Partnering for better microbial diagnostics

Transrenal DNA detection of Mycobacterium tuberculosis in patients with pulmonary tuberculosis

Background

Multiple attempts have been made to use biological samples other than sputum to diagnose tuberculosis (TB). Sputum acid-fast bacillus (AFB) microscopy is the fastest, most straightforward, and most inexpensive method for diagnosing pulmonary TB. However, urine can be used in place of sputum owing to its various advantages, such as a noninvasive method of collection, convenient handling and storage, and minimal risk of infection in health-care workers involved in sample collection. In this study, we aimed to assess the suitability of urine as a sample to obtain transrenal DNA (trDNA) to diagnose TB. This study involved several patients with TB undergoing inpatient treatment, whose AFB microscopy showed negative inversion.

Methods

Here, 51 urine samples were collected from 40 patients with TB and examined to confirm the presence of trDNA. First, we compared the efficiency of two trDNA extraction methods.

An automated magnetic bead-based method and a more efficient anchoring extraction method. Statistical analyses were performed using Excel software (Microsoft Office Professional Plus 2019).

Results

Although molecular diagnosis using GeneXpert yielded negative results, a peculiarity was observed. There was no significant difference between GeneXpert findings and our results nor was there any difference in the sequential trDNA samples obtained. However, even when GeneXpert results were negative, trDNA was detected in seven out of ten samples using the anchor extraction method.

Conclusions

Further studies are needed to establish biomarkers for the progression of TB treatment.

The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection

Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.

Tuberculosis Diagnosis by Metagenomic Next-generation Sequencing on Bronchoalveolar Lavage Fluid: a cross-sectional analysis

BACKGROUND

Metagenomic next-generation sequencing (mNGS) is an effective diagnostic method for infectious diseases, however, its clinical utility for tuberculosis (TB) diagnosis remains to be demonstrated.

METHODS

A total of 322 bronchoalveolar lavage fluid (BALF) samples were collected from 311 suspected and confirmed pulmonary TB patients and tested by mNGS, acid-fast bacillus (AFB) smear by microscopy, Xpert® MTB/RIF (Xpert), mycobacterium culture and bacterial/fungal culture. Diagnostic performance of mNGS was compared with conventional methods for detection of Mycobacterium tuberculosis complex (MTBC) and other pathogens in BALF. Underlying factors associated with positive detection in pulmonary TB patients were investigated.

RESULTS

mNGS, Xpert and culture presented a high proportion of complete matching for MTBC detection (244/322, 75.8%). In pulmonary TB patients pre-treatment the sensitivity of MTBC detection by mNGS, Xpert, culture and smear was 59.9% (85/142), 69.0% (98/142), 59.9% (85/142) and 24.6% (35/142), respectively, and 79.6% overall; MTBC was detected by mNGS in 33.2% (5/34) Xpert and culture negative samples. Positive MTBC detection by mNGS was affected by Vitamin D, erythrocyte sedimentation rate, TB initial treatment/retreatment, and cavity in chest imaging (χ² = 37.42, P < 0.001), but not by prior anti-TB therapy within 3 months. mNGS was able to detect new potential pathogens in 8.7% (28/322) of samples.

CONCLUSIONS

Combining mNGS with conventional detection methods could increase the detection rate for MTBC. Additionally, mNGS could identify pathogens in a non-targeted approach for better diagnosis of coinfection.

Transmission of Mycobacterium tuberculosis in China: a population-based molecular epidemiologic study

BACKGROUND

Understanding the transmission of Mycobacterium tuberculosis is essential for the development of efficient tuberculosis control strategies. China has the second-largest tuberculosis burden in the world. Recent transmission and infection with M. tuberculosis, particularly drug-resistant strains, may account for many new tuberculosis cases.

METHODS

We performed a population-based molecular epidemiologic study of pulmonary tuberculosis in China during 1 July 2009 to 30 June 2012. We defined clusters as cases with identical variable number tandem repeat genotype patterns and identified the risk factors associated with clustering, by logistic regression. Relative transmission rates were estimated by the sputum smear status and drug susceptibility status of tuberculosis patients.

