Clinical characteristics and drug susceptibility profiles of Mycobacterium abscessus complex infection at a medical school in Thailand.

OBJECTIVES: This study investigated the differences in epidemiological and clinical data, and antimicrobial susceptibilities among different subspecies of Mycobacterium abscessus complex (MABSC) clinical isolates at a medical school in Thailand. METHODS: A total of 143 MABSC clinical isolates recovered from 74 patients were genotypically analyzed for erm(41), rrl, and rrs mutations, and antimicrobial susceptibilities were determined using a broth microdilution method. Patient characteristics and clinical outcomes were reviewed from the medical records. RESULTS: Seventy-four patients were infected with 28/74 (37.8%) M. abscessus subspecies abscessus (MAB), 43/74 (58.1%) M. abscessus subsp. massiliense (MMA), and 3/74 (4.1%) M. abscessus subsp. bolletii (MBO). The clinical findings and outcomes were generally indistinguishable between the three subspecies. All three subspecies of MABSC clinical isolates exhibited high resistance rates to ciprofloxacin, doxycycline, moxifloxacin, TMP/SMX, and tobramycin. MAB had the highest resistance rates to clarithromycin (27.8%, 20/72) and amikacin (6.9%, 5/72) compared to MBO and MMA, with p < 0.001 and p = 0.004, respectively. In addition, the rough morphotype was significantly associated with resistance to amikacin (8.9%, 5/56), clarithromycin (26.8%, 15/56), and imipenem (76.8%, 43/56) (p < 0.001), whereas the smooth morphotype was resistant to linezolid (57.1%, 48/84) (p = 0.002). In addition, T28 of erm(41), rrl (A2058C/G and A2059C/G), and rrs (A1408G) mutations were detected in 87.4% (125/143), 16.1% (23/143), and 9.1% (13/143) of MABSC isolates, respectively. CONCLUSIONS: Three MABSC subspecies caused a variety of infections in patients with different underlying comorbidities. The drug susceptibility patterns of the recent circulating MABSC strains in Thailand were different among the three MABSC subspecies and two morphotypes.

Proteomic Profiles and Protein Network Analysis of Primary Human Leukocytes Revealed Possible Clearance Biomarkers for Staphylococcus aureus Infection.

Staphylococcus aureus is a serious pathogen that can survive within host cells after a typical course of treatment completion, leading to chronic infection. Knowledge of host proteomic patterns after clearance of this pathogen from cells is limited. Here, we looked for S. aureus clearance biomarkers produced by in vitro-infected leukocytes. Extracellular proteins from primary human leukocytes infected with S. aureus ATCC 25923 were investigated as possible treatment-monitoring clearance biomarkers by applying a proteomics approach combining liquid chromatography with tandem mass spectrometry (LC-MS/MS) and protein interaction network analysis. It was found that the expression patterns of proteins secreted by S. aureus-infected leukocytes differed among stages of infection. Proteomic profiles showed that an ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2 (ATP8A2) was expressed in the clearance stage and was not detected at any earlier stage or in uninfected controls. Protein network analysis showed that TERF2 (telomeric repeat-binding factor 2), ZNF440 (zinc finger protein 440), and PPP1R14A (phosphatase 1 regulatory subunit 14A) were up-regulated, while GLE1, an essential RNA-export mediator, was suppressed in both infection and clearance stages, suggesting their potential roles in S. aureus infection and clearance. These findings are the first to report that the ATP8A2 has potential as a clearance biomarker for S. aureus infection.

Analysis of bacterial and fungal communities in fermented fish (pla-ra) from Northeast Thailand.

