CRISPR detection of circulating cell-free Mycobacterium tuberculosis DNA in adults and children, including children with HIV: a molecular diagnostics study.

BACKGROUND: Tuberculosis remains a leading cause of global mortality, especially for adults and children living with HIV (CLHIV) underdiagnosed by sputum-based assays. Non-sputum-based assays are needed to improve tuberculosis diagnosis and tuberculosis treatment monitoring. Our aim in this study was to determine whether ultrasensitive detection of Mycobacterium tuberculosis cell-free DNA (Mtb-cfDNA) in blood can diagnose tuberculosis and evaluate tuberculosis treatment responses. METHODS: In this molecular diagnostics study we analysed archived serum from two patient populations evaluated for tuberculosis in Eswatini and Kenya to detect Mtb-cfDNA, analysing serum from all individuals who had both sufficient serum volumes and clear diagnostic results. An optimised CRISPR-mediated tuberculosis (CRISPR-TB) assay was used to detect Mtb-cfDNA in serum at enrolment from adults and children with presumptive tuberculosis and their asymptomatic household contacts, and at enrolment and during tuberculosis treatment from a cohort of symptomatic CLHIV at high risk for tuberculosis, who provided longitudinal serum at enrolment and during tuberculosis treatment. FINDINGS: CRISPR-TB identified microbiologically and clinically confirmed tuberculosis cases in the predominantly HIV-negative Eswatini adult cohort with 96% sensitivity (27 [96%] of 28, 95% CI 80-100) and 94% specificity (16 [94%] of 17, 71-100), and with 83% sensitivity (5 [83%] of 6, 36-100) and 95% specificity (21 [95%] of 22, 77-100) in the paediatric cohort, including all six cases of extrapulmonary tuberculosis. In the Kenyan CLHIV cohort, CRISPR-TB detected all (13 [100%] of 13, 75-100) confirmed tuberculosis cases and 85% (39 [85%] of 46, 71-94) of unconfirmed tuberculosis cases diagnosed by non-microbiological clinical findings. CLHIV who were CRISPR-TB positive at enrolment had a 2·4-times higher risk of mortality by 6 months after enrolment. Mtb-cfDNA signal decreased after tuberculosis treatment initiation, with near or complete Mtb-cfDNA clearance by 6 months after tuberculosis treatment initiation. INTERPRETATION: CRISPR-mediated detection of circulating Mtb-cfDNA shows promise to increase the identification of paediatric tuberculosis and HIV-associated tuberculosis, and potential for early diagnosis and rapid monitoring of tuberculosis treatment responses. FUNDING: US Department of Defense, National Institute of Child Health and Human Development, National Institute of Allergy and Infectious Diseases, University of Washington Center for AIDS Research, and the Weatherhead Presidential Endowment fund.

Cervical lymph node tuberculosis and TNF, IL8, IL10, IL12B and IFNG polymorphisms.

Cervical lymph node tuberculosis (LNTB) is the most common manifestation of extrapulmonary tuberculosis, resulting from the interaction of environmental and genetic factors. The immune response against TB is regulated by several cytokines, which have single nucleotide polymorphisms (SNPs), leading to different levels of expression. The aim of this study was to evaluate the association of LNTB with the TNF, IL8, IL10, IL12B and IFNG gene polymorphisms in Mexican patients. We investigated the association of ten SNPs in 14 patients with LNTB and 138 healthy controls. Significant differences were found for the allele TNF-238A (P=0.03) and the genotypes TNF-238GA (P=0.03), IL8+396GG (P=0.01) and IL12B+1188CC (P=0.04). Allele IL8+781C showed some association trend (P=0.08). Haplotypes TNF-AA and IL10-GTA were of susceptibility, whereas haplotype IL8-ATT was of protection. No association was found with IFNG. The association of these polymorphisms with extrapulmonary TB was compared in different populations. Our results suggest that these cytokine SNPs may influence the manifestation of LNTB in Mexican patients; however, we are aware of the limitations of our study, so it is necessary to make a replica using a larger sample of patients, as well as an increased number of cytokines with SNPs.

Identification of Differentially Expressed Genes Associated with Lymph Node Tuberculosis by the Bioinformatic Analysis Based on a Microarray.

