A systematic review and repeatability study on the use of deep learning for classifying and detecting tuberculosis bacilli in microscopic images.

Tuberculosis (TB) is among the leading causes of death worldwide from a single infectious agent. This disease usually affects the lungs (pulmonary TB) and can be cured in most cases with a quick diagnosis and proper treatment. Microscopic sputum smear is widely used to diagnose and manage pulmonary TB. Despite being relatively fast and low cost, it can be exhausting because it depends on manually counting TB bacilli (Mycobacterium tuberculosis) in microscope images. In this context, different Deep Learning (DL) techniques are proposed in the literature to assist in performing smear microscopy. This article presents a systematic review based on the PRISMA procedure, which investigates which DL techniques can contribute to classifying TB bacilli in microscopic images of sputum smears using the Ziehl-Nielsen method. After an extensive search and a careful inclusion/exclusion procedure, 28 papers were selected from a total of 400 papers retrieved from nine databases. Based on these articles, the DL techniques are presented as possible solutions to improve smear microscopy. The main concepts necessary to understand how such techniques are proposed and used are also presented. In addition, replication work is also carried out, verifying reproducibility and comparing different works in the literature. In this review, we look at how DL techniques can be a partner to make sputum smear microscopy faster and more efficient. We also identify some gaps in the literature that can guide which issues can be addressed in other works to contribute to the practical use of these methods in laboratories.

Factors Associated with the Effectiveness of Regimens for the Treatment of Tuberculosis in Patients Coinfected with HIV/AIDS: Cohort 2015 to 2019.

(1) Background: Infection with the Human Immunodeficiency Virus (HIV) is a significant challenge for tuberculosis (TB) control, with increasing mortality rates worldwide. Moreover, the loss to follow-up is very high, with low adherence to treatment, resulting in unfavorable endpoints. This study aimed to analyze the effectiveness of TB treatment in patients coinfected with HIV/AIDS and its associated factors. (2) Methods: Patients coinfected with TB and HIV/AIDS at a Reference Hospital for infectious diseases were followed up for a maximum of one year from the start of TB treatment until cure or censorship (death, abandonment, and transfer) from 2015 to 2019. The Cox proportional model was used to identify risk factors for effectiveness. (3) Results: Of the 244 patients included in the cohort, 58.2% (142/244) had no treatment effectiveness, 12.3% (30/244) died, and 11.1% (27/244) abandoned treatment. Viral suppression at the onset of TB treatment (HR = 1.961, CI = 1.123-3.422), previous use of Antiretroviral Therapy (HR = 1.676, CI = 1.060-2.651), new cases (HR = 2.407, CI = 1.197-3.501), not using illicit drugs (HR = 1.763, CI = 1.141-2.723), and using the basic TB regimen (HR = 1.864, CI = 1.084-3.205) were significant variables per the multivariate Cox regression analysis. (4) Conclusion: TB treatment for most TB patients coinfected with HIV/AIDS was not effective. This study identified that an undetectable viral load at the beginning of the disease, previous use of ART, not using illicit drugs and not having previously taken anti-TB treatment are factors associated with successful TB treatment.

The Medication Experience of TB/HIV Coinfected Patients: Qualitative Study.

Tuberculosis (TB) and human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) pharmacotherapy and the stigma related to both diseases are complex. The patients' subjective experiences with diseases and medications are of utmost importance in pharmaceutical care practice. This study aimed to understand the subjective medication experience of TB and HIV/AIDS coinfected patients. The study was based on descriptive research of a qualitative and quantitative nature using data collected during pharmaceutical care appointments and from medical records from September 2015 to December 2016 at a tertiary infectious diseases referral hospital in Southeastern Brazil. Data from 81 patients were analyzed. Regarding patient subjective medication experience, the following responses to the quantitative questionnaire were most frequent: preference for a route of administration (12.4%) and for non-pharmacological therapy (50.6%); concerns about price (11.1%) and adverse effects (18.5%); and association of a worsening of their health status with a change in medication dosage (23.5%). In the thematic analysis, adversity and socially constructed aspects were more prominent. Resolvability, associated with the patient's understanding of relief from signs and symptoms and health recovery, was observed; however, feelings of ambivalence permeated the other aspects, hence leading to treatment abandonment. The evaluation of patient medication experience can be a path to understanding and intervening in the phenomenon of treatment abandonment among TB and HIV/AIDS coinfected individuals.

Donor-Derived Tuberculosis: A Case Report and the Role of Communication Gaps in Transplantation Safety.