Our aim was to explore the microbial community composition (bacteria and fungi) of fermented fish (pla-ra) from Northeast Thailand. We also made functional predictions concerning these microbial communities. The association between the microbiota and odor intensity was also analyzed. Fourteen samples of 1-year fermented fish samples derived from seven local markets in Khon Kaen, Northeast Thailand were used. The microbial community composition of each was investigated by sequencing the V1-V9 regions of the 16S rRNA gene (bacteria) and the ITS gene (fungi) using an Illumina MiSeq platform. Functional prediction analysis was conducted through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the use of the bacterial 16S rRNA gene sequences. The bacterial communities were rich, comprising 402 genera from 28 phyla, including such genera as Tetragenococcus, Staphylococcus, Virgibacillus, Lactobacillus and Lentibacillus. The fungal communities comprised 7 phyla and 60 genera, such as Heterobasidion, Densospora, Exophiala and Monascus. The bacterial community functional analysis revealed an association with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases) with 17 subfunctions, showing the richness of bacterial community functions. Odor-association analysis revealed that Brevibacterium, Brachybacterium and Chromohalobacter were more abundant in the weak-odor group, while Noviherbaspirillum was more abundant in the strong-odor group. This study provides a preliminary analysis of pla-ra microbial community structure and function in popular traditional Thai foods. Functional prediction analysis might be helpful to improve our knowledge of the microbiota in fermented fish.

Optimized analysis parameters of variant calling for whole genome-based phylogeny of Mycobacteroides abscessus.

Whole-genome sequence (WGS) analysis provides the best resolution for reconstructing bacterial phylogeny. However, the resulting tree could vary according to parameters used in the WGS pipeline, making it difficult to compare results across multiple studies. This study compares effects on phylogenies when applying different parameter stringencies. We used as the study model to optimize parameters strains of Mycobacteroides abscessus serially isolated at various intervals, isolates known to represent persistent infection (PI) cases or re-infection (RI) cases and isolates from different subspecies. Un-optimized parameters with low stringency provided an excessive number of SNPs (823) compared to the optimized setting (3 SNPs) between paired strains isolated 1 day apart from PI cases, discordant tree topology and misclassification of subspecies and of instances of RI. We demonstrated that using high-quality variants provides more accuracy for recognizing serial isolates of the same clone versus different clones and for phylogenetic analysis of M. abscessus. Our approach might be used as a model for analyses requiring phylogenetic reconstruction of other bacteria.

Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017.

Multidrug-resistant tuberculosis (MDR TB), pre-extensively drug-resistant tuberculosis (pre-XDR TB), and extensively drug-resistant tuberculosis (XDR TB) complicate disease control. We analyzed whole-genome sequence data for 579 phenotypically drug-resistant M. tuberculosis isolates (28% of available MDR/pre-XDR and all culturable XDR TB isolates collected in Thailand during 2014-2017). Most isolates were from lineage 2 (n = 482; 83.2%). Cluster analysis revealed that 281/579 isolates (48.5%) formed 89 clusters, including 205 MDR TB, 46 pre-XDR TB, 19 XDR TB, and 11 poly-drug-resistant TB isolates based on genotypic drug resistance. Members of most clusters had the same subset of drug resistance-associated mutations, supporting potential primary resistance in MDR TB (n = 176/205; 85.9%), pre-XDR TB (n = 29/46; 63.0%), and XDR TB (n = 14/19; 73.7%). Thirteen major clades were significantly associated with geography (p<0.001). Clusters of clonal origin contribute greatly to the high prevalence of drug-resistant TB in Thailand.

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

BACKGROUND: The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS: We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS: A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS: Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).

Comparison of different hypervariable regions of 16S rRNA for taxonomic profiling of vaginal microbiota using next-generation sequencing.