To identify candidate key genes and pathways associated with lymph node tuberculosis (LNTB) and reveal the potential molecular mechanisms of LNTB development. Gene expression profile of GSE63548 was downloaded from the Gene Expression Omnibus (GEO) database. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of differentially expressed genes (DEGs) were analyzed by DAVID, and the protein-protein interaction (PPI) network was performed from STRING database. Furthermore, Cytoscape was used to integrate the network of transcription factor (TF) target and miRNA target. A total of 239 DEGs were screened out. Based on the DEGs, a miRNA of hsa-miR-4536 and 28 TFs, such as GATA1, JUND, NR2F1, POU1F1, and RELB, were obtained. Pathway enrichment analyses revealed that DEGs were mainly enriched in the pathways of regulation of lipolysis in adipocytes, vascular smooth muscle contraction, fat digestion and absorption, NOD-like receptor, and TNF signaling pathway. Furthermore, 53 nodes and 241 interactions were identified in the PPI network. In addition, the integrated regulatory network showed that CXCL9, CD36, LEP, ACACB, ALDH1A3, GPX3, STAT1, and LPL were the target genes of hsa-miR-4536. This study revealed the candidate key genes and pathways that are involved in the pathogenesis of LNTB, which will provide potential therapeutic targets for the treatment of LNTB.

Epidemiology of tuberculous lymphadenitis in Denmark: A nationwide register-based study.

BACKGROUND: Tuberculous lymphadenitis (TBLA) is the most common extrapulmonary manifestation of tuberculosis (TB), often claimed to be reactivation. We aimed to describe the epidemiology of TBLA in Denmark, as it has not previously been investigated specifically although extrapulmonary TB has been associated with an increased long-term mortality and delays in the diagnosis. METHODS: Register-based study of all patients notified with TBLA in Denmark from 2007 through 2016 utilizing six different nationwide registers. Patients were identified through the national TB surveillance register, and the diagnosis evaluated based on microbiology, pathology and/or clinical assessment. RESULTS: In total, 13.5% (n = 489) of all TB patients in Denmark had TBLA with annual proportions from 9.4 to 15.7%. Most patients were immigrants between 25-44 years. Incidence rates ranged from as high as 1,014/100,000 for Nepalese citizens to as a low as 0.06/100,000 for Danes. Danes had a significant higher median age and significant more risk factors and comorbidities, as well as an increased overall mortality, compared with immigrants (p<0.05). A significant and much higher proportion of unique MIRU-VNTR genotypes were seen among TBLA patients compared to other TB manifestations. CONCLUSION: In Denmark, TBLA is a common manifestation of TB, especially in young immigrants from high-incidence countries. In Danes, it is a rare disease manifestation and associated with higher morbidity and mortality. To our knowledge, this is the first study suggesting that TBLA is predominantly associated with reactivation of latent TB infection based on genotyping although this remains to be clarified.

Detection of Mycobacterium tuberculosis from paraffin-embedded tissues by GeneXpert MTB/RIF.

GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods.

Role of Xpert MTB/RIF in differentiating tuberculosis from sarcoidosis in patients with mediastinal lymphadenopathy undergoing EBUS-TBNA: a study of 147 patients.

BACKGROUND: In patients with intrathoracic lymphadenopathy, differentiating tuberculosis from sarcoidosis is often difficult. We hypothesized that Xpert MTB/RIF assay, a semi-automated hemi-nested PCR would help in this regard. OBJECTIVE: To evaluate the performance of Xpert MTB/RIF in the differential diagnosis of tuberculosis and sarcoidosis. METHODS: This was a retrospective analysis of patients with intrathoracic lymphadenopathy who underwent endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA), and were diagnosed as either tuberculosis or sarcoidosis. The results of Xpert MTB/RIF assay, tuberculin skin test and endosonographic characteristics (heterogeneous echotexture and coagulation necrosis sign) of the lymph nodes were compared between the two groups. RESULTS: During the study period, 465 EBUS procedures were performed and a diagnosis of sarcoidosis (n=94) or tuberculosis (n=53) was made in 147 patients. Xpert MTB/RIF was positive in 26 (49.1%) and two (2.1%) patients with tuberculosis and sarcoidosis, respectively. The sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF in the diagnosis of tuberculosis were 49.1 %, 97.9%, 92.9% and 77.3%, respectively. The presence of any of the four features namely positive Xpert MTB/RIF, positive tuberculin skin test, heterogeneous echotexture of the lymph nodes, or the presence of endosonographic coagulation necrosis sign yielded a sensitivity and negative predictive value of 83.0% and 88.0%, respectively in the diagnosis of tuberculosis versus sarcoidosis. CONCLUSIONS: Xpert MTB/RIF has good specificity and positive predictive value in the diagnosis of tuberculosis, and is a useful investigation in separating tuberculosis from sarcoidosis.

