Publications by authors named "Prasit Palittapongarnpim"

58 Publications

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids.

Front Microbiol 2021 27;12:708685. Epub 2021 Aug 27.

Division of Bioinformatics and Data Management for Research, Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR-single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the gene sequences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.708685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8431811PMC
August 2021

Local adaptation in populations of endemic to the Indian Ocean Rim.

F1000Res 2021 1;10:60. Epub 2021 Feb 1.

Institut Pasteur de Madagascar, Antananarivo, Madagascar.

Lineage 1 (L1) and 3 (L3) are two lineages of the complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.12688/f1000research.28318.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921886.2PMC
June 2021

Estimation of the global burden of Mycobacterium tuberculosis lineage 1.

Infect Genet Evol 2021 07 5;91:104802. Epub 2021 Mar 5.

Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 road, Bangkok, Thailand. Electronic address:

Tuberculosis is still problematic as it affects large numbers of people globally. Mycobacterium tuberculosis Lineage 1 (L1) or Indo Oceanic Lineage, one of widespread major lineages, has a specific geographic distribution and high mortality. It is highly diverse and endemic in several high burden countries. However, studies on the global burden of L1 and its sublineages remain limited. This may lead to the underestimation of the importance of its variance in developing and applying tuberculosis control measures. This study aimed to estimate the number of patients infected with M. tuberculosis L1 and its sublineages worldwide. The proportion of L1 among tuberculosis patients was searched in published reports from countries around the world and the number of patients was calculated based on a WHO report on country incidences and populations. The numbers of patients infected with the five major sublineages, namely L1.1.1, L1.1.2, L1.1.3, L1.2.1, and L1.2.2 were estimated where information was available. It was found that L1 accounted for 28% of global tuberculosis cases in 2012 and 2018. Over 80% of the L1 global burden was in India, the Philippines, Indonesia and Bangladesh, which are also among the countries with highest absolute numbers of tuberculosis patients in the world. Globally, the estimated number of patients infected with M. tuberculosis L1.2.1 and L1.1.2 was over 1.1 million and of patients infected with L1.1.1 was about 200,000. This study demonstrated that L1 contributes significantly to the global burden of tuberculosis. To achieve the End TB Strategy, more attention needs to be paid to the responses of M. tuberculosis L1 to various control measures.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2021.104802DOI Listing
July 2021

Transcriptional response to the host cell environment of a multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features.

Sci Rep 2021 02 4;11(1):3199. Epub 2021 Feb 4.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.

Tuberculosis is a global public health problem with emergence of multidrug-resistant infections. Previous epidemiological studies of tuberculosis in Thailand have identified a clonal outbreak multidrug-resistant strain of Mycobacterium tuberculosis in the Kanchanaburi province, designated "MKR superspreader", and this particular strain later was found to also spread to other regions. In this study, we elucidated its biology through RNA-Seq analyses and identified a set of genes involved in cholesterol degradation to be up-regulated in the MKR during the macrophage cell infection, but not in the H37Rv reference strain. We also found that the bacterium up-regulated genes associated with the ESX-1 secretion system during its intracellular growth phase, while the H37Rv did not. All results were confirmed by qRT-PCR. Moreover, we showed that compounds previously shown to inhibit the mycobacterial ESX-1 secretion system and cholesterol utilisation, and FDA-approved drugs known to interfere with the host cholesterol transportation were able to decrease the intracellular survival of the MKR when compared to the untreated control, while not that of the H37Rv. Altogether, our findings suggested that such pathways are important for the MKR's intracellular growth, and potentially could be targets for the discovery of new drugs against this emerging multidrug-resistant strain of M. tuberculosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-82905-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7862621PMC
February 2021

Identification and functional prediction of lineage-specific SNPs distributed in DosR-related proteins and resuscitation-promoting factor proteins of .

Heliyon 2020 Dec 18;6(12):e05744. Epub 2020 Dec 18.

Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.

One-third of the world population is infected by which may persist in the latent or dormant state. Bacteria can shift to dormancy when encountering harsh conditions such as low oxygen, nutrient starvation, high acidity and host immune defenses Genes related to the dormancy survival regulator (DosR) regulon are responsible for the inhibition of aerobic respiration and replication, which is required to enter dormancy. Conversely, resuscitation-promoting factor (rpf) proteins participate in reactivation from dormancy and the development of active tuberculosis (TB). Many DosR regulon and rpf proteins are immunodominant T cell antigens that are highly expressed in latent TB infection. They could serve as TB vaccine candidates and be used for diagnostic development. We explored the genetic polymorphisms of 50 DosR-related genes and 5 genes among 1,170 previously sequenced clinical genomes. Forty-three lineage- or sublineage-specific nonsynonymous single nucleotide polymorphisms (nsSNPs) were identified. Ten nsSNPs were specific to all Mtb isolates belonging to lineage 1 (L1). Two common sublineages, the Beijing family (L2.2) and EAI2 (L1.2.1), differed at as many as 26 lineage- or sublineage-specific SNPs. DosR regulon genes related to membrane proteins and the family possessed mean dN/dS ratios greater than one, suggesting that they are under positive selection. Although the T cell epitope regions of DosR-related and rpf antigens were quite conserved, we found that the epitopes in L1 had higher rates of genetic polymorphisms than the other lineages. Some mutations in immunogenic epitopes of the antigens were specific to particular lineages. Therefore, the genetic diversity of the DosR regulon and rpf proteins might impact the adaptation of to the dormant state and the immunogenicity of latency antigens, which warrants further investigation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.heliyon.2020.e05744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753917PMC
December 2020

Geno-Spatial Distribution of Mycobacterium Tuberculosis and Drug Resistance Profiles in Myanmar-Thai Border Area.