The exploration of vaginal microbiota by using next-generation sequencing (NGS) of 16S ribosomal RNA (rRNA) gene is widely used. Up to now, different hypervariable regions have been selected to study vaginal microbiota by NGS and there is no standard method for analysis. The study aimed to characterize vaginal microbiota from clinical samples using NGS targeting the 16S rRNA gene and to determine the performance of individual and concatenated hypervariable region sequences to generate the taxonomic profiles of the vaginal microbiota. Fifty-one vaginal DNA samples were subjected to 16S rRNA gene NGS based on the Ion Torrent PGM platform with the use of two primer sets spanning seven hypervariable regions of the 16S rRNA gene. Our analysis revealed that the predominant bacterial genera were Lactobacillus, Gardnerella and Atopobium, which accounted for 78%, 14% and 2%, respectively, of sequences from all vaginal bacterial genera. At the species level, Lactobacillus iners, Gardnerella vaginalis and Atopobium vaginae accounted for 72%, 10% and 6%, respectively, of the bacterial cells present. Analyses using the V3 region generally indicated the highest bacterial diversity followed by the V6-V7 and V4 regions, while the V9 region gave the lowest bacterial resolution. NGS based on the 16S rRNA gene can give comprehensive estimates of the diversity of vaginal bacterial communities. Selection of sequences from appropriate hypervariable regions is necessary to provide reliable information on bacterial community diversity.

Multi-locus Sequence Typing and Whole Genome Sequence Analysis of Cryptococcus neoformans Isolated from Clinical Specimens in Vajira Hospital, Bangkok, Thailand.

The basidiomycete yeast Cryptococcus neoformans causes disease in immunocompromized patients. Whole genome sequencing (WGS) technology provides insights into the molecular epidemiology of C. neoformans. However, the number of such studies is limited. Here we used WGS and multilocus sequence typing (MLST) to determine the genetic diversity of C. neoformans isolates and genetic structures of their populations among patients admitted to a single hospital in Bangkok, Thailand. Seven isolates from six patients collected during 1 year were identified as C. neoformans sensu stricto according to colony morphology, microscopy, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nucleotide sequence analysis of internal transcribed sequences. These isolates were sensitive to the antifungal drugs amphotericin B, fluconazole, 5-flucytosine, voriconazole, itraconazole and posaconazole and were mating type α and molecular type VNI. MLST analysis identified ST4, ST5 and ST6. We further employed WGS to determine the genetic diversity and relationships of C. neoformans isolated here combined with C. neoformans sequences data acquired from a public database (n = 42). We used the data to construct a phylogenetic tree. WGS provided additional genomics data and achieved high discriminatory power for identifying C. neoformans isolates isolated in Thailand. This report further demonstrates the applicability of WGS analysis for conducting molecular epidemiology and provides insight into the genetic diversity of C. neoformans isolates from one hospital in Thailand.

Detection and genotyping of Helicobacter pylori in saliva versus stool samples from asymptomatic individuals in Northeastern Thailand reveals intra-host tissue-specific H. pylori subtypes.

BACKGROUND: Two-thirds of the world's population is thought to be infected by Helicobacter pylori. Although most people infected with H. pylori are asymptomatic, this pathogen is associated with several gastric pathologies including cancer. The risk factors for colonization are still unclear and the genetic diversity within individual hosts has never been clearly investigated. RESULT: This study determined the prevalence of, and explored risk factors for, H. pylori infection directly from paired saliva (n = 110) and stool (n = 110) samples from asymptomatic persons in Northeast Thailand. Samples were subjected to indirect immunofluorescence assay (IFA), 16S rRNA-based real-time PCR and vacA-based semi-nested PCR. Partial vacA gene sequences of H. pylori were compared between saliva and stool samples. The overall prevalence of H. pylori infection in our asymptomatic study population was 64%. Age, gender, occupation and frequency of brushing teeth were not found to be associated with H. pylori colonization. The vacA gene was successfully sequenced from both saliva and stool samples of 12 individuals. For seven of these individuals, saliva and stool sequences fell into different clusters on a phylogenetic tree, indicating intra-host genetic variation of H. pylori. CONCLUSION: This study reports a high prevalence of H. pylori infection in asymptomatic persons in this region of Thailand and demonstrates that genotypes (vacA gene sequences) of H. pylori may differ between the oral cavity and intestinal tract.

In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer.