Donor-derived tuberculosis (DD-TB) accounts for less than 5% of TB cases and is considered a rare event. In the transplant setting, the frequency of active TB is estimated to be 20 to 74 times higher than that in the general population, and it is associated with high mortality. In this context, the main strategy to minimize the risk of DD transmission is to identify high-risk donors. Despite screening recommendations, failures may result in a breakdown of safety that ends in the transmission of potentially fatal diseases. This report describes a case of DD-TB and emphasizes communication gaps that may occur between organ procurement organizations and transplant centers. Failure in reporting results, lack of exchanging information regarding recipients from the same donor, and inefficient communication between organ procurement organizations and transplant centers are lacks that may be prevented by a more efficient approach towards screening protocols and communication.

Characterization of Mycobacterium tuberculosis heteroresistance by genotyping.

Background: Heteroresistance is the coexistence of susceptible and resistant strains in the same individual, considered the preliminary step for total resistance, and can stem from mixed infection or clonal heterogeneity. The aim of this study was to evaluate the heteroresistance of Mycobacterium tuberculosis to rifampicin and isoniazid and its characterization. Method: GenoType MTBDRplus®; Sanger sequencing of the rpoB, katG, and inhA genes; and Mycobacterial Interspersed Repetitive Unit - Variable Number Tandem Repeat (MIRU-VNTR) were performed. Results: In a total of 654 isolates, 530 were resistant, 124 were susceptible, and 29 were heteroresistant to a first-line drug. GenoType MTBDRplus® detected heteroresistance in the rpoB gene in 26/29 (89.6%), as compared to 5/29 (17.2%) in the katG gene and 2/29 (6.8%) in the inhA gene. Four isolates showed heteroresistance in these genes. The Sanger sequencing detected heteroresistance in the rpoB gene in 7/29 (24.1%), as compared to 3/29 (10.3%) in the katG gene. In one isolate, heteroresistance was concomitant in both the rpoB and katG genes. MIRU-VNTR detected mixed infection in three heteroresistant isolates, while four isolates showed clonal heterogeneity. Conclusions: GenoType MTBDRplus® detected more cases of heteroresistance when compared to sequencing. It was also possible to characterize mixed infection and clonal heterogeneity by MIRU-VNTR.

The activity-based cost of drug-susceptibility test of Mycobacterium tuberculosis through Kit SIRE Nitratase® Plastlabor.

Background: Drug-resistant tuberculosis (TB) is an ongoing health threat, and the greatest challenge to adequate control of TB in many countries lies in the lack of proper laboratory drug-susceptibility test. The aim of this study was to evaluate the activity-based costs (ABC) of Kit SIRE Nitratase® (Kit SIRE) and compare its values with the conventional drug-susceptibility test. Methods: The ABC was calculated for three different approaches: Kit SIRE (clinical samples and cultures), proportion methods in Lowenstein Jensen (PM-LJ), and the Bactec™ MGIT™ 960 system based on Mycobacterial Research Laboratory's routine. Results: The ABC of Kit SIRE from cultures was US$ 148.54, while from clinical samples was US$ 136.12. In the case of conventional tests, the ABC of Bactec™ MGIT™ 960 was US$ 227.63 and of the PM-LJ was US$ 132.64. The Kit SIRE has a lower ABC when clinical samples are used instead of cultures. Compared to conventional tests, the ABC is similar to the PM-LJ and lower the Bactec™ MGIT™ 960. Conclusion: The Kit SIRE should be used as a screening method in clinical specimens and in culture for laboratories that do not have Bactec™ MGIT™ 960. Therefore, it can be incorporated into the routine of laboratories in countries with low resources and a high burden of TB and drug-resistant TB.

Rapid detection of Mycobacterium tuberculosis DNA and genetic markers for Isoniazid resistance in Ziehl-Neelsen stained slides.

BACKGROUND: Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES: To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS: Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS: The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS: qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.

Multicenter evaluation of TB-SPRINT 59-Plex Beamedex®: accuracy and cost analysis.

BACKGROUND: Molecular tests can allow the rapid detection of tuberculosis (TB) and multidrug-resistant TB (MDR-TB). TB-SPRINT 59-Plex Beamedex® is a microbead-based assay developed for the simultaneous spoligotyping and detection of MDR-TB. The accuracy and cost evaluation of new assays and technologies are of great importance for their routine use in clinics and in research laboratories. The aim of this study was to evaluate the performance of TB-SPRINT at three laboratory research centers in Brazil and calculate its mean cost (MC) and activity-based costing (ABC). METHODS: TB-SPRINT data were compared with the phenotypic and genotypic profiles obtained using Bactec™ MGIT™ 960 system and Genotype® MTBDRplus, respectively. RESULTS: Compared with MGIT, the accuracies of TB-SPRINT for the detection of rifampicin and isoniazid resistance ranged from 81 to 92% and 91.3 to 93.9%, respectively. Compared with MTBDRplus, the accuracies of TB-SPRINT for rifampicin and isoniazid were 99 and 94.2%, respectively. Moreover, the MC and ABC of TB-SPRINT were USD 127.78 and USD 109.94, respectively. CONCLUSION: TB-SPRINT showed good results for isoniazid and rifampicin resistance detection, but still needs improvement to achieve In Vitro Diagnostics standards.

