentiate nontuberculous mycobacteria (NTM) pulmonary diseases from pulmonary tuberculosis (PTB) by analyzing the CT radiomics features of their cavity. Methods 73 patients of NTM pulmonary diseases and 69 patients of PTB with the cavity in Shandong Province Chest Hospital and Qilu Hospital of Shandong University were retrospectively analyzed. 20 patients of NTM pulmonary diseases and 20 patients of PTB with the cavity in Jinan Infectious Disease Hospitall were collected for external validation of the model. 379 cavities as the region of interesting (ROI) from chest CT images were performed by 2 experienced radiologists. 80% of cavities were allocated to the training set and 20% to the validation set using a random number generated by a computer. 1409 radiomics features extracted from the Huiying Radcloud platform were used to analyze the two kinds of diseases' CT cavity characteristics. Feature selection was performed using analysis of variance (ANOVA) and least absolute shrinkage and selection operator (LASSO) methods, and six supervised learning classifiers (KNN, SVM, XGBoost, RF, LR, and DT models) were used to analyze the features. Results 29 optimal features were selected by the variance threshold method, K best method, and Lasso algorithm.and the ROC curve values are obtained. In the training set, the AUC values of the six models were all greater than 0.97, 95% CI were 0.95–1.00, the sensitivity was greater than 0.92, and the specificity was greater than 0.92. In the validation set, the AUC values of the six models were all greater than 0.84, 95% CI were 0.76–1.00, the sensitivity was greater than 0.79, and the specificity was greater than 0.79. In the external validation set, The AUC values of the six models were all greater than 0.84, LR classifier has the highest precision, recall and F1-score, which were 0.92, 0.94, 0.93. Conclusion The radiomics features extracted from cavity on CT images can provide effective proof in distinguishing the NTM pulmonary disease from PTB, and the radiomics analysis shows a more accurate diagnosis than the radiologists. Among the six classifiers, LR classifier has the best performance in identifying two diseases.

Mycobacterium abscessus Genetic Determinants Associated with the Intrinsic Resistance to Antibiotics

Mycobacterium abscessus subsp. abscessus (MAB) is a fast-growing nontuberculous mycobacterium causing pulmonary infections in immunocompromised and immunocompetent individuals. The treatment of MAB infections in clinics is extremely challenging, as this organism is naturally resistant to most available antibiotics. There is limited knowledge on the mechanisms of MAB intrinsic resistance and on the genes that are involved in the tolerance to antimicrobials. To identify the MAB genetic factors, including the components of the cell surface transport systems related to the efflux pumps, major known elements contributing to antibiotic resistance, we screened the MAB transposon library of 2000 gene knockout mutants. The library was exposed at either minimal inhibitory (MIC) or bactericidal concentrations (BC) of amikacin, clarithromycin, or cefoxitin, and MAB susceptibility was determined through the optical density. The 98 susceptible and 36 resistant mutants that exhibited sensitivity below the MIC and resistance to BC, respectively, to all three drugs were sequenced, and 16 mutants were found to belong to surface transport systems, such as the efflux pumps, porins, and carrier membrane enzymes associated with different types of molecule transport. To establish the relevance of the identified transport systems to antibiotic tolerance, the gene expression levels of the export related genes were evaluated in nine MAB clinical isolates in the presence or absence of antibiotics. The selected mutants were also evaluated for their ability to form biofilms and for their intracellular survival in human macrophages. In this study, we identified numerous MAB genes that play an important role in the intrinsic mechanisms to antimicrobials and further demonstrated that, by targeting components of the drug efflux system, we can significantly increase the efficacy of the current antibiotics.

More on search for causes of sensitization to tuberculin PPD for mammals in cattle

Despite the large number of papers dealing with the description of proposed methods for bovine tuberculosis diagnosis and mechanisms of non-specific reaction development in diseased and healthy animals, various aspects require further study. Many specialists are still of the view, formulated when studying causes of pseudoallergic reactions, that the agents of actinomycosis, trematode infections etc. can cause sensitization of the animal body to tuberculin PPD for mammals. The possibility of sensitization of cattle body to Аctinomyces bovis tuberculin was studied in 240 animals identified as actinomycosis diseased among 3,473 tested animals. Only 11 (4.6%) of the total number of diseased animals were reactors to tuberculin PPD for mammals. During bacteriological tests of material from animals euthanized for diagnostic purposes (tuberculin reactors and nonreactors with a confirmed postmortem diagnosis of actinomycosis), acid-tolerant nontuberculous mycobacterium (NTM) cultures were isolated. The results of the experiment conducted in 628 cows of a dairy holding confirmed that Actinomyces bovis lacks tuberculin-associated allergenicity: actinomycosis was detected only in one of 96 (15.2%) tuberculin reactors. The conducted clinical tests with high significance level (Р < 0.005) showed that there is no association between allergic reaction to tuberculin PPD for mammals and actinomycosis infection. The obtained results are indicative of imperfections in differential diagnosis, and further studies in this field should significantly contribute to gaining a better insight into non-specific sensitization of cattle body to tuberculin.