RESULTS

Among 2274 culture-positive tuberculosis patients with genotyped isolates, there were 705 (31.0%) tuberculosis patients in 287 clusters. Multidrug-resistant (MDR) tuberculosis (adjusted odds ratio [aOR], 1.86; 95% confidence interval [CI], 1.25-2.63) and infection with a Beijing family strain (aOR, 1.56; 95% CI, 1.23-2.96) were associated with clustering. Eighty-four of 280 (30.0%) clusters had a putative source case that was sputum smear negative, and 30.6% of their secondary cases were attributed to transmission by sputum smear-negative patients. The relative transmission rate for sputum smear negative compared with sputum smear-positive patients was 0.89 (95% CI, .68-1.10), and was 1.51 (95% CI, 1.00-2.24) for MDR tuberculosis vs drug-susceptible tuberculosis.

CONCLUSIONS

Recent transmission of M. tuberculosis, including MDR strains, contributes substantially to tuberculosis disease in China. Sputum smear-negative cases were responsible for at least 30% of the secondary cases. Interventions to reduce the transmission of M. tuberculosis should be implemented in China.

Tuberculosis in the African continent: A comprehensive review

Tuberculosis continues to be a major global health problem, causing an estimated 8.8 million new cases and 1.45 million deaths annually. New drugs in the 1940s made it possible to beat the disease, and consequently, the number of cases reduced drastically. Fast-forward a few decades, drugresistant strains of varied virulence are reported consistently, disease is again on the rise and the treatment has not kept pace. Tuberculosis is the leading cause of death among HIV-infected persons in many resource-constrained settings however, it is curable and preventable. The unprecedented growth of the tuberculosis epidemic in Africa is attributable to several factors, the most important being the HIV epidemic. Analysis of molecular-based data have shown diverse genetic backgrounds among both drug-sensitive and MDR TB isolates in Africa presumably due to underlying genetic and environmental differences. The good news is that there have been important advances recently in TB drugs and diagnostics. Despite the availability of revolutionary tests that allow for faster diagnosis and of new drugs and regimens that offer better and safer treatment it is now becoming clearer that national efforts on TB control should be enhanced and focus on improving the quality of prevention, diagnosis, treatment and care services; strengthening program management, implementation and supervision. This review is an assessment of the trend in TB in Africa.

Immunofluorescence microtip sensor for point-of-care tuberculosis (TB) diagnosis

A immunofluorescence microtip sensor was developed for specific detection of Mycobacterium cells in sputum samples by the combination of electric field, streaming flow, and immuno-affinity binding. The detection limit was 200 CFU/mL in human sputum, which was comparable to PCR but without requiring bacteriological culture, centrifugation, or nucleic acid amplification. In spite of the complex nature of physical, chemical, and biological mechanisms, the simple operation of "dipping and withdrawal" of tips will allow for screening by minimally trained personnel within 30 min. In addition, the minimal power requirement (5 W) combined with low assay cost is ideal for point-of-care (POC) screening in resource-limited settings.

Immunosensor towards low-cost, rapid diagnosis of tuberculosis

A rapid, accurate tuberculosis diagnostic tool that is compatible with the needs of tuberculosis-endemic settings is a long-sought goal. An immunofluorescence microtip sensor is described that detects Mycobacterium tuberculosis complex cells in sputum in 25 minutes. Concentration mechanisms based on flow circulation and electric field are combined at different scales to concentrate target bacteria in 1 mL samples onto the surfaces of microscale tips. Specificity is conferred by genus-specific antibodies on the microtip surface. Immunofluorescence is then used to detect the captured cells on the microtip. The detection limit in sputum is 200 CFU mL(-1) with a success rate of 96%, which is comparable to PCR.

Biomarkers and diagnostics for tuberculosis: progress, needs, and translation into practice

Human infection with Mycobacterium tuberculosis can progress to active disease, be contained as latent infection, or be eradicated by the host response. Tuberculosis diagnostics classify a patient into one of these categories. These are not fixed distinct states, but rather are continua along which patients can move, and are affected by HIV infection, immunosuppressive therapies, antituberculosis treatments, and other poorly understood factors. Tuberculosis biomarkers-host or pathogen-specific-provide prognostic information, either for individual patients or study cohorts, about these outcomes. Tuberculosis case detection remains difficult, partly because of inaccurate diagnostic methods. Investments have yielded some progress in development of new diagnostics, although the existing pipeline is limited for tests for sputum-smear-negative cases, childhood tuberculosis, and accurate prediction of reactivation of latent tuberculosis. Despite new, sensitive, automated molecular platforms for detection of tuberculosis and drug resistance, a simple, inexpensive point-of-care test is still not available. The effect of any new tests will depend on the method and extent of their introduction, the strength of the laboratories, and the degree to which access to appropriate therapy follows access to diagnosis. Translation of scientific progress in biomarkers and diagnostics into clinical and public health programmes is possible-with political commitment, increased funding, and engagement of all stakeholders.