Trop Med Infect Dis 2020 Sep 30;5(4). Epub 2020 Sep 30.

Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.

Worldwide, studies investigating the relationship between the lineage of (MTB) across geographic areas has empowered the "End TB" program and understand transmission across national boundaries. Genomic diversity of MTB varies with geographical locations and ethnicity. Genomic diversity can also affect the emergence of drug resistance. In Myanmar, we still have limited genetic information about geographical, ethnicity, and drug resistance linkage to MTB genetic information. This study aimed to describe the geno-spatial distribution of MTB and drug resistance profiles in Myanmar-Thailand border areas. A cross-sectional study was conducted with a total of 109 sequenced isolates. The lineages of MTB and the potential associated socio-demographic, geographic and clinical factors were analyzed using Fisher's exact tests. value of statistically significance was set at < 0.05. We found that 67% of the isolates were lineage 1 (L1)/East-African-Indian (EAI) (n = 73), followed by lineage 2 (L2)/Beijing (n = 26), lineage 4 (L4)/European American (n = 6) and lineage 3 (L3)/Delhi/Central Asian (n = 4). "Gender", "type of TB patient", "sputum smear grading" and "streptomycin resistance" were significantly different with the lineages of MTB. Sublineages of L1, which had never been reported elsewhere in Myanmar, were detected in this study area. Moreover, both ethnicity and lineage of MTB significantly differed in distribution by patient location. Diversity of the lineage of MTB and detection of new sublineages suggested that this small area had been resided by a heterogeneous population group who actively transmitted the disease. This information on distribution of lineage of MTB can be linked in the future with those on the other side of the border to evaluate cross-border transmission.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/tropicalmed5040153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709706PMC
September 2020

Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country.

Tuberculosis (Edinb) 2020 12 11;125:101991. Epub 2020 Sep 11.

National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand; Pornchai Matangkasombut Centre of Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand. Electronic address:

Whole-genome sequencing (WGS) analysis has great discriminative power for detecting similar molecular fingerprints of suspected tuberculosis (TB) clusters. The proportion of TB cases within clusters and the associated risk factors are important epidemiological parameters guiding appropriate outbreak control strategies in endemic settings. We conducted a hospital-based TB case-cohort study between 2003 and 2011 in the northernmost province of Thailand. We identified TB clusters by Mycobacterium tuberculosis WGS and analysed the risks of TB clustering and the characteristics of large clusters compared with small clusters. Among 1146 TB isolates, we identified 77 clusters with 251 isolates defined by a 5-single-nucleotide variant (SNV) cutoff and 112 clusters with 431 isolates defined by a 12-SNV cutoff. Twelve large clusters with 6 isolates or more in each cluster were identified by a 12-SNV cutoff. Sublineage 2.2.1 (both Ancestral and Modern) strains and imprisonment were independently associated with large clusters. Furthermore, although large clusters of Lineage 2.2.1/Ancestral strains included a high number of prisoners, Lineage 2.2.1/Modern strain clusters were only associated with treatment failures and drug resistance. Heterogeneity among lineage strains was observed with respect to large-cluster characteristics. Patients with an increased TB-transmission tendency should be priority targets for contact investigations and outbreak interventions to prevent ongoing transmission.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tube.2020.101991DOI Listing
December 2020

The geno-spatio analysis of Mycobacterium tuberculosis complex in hot and cold spots of Guangxi, China.

BMC Infect Dis 2020 Jul 1;20(1):462. Epub 2020 Jul 1.

Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, 530028, Guangxi, China.

Background: At present, there are few studies on polymorphism of Mycobacterium tuberculosis (Mtb) gene and how it affects the TB epidemic. This study aimed to document the differences of polymorphisms between tuberculosis hot and cold spot areas of Guangxi Zhuang Autonomous Region, China.

Methods: The cold and hot spot areas, each with 3 counties, had been pre-identified by TB incidence for 5 years from the surveillance database. Whole genome sequencing analysis was performed on all sputum Mtb isolates from the detected cases during January and June 2018. Single nucleotide polymorphism (SNP) of each isolate compared to the H37Rv strain were called and used for lineage and sub-lineage identification. Pairwise SNP differences between every pair of isolates were computed. Analyses of Molecular Variance (AMOVA) across counties of the same hot or cold spot area and between the two areas were performed.