Associations between Diabetes Mellitus and Nontuberculous Mycobacterium-Caused Diseases in Taiwan: A Nationwide Cohort Study

Patients with diabetes mellitus (DM) are at greater risk of developing active tuberculosis and other intracellular bacterial infections, although the risk of acquiring infections from nontuberculous Mycobacterium (NTM) remains undefined. This study evaluated associations between DM and incidence of NTM infection-caused pulmonary and cutaneous diseases. Data for DM patients were extracted from the National Health Insurance Research Database of Taiwan. The DM cohort included 136,736 patients, and cases were matched randomly by age, gender, and index year with non-DM patients. Multivariate Cox proportional hazards regression was used to calculate adjusted hazard ratios of incident NTM-caused diseases in the DM cohort compared with non-DM control subjects. The frequency of incident NTM-caused diseases was significantly greater in DM patients (0.12%) than in non-DM patients (0.08%) (P < 0.05), including patients with type 1 DM (0.12%) and type 2 DM (0.12%) (all P < 0.05). Adjusted multivariate Cox regression analysis revealed that the incidence of NTM-caused diseases in DM patients was 1.43-fold greater than that in non-DM patients overall (P < 0.05), particularly in pulmonary (1.13-fold), other specific (excluding pulmonary, cutaneous, and disseminated diseases; 3.88-fold), and unspecific (atypical NTM infection; 1.54-fold) diseases (all P < 0.05). In conclusion, both type 1 DM and type 2 DM patients have high risk of NTM-caused diseases, suggesting that physicians need to pay more attention to this issue concerning the high risk of NTM-caused infection in DM patients.

Dissemination of Mycobacterium abscessus via global transmission networks

Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of global transmission networks of M. abscessus. How and when these clones emerged and spread globally is unclear. Here, we use evolutionary analyses of isolates from individuals both with and without CF to reconstruct the population history, spatiotemporal spread and recent transmission networks of the DCCs. We demonstrate synchronous expansion of six unrelated DCCs in the 1960s, a period associated with major changes in CF care and survival. Each of these clones has spread globally as a result of rare intercontinental transmission events. We show that the DCCs, but not environmentally acquired isolates, exhibit a specific smoking-associated mutational signature and that current transmission networks include individuals both with and without CF. We therefore propose that the DCCs initially emerged in non-CF populations but were then amplified and spread through the CF community. While individuals with CF are probably the most permissive host, non-CF individuals continue to play a key role in transmission networks and may facilitate long-distance transmission.

Mycobacterium fortuitum abortion in a sow

Two aborted Chester White pig fetuses were presented to a veterinary diagnostic laboratory in Illinois. Postmortem examination identified no gross abnormalities. Histologic evaluation revealed multifocal necrosis of chorionic epithelial cells, coalescing areas of mineralization in the placenta, and focal accumulations of viable and degenerate neutrophils in the lung. Intra- and extracellular acid-fast bacilli were identified in the lesions in both the placenta and lungs. Bacterial culture of stomach contents yielded heavy growth of Mycobacterium fortuitum, a rapidly growing nontuberculous mycobacterium (NTM), which was further confirmed through whole-genome sequencing. NTM are opportunistic pathogens commonly found in the soil and in contaminated water supplies. In animals, M. fortuitum is typically introduced through cutaneous wounds leading to infections limited to the skin, with systemic infection being uncommon. To our knowledge, abortion caused by M. fortuitum has not been reported previously.

DNA Methylation Profiling for the Diagnosis and Prognosis of Patients with Nontuberculous Mycobacterium Lung Disease

The incidence of nontuberculous Mycobacterium (NTM) lung disease is rapidly increasing; however, its diagnosis and prognosis remain unclear while selecting patients who will respond to appropriate treatment. Differences in DNA methylation patterns between NTM patients with good or poor prognosis could provide important therapeutic targets. We used the Illumina MethylationEPIC (850k) DNA methylation microarray to determine the pattern between differentially methylated regions (DMRs) in NTM patients with good or poor prognosis (n = 4/group). Moreover, we merged and compared 20 healthy controls from previous Illumina Methylation450k DNA methylation microarray data. We selected and visualized the DMRs in the form of heatmaps, and enriched terms associated with these DMRs were identified by functional annotation with the “pathfinder” package. In total, 461 and 293 DMRs (|Log2 fold change| > 0.1 and p < 0.03) were more methylated in patients with four poor and four good prognoses, respectively. Furthermore, 337 and 771 DMRs (|Log2 fold change| > 0.08 and p < 0.001) were more methylated in eight NTM patients and 20 healthy controls, respectively. TGFBr1 was significantly less methylated, whereas HLA-DR1 and HLA-DR5 were more methylated in patients with poor prognosis (compared to those with good prognosis). LRP5, E2F1, and ADCY3 were the top three less-methylated genes in NTM patients (compared with the controls). The mTOR and Wnt signaling pathway-related genes were less methylated in patients with NTM. Collectively, genes related to Th1-cell differentiation, such as TGFBr1 and HLA-DR, may be used as biomarkers for predicting the treatment response in patients with NTM lung disease.