BACKGROUND: Whole-genome sequencing is increasingly used in clinical diagnosis of tuberculosis and study of Mycobacterium tuberculosis complex (MTC). MTC consists of several genetically homogenous mycobacteria species which can cause tuberculosis in humans and animals. Regions of difference (RDs) are commonly regarded as gold standard genetic markers for MTC classification. RESULTS: We develop RD-Analyzer, a tool that can accurately infer the species and lineage of MTC isolates from sequence reads based on the presence and absence of a set of 31 RDs. Applied on a publicly available diverse set of 377 sequenced MTC isolates from known major species and lineages, RD-Analyzer achieved an accuracy of 98.14 % (370/377) in species prediction and a concordance of 98.47 % (257/261) in Mycobacterium tuberculosis lineage prediction compared to predictions based on single nucleotide polymorphism markers. By comparing respective sequencing read depths on each genomic position between isolates of different sublineages, we were able to identify the known RD markers in different sublineages of Lineage 4 and provide support for six potential delineating markers having high sensitivities and specificities for sublineage prediction. An extended version of RD-Analyzer was thus developed to allow user-defined RDs for lineage prediction. CONCLUSIONS: RD-Analyzer is a useful and accurate tool for species, lineage and sublineage prediction using known RDs of MTC from sequence reads and is extendable to accepting user-defined RDs for analysis. RD-Analyzer is written in Python and is freely available at https://github.com/xiaeryu/RD-Analyzer .

RISK FACTORS FOR LATENT TUBERCULOSIS INFECTION AMONG HEALTH-CARE WORKERS IN NORTHEASTERN THAILAND.

Health-care workers (HCWs) are a high-risk population for acquiring Mycobacterium tuberculosis infection. Understanding the risk factors for latent tuberculosis infection (LTBI) could provide information to facilitate an appropriate tuberculosis (TB) control program. We aimed to determine the prevalence of, and risk factors for LTBI among HCWs in northeastern Thailand. Between 1 November 2013 and 30 September 2015, we examined 112 HCWs at Srinagarind Hospital, Khon Kaen Province in northeastern Thailand using the QuantiFERON®-TB Gold In-Tube (QFT) assay. Twenty-one [18.8%; 95% confidence interval (CI): 11.5- 26.0%] HCWs had a positive QFT result ­ all of whom were determined to have LTBI. The exposure risks and demographic data obtained from a questionnaire were compared between the 21 subjects who had a positive QFT assay and the 91 subjects who had a negative QFT assay. Multivariate analysis showed factors significantly associated with a positive QFT assay were: age ≥30 years (OR=18.88; 95%CI: 1.52-234.36), having worked as a nurse (OR=2.78; 95%CI: 1.19-6.49), having been employed at that job for ≥10 years (OR=8.78; 95%CI: 1.26-61.29) and having been exposed to known TB patients (OR=13.32: 95%CI: 1.61-110.04). Appropriate guidelines need to be developed, especially for these at-risk workers to prevent LTBI. These high-risk workers should also be considered for regular TB screening.

SXT ELEMENT, CLASS 1 INTEGRON AND MULTIDRUG-RESISTANCE GENES OF VIBRIO CHOLERAE ISOLATED FROM CLINICAL AND ENVIRONMENTAL SOURCES IN NORTHEAST THAILAND.