Frequency of the Mycobacterium tuberculosis RDRio genotype and its association with multidrug-resistant tuberculosis.

BACKGROUND: In recent decades, Mycobacterium tuberculosis with the RDRio genotype, frequently isolated from tuberculosis patients in Rio de Janeiro, has become part of the Latin American - Mediterranean (LAM) family and has been associated with multidrug-resistant tuberculosis (MDR-TB). The aim of this study was to investigate the frequency of M. tuberculosis RDRio in the state of Minas Gerais, Brazil, and its relationship with MDR-TB. METHODS: For convenience, 172 susceptible and 63 MDR M. tuberculosis isolates were taken from pulmonary samples from patients diagnosed between January 2007 and December 2011. The DNA extracted from these isolates was analyzed by spoligotyping, PCR-RFLP to characterize fbpC103/Ag85C103, multiplex PCR to detect RDRio and RD174, and MIRU-VNTR 24 loci. RESULTS: Among the 235 isolates, the RDRio pattern was identified in 122 (51.9%) isolates (IC 0.45-0.58), with 100 (42.5%) wild-type and 13 (5.5%) mixed pattern isolates, whereas RD174 was identified in 93 of the 122 RDRio positive samples (76.3%). The LAM family and the LAM9 lineage were the most frequently identified among the isolates in this study. Among the 63 MDR isolates, 41 (65.1%) were RDRio and 28 (44.4%) RD174. CONCLUSION: The association of both deletions with MDR proved to be statistically significant, corroborating the few reports that have associated RDRio with MDR.

Genetic diversity and molecular epidemiology of multidrug-resistant Mycobacterium tuberculosis in Minas Gerais State, Brazil.

BACKGROUND: We aimed to characterize the genetic diversity of drug-resistant Mycobacterium tuberculosis (MTb) clinical isolates and investigate the molecular epidemiology of multidrug-resistant (MDR) tuberculosis from Minas Gerais State, Brazil. METHODS: One hundred and four MTb clinical isolates were assessed by IS6110-RFLP, 24-locus mycobacterial interspersed repetitive units variable-number tandem repeats (MIRU-VNTR), TB-SPRINT (simultaneous spoligotyping and rifampicin-isoniazid drug-resistance mutation analysis) and 3R-SNP-typing (analysis of single-nucleotide polymorphisms in the genes involved in replication, recombination and repair functions). RESULTS: Fifty-seven different IS6110-RFLP patterns were found, among which 50 had unique patterns and 17 were grouped into seven clusters. The discriminatory index (Hunter and Gaston, HGDI) for RFLP was 0.9937. Ninety-nine different MIRU-VNTR patterns were found, 95 of which had unique patterns and nine isolates were grouped into four clusters. The major allelic diversity index in the MIRU-VNTR loci ranged from 0.6568 to 0.7789. The global HGDI for MIRU-VNTR was 0.9991. Thirty-two different spoligotyping profiles were found: 16 unique patterns (n = 16) and 16 clustered profiles (n = 88). The HGDI for spoligotyping was 0.9009. The spoligotyped clinical isolates were phylogenetically classified into Latin-American Mediterranean (66.34 %), T (14.42 %), Haarlem (5.76 %), X (1.92 %), S (1.92 %) and U (unknown profile; 8.65 %). Among the U isolates, 77.8 % were classified further by 3R-SNP-typing as 44.5 % Haarlem and 33.3 % LAM, while the 22.2 % remaining were not classified. Among the 104 clinical isolates, 86 were identified by TB-SPRINT as MDR, 12 were resistant to rifampicin only, one was resistant to isoniazid only, three were susceptible to both drugs, and two were not successfully amplified by PCR. A total of 42, 28 and eight isolates had mutations in rpoB positions 531, 526 and 516, respectively. Correlating the cluster analysis with the patient data did not suggest recent transmission of MDR-TB. CONCLUSIONS: Although our results do not suggest strong transmission of MDR-TB in Minas Gerais (using a classical 100 % MDR-TB identical isolates cluster definition), use of a smoother cluster definition (>85 % similarity) does not allow us to fully eliminate this possibility; hence, around 20-30 % of the isolates we analyzed might be MDR-TB transmission cases.