Relationship between human LTA4H polymorphisms and extra-pulmonary tuberculosis in an ethnic Han Chinese population in Eastern China.

Two single nucleotide polymorphisms in Leukotriene A4 hydrolase (LTA4H) gene were reported to be associated with protection from pulmonary tuberculosis in Vietnamese population. But these associations were not found in the Russians. To investigate the association of LTA4H polymorphisms with tuberculosis in a Han Chinese population in Eastern China, we genotyped 5 SNPs of LTA4H gene in 743 of pulmonary tuberculosis patients, 372 of extra-pulmonary tuberculosis patients and 888 of healthy controls individuals. The CC and TT homozygotes of rs1978331 and rs2540474 were identified to have higher rates (P < 0.01) and be risk factors in the patients with extra-pulmonary tuberculosis (OR = 1.412; 95% CI = 1.104-1.804 and(OR = 1.380; 95% CI = 1.080-1.764). However, no significant association was found between any of the SNPs and pulmonary tuberculosis. In the extra-pulmonary tuberculosis subgroups. LTA4H gene were significantly associated with tuberculous meningitis, lymph node tuberculosis, bone tuberculosis and other extra-pulmonary tuberculosis except for pleural tuberculosis. The present findings suggest that polymorphisms in the LTA4H gene may affect susceptibility to extra-pulmonary tuberculosis and change the risk of developing the disease in the Han nationality in the East China.

Mannose-binding lectin gene polymorphisms and mycobacterial lymphadenitis in young patients.

BACKGROUND: Tuberculosis (TB) has recently re-emerged as a major public health threat worldwide. There is strong evidence that host genetic factors influence individual susceptibility to TB and that, once infected, young children and immunocompromised patients are at increased risk for mycobacterial disease and progression to extrapulmonary lymphadenitis. METHODS: The association between polymorphisms of mannose-binding lectin and the susceptibility of 139 children with cervical mycobacterial lymphadenitis and infected with Mycobacterium tuberculosis was investigated. RESULTS: The frequencies of genotypes A/B and B/B, based on codon 54 polymorphisms, were significantly different in TB-infected versus healthy control subjects. The frequency of the A/B genotype was significantly lower in TB-infected children (odds ratio = 0.56; 95% confidence interval: 0.36-0.87; P = 0.01), and the B/B genotype was significantly higher in TB-infected children (odds ratio = 4.68; 95% confidence interval: 1.35-16.3; P = 0.01) compared with healthy controls. The HYB haplotype appeared significantly more often to be protective in the healthy control population (odds ratio = 0.23; 95% confidence interval: 0.05-0.96; P = 0.046). Ex vitro phagocytosis assays indicated that high-expression mannose-binding lectin genotypes are associated with an increased risk of infection with M. tuberculosis. CONCLUSIONS: The present study suggests that mannose-binding lectin can protect against TB or predispose the host to the disease depending on the haplotype pair of the host. The low-expression genotype A/B and the HYB haplotype may be associated with protection against intracellular mycobacterial infections, whereas the high-expression genotype A/A may confer susceptibility to disease.

Genetic association study suggests a role for SP110 variants in lymph node tuberculosis but not pulmonary tuberculosis in north Indians.