Tuberculosis, drug resistance, and HIV/AIDS: a triple threat

The worldwide epidemics of tuberculosis (TB) and HIV/AIDS have been joined by an insidiously developing third epidemic of TB drug resistance. Fueled by the disruption of TB control programs and the explosive growth of HIV/AIDS, the presence of TB drug resistance, particularly multiple drug resistance, is worldwide and threatens the gains made in the past decades in the treatment of both TB and HIV. Although treatment success is possible, the diagnosis and treatment of drug-resistant TB is difficult. Advances in TB diagnosis and treatment have been minimal in the past 40 years, and there is an urgent need for wider distribution of available diagnostic technology and for the development and testing of newer rapid molecular diagnostic techniques and therapeutic agents. This review discusses current information about the distribution of multiple drug-resistant and newer extensively drug-resistant TB as well as available diagnostic and therapeutic strategies with an emphasis on the relationship between TB drug resistance and HIV/AIDS.

Assessing proficiency of interpretation of rapid human immunodeficiency virus assays in nonlaboratory settings: ensuring quality of testing

Rapid antibody tests for the detection of human immunodeficiency virus (HIV) offer an effective means of providing a timely result of HIV serostatus to individuals. The increased use of rapid HIV antibody tests outside the laboratory has highlighted the need for new, cost-effective quality assurance methods to be developed for use in nonlaboratory-based and resource-limited settings. Photographed rapid HIV test results were used in a modified external quality assessment scheme to assess the interpretation proficiency and, therefore, to assess the feasibility of using this method as a basis for a quality assessment program for nonlaboratory-based testing. Participants (n = 148), both experienced and inexperienced in the performance and interpretation of rapid HIV testing, interpreted the photographed results of five rapid HIV assays. These were scored according to the degree of technical discordance. Error scores were grouped according to each participant's technical experience. The accuracy of interpretation for four of the five assays was between 80 and 97%, indicating that the photographed results of samples, including those difficult to read or borderline difficult to read, can be used to assess the proficiency of test operators in interpreting results. Participants had greater difficulty in interpreting samples of weak reactivity; this was consistent across the five assays. Experience played an important role in accurate interpretation, with experienced laboratory participants exhibiting greater proficiency (P < 0.05) in interpreting the results of three of the five rapid HIV assays. It was established that photographed results of rapid HIV assays could be interpreted with accuracy and demonstrated that prior experience resulted in a more accurate interpretation performance.

T-cell assays for the diagnosis of latent tuberculosis infection: moving the research agenda forward

For nearly a century, the tuberculin skin test was the only tool available for the detection of latent tuberculosis infection. A recent breakthrough has been the development of T-cell-based interferon-gamma release assays. Current evidence suggests interferon-gamma release assays have higher specificity than the tuberculin skin test, better correlation with surrogate markers of exposure to Mycobacterium tuberculosis in low-incidence settings, and less cross-reactivity as a result of BCG vaccination compared with the tuberculin skin test. The body of literature supporting the use of interferon-gamma release assays has rapidly expanded. However, several unresolved and unexplained issues remain. To address these issues, a group of experts met in Geneva, Switzerland, in March, 2006, to discuss the research evidence on T-cell-based assays, their clinical usefulness, limitations, and directions for future research, with a specific focus on resource-limited and high HIV prevalence settings. On the basis of 2 days of discussions, a comprehensive research agenda was generated, which will propel the field forward by stimulating focused high-impact research and encourage the investment of resources needed to tackle priority research questions, especially in resource-limited settings. Ultimately, if adequately financed, the research findings will inform appropriate use of novel latent tuberculosis infection diagnostics in global tuberculosis control.