Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

RpoB Gene Mutation Characteristics of Rifampicin-resistant Tuberculosis in Anqing, China

Background: Rifampicin resistant tuberculosis is a serious problem faced by tuberculosis control in China, and rapid detection of rifampicin resistance is urgently needed. Objectives: This study aimed to describe the molecular characteristics and frequency of RNA polymerase β subunit (rpoB) gene mutations in rifampicin-resistant tuberculosis (RR-TB) in the Anqing area. Methods: The rpoB gene fragment was amplified by polymerase chain reaction (PCR), and all isolates were sequenced for mutations in the rpoB gene. The mutations were obtained by comparing the sequencing results with the MUBII database. In addition, logistic regression was used to analyze the relationship between rpoB mutations and rifampicin (RIF) resistance. Results: There were 152 males and 42 females in this study, and the mean age was 56.60 ± 17.91 years. Mutations in the rpoB gene were a risk factor for rifampicin resistance (β = 5.271, P < 0.001 OR = 195.192). Among the 19 RR-TB strains, 16 (84.21%) had mutations in the ropB gene, and three (1.71%) of 175 rifampicin-sensitive strains were mutated. The mutation sites of five strains (31.58%) were at the codon 526 and five strains (31.58%) at the codon 531. However, there were two strains at the codon 513 and two strains at the codon 533 (15.79%), and two strains (10.53%) were double mutations. Conclusions: The mutation characteristics of the rpoB gene in the Anqing area are complex, and rpoB mutation detection can be used as an indicator to screen drug resistance of RIF.

The first diagnostic test for specific detection of Mycobacterium simiae using an electrochemical label-free DNA nanobiosensor

Mycobacterium simiae has been reported to be the most prevalent species of Nontuberculous mycobacteria (NTM) in many countries. As both phenotypic and molecular detection of M. simiae and other NTMs have limitations, finding an accurate, fast, and low-cost diagnostic method is critical for the management of infections. Here, we report the development of a new type of label-free electrochemical biosensor using a gold electrode decorated with l-cysteine/PAMAM dendrimer for specific targeting of M. simiae ITS sequence. DNA hybridization was monitored by measuring changes in the free guanine electrical signal with changing ssDNA target concentrations by differential pulse voltammetry (DPV) method. Response surface methodology (RSM) was applied for the optimization of variables affecting biosensor response. Under optimal conditions, the biosensor revealed a wide linear range from 10^-14 M to 10^-6 M and a detection limit of 1.40 fM. The fabricated biosensor showed an excellent selectivity to M. simiae in the presence of other similar pathogenic bacteria. Moreover, experimental results confirmed that this biosensor exhibited great precision and high reproducibility, hence provides a low-cost, label-free, and faster detection analysis, representing a novel strategy in detecting other NTMs.

Differential diagnosis of disseminated Mycobacterium avium and Mycobacterium tuberculosis infection in HIV patients using duplex PCR

Background: Disseminated Mycobacterium avium complex (MAC) and Mycobacterium tuberculosis infections have almost similar clinical presentations but require different therapeutic management. Materials & methods: A duplex PCR was designed based on the sequence variation between the genes encoding catalase-peroxidase (KatG) of M. avium complex and M. tuberculosis, so as to discriminate MAC, M. tuberculosis and mixed mycobacterial (MAC + M. tuberculosis) infections in HIV patients. Results: An accurate, single-step differential diagnosis of disseminated mycobacterial infections in HIV patients was achieved with specific detection of a single band each for M. avium (120 bp) and M. tuberculosis (90 bp) and two bands for the mixed (120 and 90 bp) infections. Conclusion: katG gene-based duplex PCR can facilitate quick differential diagnosis of disseminated MAC and M. tuberculosis infections in HIV patients.

Genotypic and phenotypic characterization of Mycobacterium tuberculosis resistance against fluoroquinolones in the northeast of Iran

BACKGROUND

Fluoroquinolones are broad-spectrum antibiotics that are recommended, and increasingly important, for the treatment of multidrug-resistant tuberculosis (MDR-TB). Resistance to fluoroquinolones is caused by mutations in the Quinolone Resistance Determining Region (QRDR) of gyrA and gyrB genes of Mycobacterium tuberculosis. In this study, we characterized the phenotypic and genotypic resistance to fluoroquinolones for the first time in northeast Iran.

METHODS

A total of 123 Mycobacterium tuberculosis isolates, including 111 clinical and 12 collected multidrug-resistant isolates were studied. Also, 19 WHO quality control strains were included in the study. The phenotypic susceptibility was determined by the proportion method on Löwenstein-Jensen medium. The molecular cause of resistance to the fluoroquinolone drugs ofloxacin and levofloxacin was investigated by sequencing of the QRDR region of the gyrA and gyrB genes.