Ethnic specificity is a key determinant in understanding the association of genetic variants with outcome of disease susceptibility. SP110, a component of the nuclear body, has been subjected to association studies with conflicting results. In this study we probed SP110 variants in pulmonary (PTB) and lymph node tuberculosis (LNTB) cases to explore their role in controlling susceptibility to Mycobacterium tuberculosis infection in north Indians. We genotyped 24 SP110 variants in over 140 north Indian tuberculosis cases and 78 ethnicity-matched controls. The SP110 gene variants were available from public databases. The cases and controls were free of any population stratification when subjected to Eigenstrat principal component analysis. Genotyping was carried out using the Sequenom MassARRAY platform. Applying exclusion criteria, 11 single nucleotide polymorphisms (SNPs) of the LNTB panel and 13 SNPs of the PTB panel passed all filters and were analyzed further. No significant association was observed between SP110 variants and PTB. Surprisingly, we discovered evidence of an association of SP110 variants with LNTB, a form of extrapulmonary tuberculosis, at 3 loci, namely, rs6436915, rs1427294, and rs1346311. When permutations analysis (n = 10,000) of allelic p values was undertaken, only rs1427294 passed the test with its p value remaining statistically significant. The C allele of rs1427294 exhibited a 5-fold risk of developing LNTB. No significant haplotypes were observed. In the pilot study presented here, our results provide evidence for the first time that SP110 may be a risk determinant locus in LNTB while confirming a doubtful role of SP110 in PTB in north Indians. In general, the results might indicate a role of SP110 variants in extrapulmonary tuberculosis rather than PTB.

A novel mutation of the IL12RB1 gene in a child with nocardiosis, recurrent salmonellosis and neurofibromatosis type I: first case report from Thailand.

Genetic defects of interleukin (IL)-12/23-and interferon (IFN)-gamma-mediated immunity can cause increased susceptibility to intracellular microbes. Among these defects, a mutation of the gene encoding the IL-12 receptor beta1 (IL-12Rbeta1) is the most common worldwide. A 12-year old Thai boy with pre-existing neurofibromatosis type 1 (NF1) was evaluated for primary immunodeficiency after a history of tuberculous lymphadenitis, recurrent Salmonella infections and nocardiosis. Flow cytometry of phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) revealed a defect in the IL-12Rbeta1 surface expression. A genetic study showed a novel nonsense homozygous mutation of the IL12RB1 gene in exon 4 (402C > A), confirming the diagnosis of IL-12Rbeta1 deficiency. This is the first case report of a primary IL-12Rbeta1 deficiency in Thailand with the interesting finding of a coexisting NF1.

[The phenotypes of haptoglobin and the level of acute-phasic proteins in the sera of children with local form of intrathoracic tuberculosis]. / Fenotipy gaptoglobina i uroven' ostrofaznykh belkov v syvorotke krovi u detei s lokal'nymi formami vnutrigrudnogo tuberkuleza.

Seventy-seven children aged 4-12 years who had local forms of primary intrathoracic tuberculosis were examined. On admission to and discharge from hospital, haptoglobin (Hp) was phenotyped and the content of Hp was measured, and the activity of alpha1-antitrypsin (alpha1-AT) was determined. In all ill children, the distribution of Hp phenotypes did not differ from the normal level, but all patients with tuberculous pleurisy were found to be carriers of Hp1 gene (among them the phenotype Hp 2-2 was absent and the minor variant of Hp 1-1 was detectable in half the cases). In patients of this group, alpha1-AT acted as a typical acute phase reagent and remained moderately increased by the termination of treatment in the vast majority of the examinees. On the contrary, on admission the content of Hp was to be decreased. Its increase was natural only in patients with tuberculous pleurisy. The level of Hp was associated with its phenotype. Carriers of Hp1-1 had elevated levels of Hp in the overwhelming majority of cases whereas those of Hp 2-2 had its decreased levels. It is concluded that in children with primary tuberculosis, the serum level of Hp may not be used as an indicator of the activity of the process. Possible causes and the values of decreased levels of circulating Hp in children with primary tuberculosis are discussed in the paper.

The Arg753GLn polymorphism of the human toll-like receptor 2 gene in tuberculosis disease.

Toll-like receptor 2 (TLR2), a member of the Toll-like receptor family, plays an important role in recognition of, and subsequent immune response activation against, mycobacteria. The genetic polymorphism of TLR2 (arginine to glutamine substitution at residue 753 (Arg753Gln)) has been associated with a negative influence on TLR2 function, which may, in turn, determine the innate host response to mycobacteria. The aim of the present study was to investigate the Arg753Gln single nucleotide polymorphism of the TLR2 gene in tuberculosis (TB) patients compared to healthy controls. A retrospective case/control study was carried out. The Arg753Gln polymorphism of the TLR2 gene was studied in 151 TB patients compared to 116 ethnically and age-matched healthy control subjects. The TLR2 polymorphism (adenine (A) allele) was observed in 17.9 and 7.7% of TB patients and controls, respectively. When the ratios of the three genotypes were compared between the two groups, the AA genotype was found to be more significantly associated with TB. Allele frequencies for guanine (G) and A were found to be 0.95 and 0.05 in the control group and 0.86 and 0.14 in the TB patient group, respectively. The risk of developing TB disease was increased 6.04- and 1.60-fold for carriers of the AA and GA genotypes, respectively. In conclusion, the present data suggest that the arginine to glutamine substitution at residue 753 polymorphism of the Toll-like receptor 2 gene influences the risk of developing tuberculosis.