Emergence of multiple drug resistance in Vibrio cholerae has been increasing around the world including Northeast Thailand. In this study, 92 isolates of V. cholerae (50 O1 and 42 non-O1/non-O139 isolates) from clinical and environmental sources in Northeast Thailand were randomly selected and investigated for the presence of SXT element, class 1 integron and antimicrobial resistance genes. Genotypic-phenotypic concordance of antimicrobial resistance was also determined. Using PCR-based assays, 79% of V. cholerae isolates were positive for SXT element, whereas only 1% was positive for class 1 integron. SXT element harbored antimicrobial resistance genes, dfrA1 or dfr18, floR, strB, sul2, and tetA. Overall phenotypic-genotypic concordance of antimicrobial resistance was 78%, with highest and lowest value being for trimethoprim (83%) and chloramphenicol (70%), respectively. Ninety-two percent of V. cholerae O1 strains isolated from clinical sources harbored both dfrA1 (O1-specific trimethoprim resistance gene) and dfr18 (non-O1-specific trimethoprim resistance gene), whereas only 5% of V. cholerae non-O1/non-O139 strains harbored both genes. All V. cholerae O1 isolated from environmental source harbored dfr18 but 48% of V. cholerae non-O1/non-O139 harbored dfrA1. This study indicates that SXT element was the main contributor to the circulation of multiple-drug resistance determinants in V. cholerae strains in Northeast Thailand and that genetic exchange of SXT element can occur in both V. cholerae O1 and non-O1/non-O139 strains from clinical and environmental sources.

DOUBLE-STEP MULTIPLEX REAL TIME PCR WITH MELTING CURVE ANALYSIS FOR DETECTION AND DIFFERENTIATION OF MYCOBACTERIA IN SPUTUM.

Mycobacterium tuberculosis (M. tb) is a causative agent of tuberculosis, a worldwide public health problem. In recent years, the incidence of human mycobacterial infection due to species other than M. tb has increased. However, the lack of specific, rapid, and inexpensive methods for identification of mycobacterial species remains a pressing problem. A diagnostic test was developed for mycobacterial strain differentiation utilizing a double-step multiplex real time PCR together with melting curve analysis for identifying and distinguishing among M. tb, M. bovis BCG, other members of M. tb. complex, M. avium, and non-tuberculosis mycobacteria. The assay was tested using 167 clinical sputum samples in comparison with acid-fast staining and culturing. Using only the first step (step A) the assay achieved sensitivity and specificity of 81% and 95%, respectively. The detection limit was equivalent to 50 genome copies.

TRANSMISSION AND RISK FACTORS FOR LATENT TUBERCULOSIS INFECTIONS AMONG INDEX CASE-MATCHED HOUSEHOLD CONTACTS.

An understanding of the risk factors associated with acquiring and transmitting Mycobacterium tuberculosis (MTB) is required for controlling tuberculosis (TB). We aimed to determine the risk factors and transmission factors for latent tuberculosis infection (LTBI) in northeastern Thailand. Household contact persons (n = 70) and matched index patients with pulmonary TB (n = 42) who presented to Srinagarind Hospital, Khon Kaen, Thailand were interviewed from September 1, 2012 to March 31, 2014. LTBI was determined by positive results on both a tuberculin skin test and the QuantiFERON-TB Gold In-Tube test. Multivariate analysis of host and environmental risk factors was performed. Among contact persons, being aged 20 years (adjusted OR=14.0; 95% CI: 1.2-159.5), having a family relationship with a TB subject such as being a spouse or parent (adjusted OR=24.9; 95% CI: 2.4-263.9) and exposure to a TB subject for 5 hours/day (adjusted OR=9.2; 95% CI: 1.4-58.1) were risk factors for LTBI. Having a high bacillary load (adjusted OR=2; 95% CI: 1.26-3.17) or a moderate bacillary load (adjusted OR=1.39; 95% CI: 1.04-1.84) among TB subjects correlated with increased transmissibility compared to having a low bacillary load. The type of dwelling and density of household members were not found to be risk factors for LTBI in our study. We conclude being aged 20 years and having a relationship with a TB patient as a spouse or parent were risk factors for acquiring LTBI, and having a higher bacillary load was a risk factor for transmitting TB. Keywords: latent tuberculosis infection, transmission factor, risk factor, Mycobacterium tuberculosis, interferon-gamma release assay, Thailand

Evaluation of the QuantiFERON?-TB Gold In-Tube assay and tuberculin skin test for the diagnosis of Mycobacterium tuberculosis infection in northeastern Thailand.