In-house PCR with DNA extracted directly from positive slides to confirm or exclude the diagnosis of tuberculosis: focus on biosafety.

The possibility to obtain DNA from smears is a valuable alternative to remedy the lack of samples when they are totally used for bacilloscopy; this technique solves the biosafety problem related to a possible accident with the transportation of flasks containing potentially transmissible clinical samples. Hence, the purpose of this study was to utilize the insertion sequence IS6110 for amplification of DNA from a smear-positive sample for tuberculosis (TB) diagnosis. Among the 52 positive bacilloscopies, sensitivity, specificity, positive predictive value and negative predictive value were 52.3%, 100%, 100% and 89.7%, respectively whereas accuracy was 90.7%. The IS6110-based PCR for TB diagnosis developed in DNA extracted from a positive smear is a fast, simple, specific, and safe method.

In-house PCR with DNA extracted directly from positive slides to confirm or exclude the diagnosis of tuberculosis: focus on biosafety. / In-house PCR with DNA extracted directly from positive slides to confirm or exclude the diagnosis of tuberculosis: focus on biosafety.

The possibility to obtain DNA from smears is a valuable alternative to remedy the lack of samples when they are totally used for bacilloscopy; this technique solves the biosafety problem related to a possible accident with the transportation of flasks containing potentially transmissible clinical samples. Hence, the purpose of this study was to utilize the insertion sequence IS6110 for amplification of DNA from a smear-positive sample for tuberculosis (TB) diagnosis. Among the 52 positive bacilloscopies, sensitivity, specificity, positive predictive value and negative predictive value were 52.3

, 100

, 100

and 89.7

, respectively whereas accuracy was 90.7

. The IS6110-based PCR for TB diagnosis developed in DNA extracted from a positive smear is a fast, simple, specific, and safe method.

Evaluation of six different DNA extraction methods for detection of Mycobacterium tuberculosis by means of PCR-IS6110: preliminary study.

BACKGROUND: Developments in molecular detection and strain differentiation of members of Mycobacterium tuberculosis complex have proved to be useful. The DNA extraction method influences the amplification efficiency, causing interference on the sensitivity and respective inhibitors. The aim of this study was to standardize a simple and fast DNA extraction method, providing DNA amplification by IS6110-PCR effectively free from undue interferences. FINDINGS: The efficiency of the six different protocols tested in M. tuberculosis cultures has varied from 75% to 92.5%. This preliminary study evaluating the IS6110 PCR sensitivity and specificity was developed in DNA extracted from microscope slides, and achieved 100% of efficiency. CONCLUSIONS: DNA extraction by Chelex + NP-40 method from both, cultures of M. tuberculosis and smear slides, resulted in good quantity of interference free DNA, especially in samples with low concentrations of genetic material; therefore, such technique may be used for the molecular diagnosis of tuberculosis.

Functional profile of patients with tuberculosis sequelae in a university hospital.

OBJECTIVE: To describe data related to the pulmonary function of patients with sequelae of pulmonary tuberculosis, pleural tuberculosis or both. METHODS: In the outpatient clinic of a university hospital, 218 patients were evaluated. Of those 218, 56 had sequelae of tuberculosis (pulmonary, pleural or both), and 162 had other types of tuberculosis. All patients were evaluated in the pulmonary function laboratory between February 2000 and July 2004, and 43 were found to be eligible for inclusion in the study. Patients with a history of asthma, chronic pulmonary obstructive disease, cardiac insufficiency, collagen diseases, silicosis or thoracic surgery, as well as those for whom spirometry yielded unacceptable results or was not performed, were excluded. The lung fields were divided into six zones, and radiographic results were classified by degree: I (involvement of only one zone with no cavitation); II (involvement of two or three zones or of one zone with cavitation); or III (extensive involvement of three or more zones with or without cavitation). RESULTS: The final study sample comprised 50 patients, 44 (88%) of whom had pulmonary tuberculosis. The most prevalent form (17/50; 34%) was mixed ventilatory disturbance. Severe disturbances were more significant in degree III radiographs (p = 0.0002) and normal pulmonary function was predominant among patients presenting degree I and II radiographs (p = 0.002). CONCLUSION: The early discovery and treatment of tuberculosis contribute to reduce the number of cases, as well as the incidence of tuberculosis sequelae, thereby improving the quality of life of tuberculosis patients. Further studies, involving longitudinal, sequential analysis and larger samples of patients with tuberculosis sequelae, should be conducted in referral centers in Brazil.