RESULTS

Among 123 isolates, six (4.8%) were fluoroquinolone-resistant according to phenotypic methods, and genotypically three of them had a mutation at codon 94 of the gyrA gene (Asp→ Gly) which was earlier reported to cause resistance. All three remaining phenotypically resistant isolates had a nucleotide change in codon 95. No mutations were found in the gyrB gene. Five of the 19 WHO quality control strains, were phenotypically fluoroquinolone-resistant, four of them were genotypically resistant with mutations at codon 90, 91 of the gyrA gene and one resistant strain had no detected mutation.

CONCLUSIONS

Mutation at codon 94 of the gyrA gene, was the main cause of fluoroquinolone resistance among M. tuberculosis isolates in our region. In 3/6 fluoroquinolone-resistant isolates, no mutations were found in either gyrA or gyrB. Therefore, it can be concluded that various other factors may lead to fluoroquinolone resistance, such as active efflux pumps, decreased cell wall permeability, and drug inactivation.

COVID-19 target: A specific target for novel coronavirus detection

An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. We, for the first time, detected ORF8 gene as a potential target for the detection of the novel coronavirus. Unlike previous reported genes (RdRP, E and N genes), ORF8 is entirely specific to the novel coronavirus (COVID-19) and has no cross-reactivity with other kinds of coronavirus. Accordingly, ORF8 gene can be used as an additional confirmatory assay.

Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay

The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.

Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of Mycobacterium Species: A Pilot Study

BACKGROUND

The line probe assay (LPA) is one of the most accurate diagnostic tools for detection of different Mycobacterium species. Several commercial kits based on the LPA for detection of Mycobacterium species are currently available. Because of their high cost, especially for underdeveloped and developing countries, and the discrepancy of non-tuberculous mycobacteria (NTM) prevalence across geographic regions, it would be reasonable to consider the development of an in-house LPA. The aim of this study was to develop an LPA to detect and differentiate mycobacterial species and to evaluate the usefulness of PCR-LPA for direct application on clinical samples.

METHODS

One pair of biotinylated primers and 15 designed DNA oligonucleotide probes were used based on multiple aligned internal transcribed spacer (ITS) sequences. Specific binding of the PCR-amplified products to the probes immobilized on nitrocellulose membrane strips was evaluated by the hybridization method. Experiments were performed three times on separate days to evaluate the assay's repeatability. The PCR-LPA was evaluated directly on nine clinical samples and their cultivated isolates.

RESULTS

All 15 probes used in this study hybridized specifically to ITS sequences of the corresponding standard species. Results were reproducible for all the strains on different days. Mycobacterium species of the nine clinical specimens and their cultivated isolates were correctly identified by PCR-LPA and confirmed by sequencing.

CONCLUSION

In this study, we describe a PCR-LPA that is readily applicable in the clinical laboratory. The assay is fast, cost-effective, highly specific, and requires no radioactive materials.

Candida coinfection among patients with pulmonary tuberculosis in Asia and Africa; A systematic review and meta-analysis of cross-sectional studies

Diagnosis of fungal co-infections in patients suffering from pulmonary tuberculosis has critical importance. Therefore, we aimed to determine the prevalence of candida coinfection in patients with pulmonary tuberculosis. The present systematic review of cross-sectional studies was conducted based on the Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) Protocol. Studies published online in English from January 2001 to March 2019 were assessed. Literature search was done in Web of Science, MEDLINE/PubMed, and Scopus databases and search engines using keywords combinations of "pulmonary fungi", "pulmonary coinfection", OR "pulmonary mycosis", "pulmonary fungal infections/agents", OR "polymicrobial infection", OR "secondary infection", OR "mixed infections", "pulmonary candidiasis", "fungi coinfection", "fungal co-colonization", AND "pulmonary tuberculosis", OR "pulmonary TB", AND "Asia", AND "Africa". Data was analyzed using Comprehensive Meta-Analysis software (CMA). Heterogeneity between studies was evaluated by Cochran's Q and I² tests. The pooled prevalence of candida coinfection among patients with pulmonary tuberculosis was 25.7% (95% CI: 23.7-27.9). C. albicans was the most prevalent Candida spp. with a pooled prevalence of 65.8% (95% CI: 54.3-75.7). Risk factors of candida coinfection were smoking, diabetes, advanced age, and low body mass index. The present review showed a high rate of candida coinfection among patients suffering from pulmonary tuberculosis. So, appropriate measures are necessary to early diagnose and treat these infections.