BACKGROUND: The diagnosis of latent Mycobacterium tuberculosis infection (LTBI) is currently based on the immunological response of T-cells to M. tuberculosis (MTB) antigens. However, the QuantiFERON®-TB Gold In-Tube assay (QFT) has not yet been evaluated in the Thai adult population. OBJECTIVE: To evaluate the diagnostic performance and determine predictors of discordant results between the QFT and tuberculin skin test (TST). METHODS: Active tuberculosis (ATB) patients (n=54), close contacts (CCs) living in the same household as a TB patient (n=100) and healthy controls (HCs) (n=60) were interviewed and underwent the QFT and TST at Srinagarind Hospital in Thailand. Various cut-off values for the QFT (0.25-0.35 IU/mL) and TST (5-15 mm) were applied. RESULTS: The maximum agreement rate between the tests was 71.5% (κ=0.41) with cut-offs of 0.35 IU/mL and 10 mm or 0.25 IU/mL and 10 mm. Based on standard cut-off values (0.35 IU/mL and 10 mm) and using ATB patients and HCs as positive and negative controls, the TST was more sensitive than the QFT (87.0% vs. 66.7%, respectively), whereas the QFT was more specific than the TST (83.3% vs. 70.0%, respectively). Being underweight (OR 3.86, 95%CI 1.3-11.48) or overweight (OR 5.9, 95%CI 1.24-28.16) was significantly associated with TST+/QFT- results. Diabetes (OR 32.56, 95%CI 1.73-613.49) and poor or fair nutrition (OR 7.4, 95%CI 1.23-44.57) were significantly associated with TST-/QFT+ results. CONCLUSION: The TST should be used as a screening test based on its higher sensitivity, whereas the QFT should be used as a confirmatory test because of its higher specificity.

Epidemiology and identification of potential fungal pathogens causing invasive fungal infections in a tertiary care hospital in northeast Thailand.

Invasive fungal infections (IFIs) are life threatening and associated with a high mortality rate. Here, we describe the distribution of pathogens, host risk factors, and significance of fungi isolated from patients with IFIs. The study included 861 fungal isolates recovered between 2006 and 2011 from 802 patients at Srinagarind Hospital, Thailand. Based on the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group 2008 criteria, 28.5% (245/861 isolates) of the fungal isolates were considered to be causative agents of IFIs. The most common fungus was Candida albicans (46%, 396/861 isolates). However, the most common yeast causing IFIs was Cryptococcus neoformans (34.7%, 85/245 isolates), while the most common mould was Penicillium marneffei (10.6%, 26/245 isolates). Cryptococcosis was significantly associated with human immunodeficiency virus infections (P < 0.001). Trend analysis revealed that there was no significant increase in IFI cases (P = 0.34) from 2006 to 2011 or from 2007 to 2011 (P = 0.05), but there was a trend toward significant increases in candidiasis (P = 0.04). The fungal isolates were categorized according to the positive predictive value of their recovery in cultures as being true (>95%), moderate (5%-95%), and rare (<5%) pathogens. This classification system could facilitate the prediction of the likelihood of diseases caused by the isolated fungi.

Development of single-tube multiplex PCR for classification of Mycobacterium tuberculosis lineages based on large sequence polymorphisms.

Large sequence polymorphisms (LSPs) or regions of differences (RDs) are molecular epidemiological and evolutionary markers used to classify Mycobacterium tuberculosis (MTB) into East Asian (Beijing), Indo-Oceanic (IO), Euro-American (EuA) and East African Indian (EAI) lineages. The most used method is separate PCR and sequencing for each RD. We developed a single-tube multiplex PCR using four primer pairs specific to the four MTB lineages and a primer pair for species-specific RD9 with genomic DNA extracted from isolated colonies. The single-tube multiplex PCR produced lineage-specific amplicon patterns capable of differentiating the four MTB lineages. Sensitivity and specificity of the assay were 100% when differentiating MTB lineages from other species and strains of bacteria. The limit of detection of genomic MTB DNA was 12.5 ng. This single-tube multiplex PCR method offers a simple, rapid and reliable method for classification of MTB lineages based on LSPs.