Aspiration cytology for diagnosis of tuberculosis--perspectives in India.

Tuberculosis (TB) a common cause of mortality can readily be diagnosed by fine needle aspiration. The technique is a simple, cost effective, out patient procedure with a high diagnostic accuracy both in adults and children. The diagnostic morphologic findings comprise of epithelioid cell granulomas and giant cells with or without necrosis. Often an acute inflammatory exudate is obtained. Stain for acid fast bacilli immensely augments diagnosis especially in cases where necrosis or an inflammatory exudate is obtained. Culture studies on aspirated material are time consuming though diagnosis is enhanced. PCR can be applied to detect mycobacterial DNA and has been applied on aspirated material and found to be more sensitive in the detection of tuberculosis. In children TB of lymph nodes is readily identified and so also from other sites such as bone and soft tissues. In children FNAC also plays a role in detection of BCG adenitis, infection with atypical mycobacteria and co-existing infections such as HIV and AIDS.

Quantitative PCR of mycobacterial and propionibacterial DNA in lymph nodes of Japanese patients with sarcoidosis.

BACKGROUND: The causes of sarcoidosis are not known. The DNA of Mycobacterium tuberculosis has been detected in some sarcoid lesions. In Japan, Propionibacterium acnes has been isolated from such lesions, but whether this indigenous bacterium is related to the disease is unclear. We used PCR to estimate the number of genomes of these bacteria in sarcoid lesions, to identify any link between sarcoidosis and these two bacterial species. METHODS: We examined formalin-fixed and paraffin-embedded sections of biopsy and surgical samples from lymph nodes of 15 patients with sarcoidosis, 15 patients with tuberculosis, and 15 patients with gastric cancer (controls). Quantitative PCR was done to amplify segments of 16 S ribosomal RNA of P. acnes and P. granulosum and of insertion sequence 6110 of M. tuberculosis. PCR products were identified and the quantities of the products were estimated in terms of the fluorescence of oligonucleotide reporter probes. The numbers of bacterial genomes in samples were estimated from standard curves of serially diluted bacterial DNA. FINDINGS: Genomes of M. tuberculosis were found in samples from all 15 patients with tuberculosis, from three patients with sarcoidosis, and in one control sample. Genomes of P. acnes were found in 12 of the 15 patients with sarcoidosis, in two tuberculosis patients, and three controls. The difference in the estimated number of P. acnes genomes between individuals with and without sarcoidosis was similar to that in the number of M. tuberculosis between people with and without tuberculosis. There were 5x10(5) P. acnes genomes in sarcoidosis and 3x10(6) M. tuberculosis genomes in tuberculosis, respectively, on average per microg of total DNA. The three patients with sarcoidosis but without P. acnes all had P. granulosum DNA in their biopsy samples; the number of genomes of the bacterium was 5x10(5). INTERPRETATION: These findings suggest that propionibacteria had resided or proliferated ectopically in the sarcoid lesions, whether there was a connection with the disease or not. Propionibacteria are a more likely cause than mycobacteria of sarcoidosis.

Polymerase chain reaction for detection of Mycobacterium tuberculosis.

Rapid diagnosis of tuberculosis is essential, and therefore we use a polymerase chain reaction. In this report, we describe two cases of tuberculous lymphadenitis in childhood. Although histopathological findings were not specific for tuberculosis in both cases, distinct positive bands were amplified. For DNA diagnosis of tuberculosis, a lysis method of extracting chromosomal DNA from lipid-rich cell walls of mycobacteria is of critical importance. We made use of a simple lysozyme-proteinase K treatment for biopsied tissues. Although this extraction procedure was less efficient than those reported previously, it was considered sufficient for detecting mycobacterial DNA with the use of a highly sensitive polymerase chain reaction. We conclude that DNA amplification in combination with lysozyme lysis can be used routinely in clinical laboratories as a rapid and sensitive test for the diagnosis of tuberculosis.