T-CELL RESPONSES ASSESSED USING IGRA AND TST ARE NOT CORRELATED WITH AFB GRADE AND CHEST RADIOGRAPH IN PULMONARY TUBERCULOSIS PATIENTS.

A definitive marker determining the bacillary load of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), and hence disease severity, is required for patient monitoring and management. In this study, the association among T-cell responses based on the interferon-gamma release assay (IGRA) and the tuberculin skin test (TST), the sputum acid-fast bacilli (AFB) grade and types of radiological lesions were analyzed in new cases of pulmonary TB patients (n = 54) at Srinagarind Hospital, Khon Kaen, Thailand between September 1, 2012 and March 31, 2014. It was found that infiltrative and cavitary lesions from chest radiographs were associated with high sputum AFB grade (p = 0.048). T-cell responses from both IGRA and TST were not correlated with sputum AFB grade. Neither IGRA nor TST was correlated with the bacillary load as defined by AFB grade and chest radiographs. Patients with cavitary lesions on chest radiographs tended to have high IFN-γ concentrations and large TST indurations. In addition, TB patients with previous BCG vaccination showed significantly higher IFN-γ induction compared to the non-vaccinated group (p = 0.001). This study showed T-cell responses based on both IGRA and TST were not correlated with AFB grade and chest radiograph. In areas of high rates of BCG vaccination, as in Thailand, the BCG may affect IGRA and TST interpretations.

Cloning, expression and characterization of Mycobacterium tuberculosis sirR.

Identification of new drug targets is important for the improvement of chemotherapy for tuberculosis treatment. Metal-associated gene products are candidates for novel drug development. A Mycobacterium tuberculosis (MTB) sirR-encoded protein has been proposed, but the function of MTB SirR has not yet been elucidated. Bioinformatics analysis revealed that MTB SirR contains iron binding domains with 34%-59% similarity to previously described metal-dependent gene regulators and that the gene lies in Rv2787-sirR operon. RT-PCR revealed that the Rv2787-sirR operon is transcribed a single bicistronic mRNA. Heterologous expression, purification and characterization of recombinant MTB His-tagged SirR demonstrated a 25 kDa protein (by SDS-PAGE and immunoblotting) that exists as a dimer (native PAGE). Based on electrophoretic mobility shift assay, MTB SirR bound a cis element located at -85 bp upstream of its operon. As Rv2787-sirR operon is unique only to MTB (and M. bovis), further studies on its regulation and other functions of the encoded proteins should provide leads towards the discovery of novel anti-TB drugs.

Characterization of a novel two-component system response regulator involved in biofilm formation and a low-iron response of Burkholderia pseudomallei.

Two-component systems (TCSs) regulate an adaptive response to environmental conditions, leading to changes in bacterial cellular processes. In this study, we identified a novel TCS response regulator gene, designated as bfmR (biofilm formation-associated regulator) that regulates biofilm formation by Burkholderia pseudomallei (Bp). An insertion mutant of the Bp bfmR gene resulted in a significant decrease in expression of fimbriae chaperone-usher assembly genes (BPSL2O28 and BPSL22 7), leading to suppression of assembly of fimbriae on the cell surface and reduced biofilm formation. The defective phenotypes of the mutant strain were restored by introducing a complementing plasmid having an intact bfmR gene. Using RT-PCR analyses, we found that bfmR gene expression was upregulated under low-iron growth conditions. In addition, the bfmR mutant strain showed retarded growth in low-iron medium and in phagocytic cells compared to the wild-type strain. These results indicate that bfmR is a novel positive regulator for controlling assembly of fimbriae and biofilm formation, and is upregulated under low-iron conditions.