Results: As a whole, 59.8% (57.7% sub-lineage 2.2 and 2.1% sub-lineage 2.1) and 39.8% (17.8% sub-lineage 4.4, 6.5% sub-lineage 4.2 and 15.5% sub-lineage 4.5) of the Mtb strains were Lineage 2 and Lineage 4 respectively. The percentages of sub-lineage 2.2 (Beijing family strains) are significantly higher in hot spots. Through the MDS dimension reduction, the genomic population structure in the three hot spot counties is significantly different from those three cold spot counties (T-test p = 0.05). The median of SNPs distances among Mtb isolates in cold spots was greater than that in hot spots (897 vs 746, Rank-sum test p < 0.001). Three genomic clusters, each with genomic distance ≤12 SNPs, were identified with 2, 3 and 4 consanguineous strains. Two clusters were from hot spots and one was from cold spots.

Conclusion: Narrower genotype diversity in the hot area may indicate higher transmissibility of the Mtb strains in the area compared to those in the cold spot area.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12879-020-05189-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329418PMC
July 2020

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis.

Sci Rep 2020 05 15;10(1):8024. Epub 2020 May 15.

Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.

Homoplastic mutations are mutations independently occurring in different clades of an organism. The homoplastic changes may be a result of convergence evolution due to selective pressures. Reports on the analysis of homoplastic mutations in Mycobacterium tuberculosis have been limited. Here we characterized the distribution of homoplastic single nucleotide polymorphisms (SNPs) among genomes of 1,170 clinical M. tuberculosis isolates. They were present in all functional categories of genes, with pe/ppe gene family having the highest ratio of homoplastic SNPs compared to the total SNPs identified in the same functional category. Among the pe/ppe genes, the homoplastic SNPs were common in a relatively small number of homologous genes, including ppe18, the protein of which is a component of a promising candidate vaccine, M72/AS01E. The homoplastic SNPs in ppe18 were particularly common among M. tuberculosis Lineage 1 isolates, suggesting the need for caution in extrapolating the results of the vaccine trial to the population where L1 is endemic in Asia. As expected, homoplastic SNPs strongly associated with drug resistance. Most of these mutations are already well known. However, a number of novel mutations associated with streptomycin resistance were identified, which warrants further investigation. A SNP in the intergenic region upstream of Rv0079 (DATIN) was experimentally shown to increase transcriptional activity of the downstream gene, suggesting that intergenic homoplastic SNPs should have effects on the physiology of the bacterial cells. Our study highlights the potential of homoplastic mutations to produce phenotypic changes. Under selective pressure and during interaction with the host, homoplastic mutations may confer advantages to M. tuberculosis and deserve further characterization.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-64895-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229016PMC
May 2020

Genetic variation in the cag pathogenicity island of Helicobacter pylori strains detected from gastroduodenal patients in Thailand.

Braz J Microbiol 2020 Sep 15;51(3):1093-1101. Epub 2020 May 15.

Department of Microbiology, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.

There is a lack of evidence of genetic variation in the Helicobacter pylori cag-PAI in Thailand, a region with the low incidence of gastric cancer. To clarify this issue, variation in the H. pylori cag-PAI in strains detected in Thailand was characterized and simultaneously compared with strains isolated from a high-risk population in Korea. The presence of ten gene clusters within cag-PAI (cagA, cagE, cagG, cagH, cagL, cagM, cagT, orf13, virB11, and orf10) and IS605 was characterized in H. pylori strains detected from these two countries. The cagA genotypes and EPIYA motifs were analyzed by DNA sequencing. The overall proportion of the ten cag-PAI genes that were detected ranged between 66 and 79%; additionally, approximately 48% of the strains from Thai patients contained an intact cag-PAI structure, while a significantly higher proportion (80%) of the strains from Korean patients had an intact cag-PAI. A significantly higher proportion of IS605 was detected in strains from Thai patients (55%). Analysis of cagA genotypes and EPIYA motifs revealed a higher frequency of Western-type cagA in Thai patients (87%) relative to Korean patients (8%) who were predominately associated with the East Asian-type cagA (92%). Variations in the Western-type cagA in the Thai population, such as EPIYA-BC patterns and EPIYA-like sequences (EPIYT), were mainly detected as compared with the Korean population (p < 0.05). In summary, H. pylori strains that colonize the Thai population tend to be associated with low virulence due to distinctive cag-PAI variation, which may partially explain the Asian paradox phenomenon in Thailand.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s42770-020-00292-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455669PMC
September 2020

First meeting in Asia of the Asia Pacific Research Integrity network.

Account Res 2020 02 14;27(2):99-106. Epub 2020 Jan 14.

Department of Biological Science and Technology, National Chiao Tung University.

In 2017, the University of Hong Kong and the University of California San Diego co-hosted the first Asian meeting of the recently formed Asia Pacific Research Integrity (APRI) network in Hong Kong. Aligned with planning meetings in 2015 and 2016 funded in part by the US Office of Research Integrity (ORI), the Hong Kong meeting was designed by a multi-national planning committee to address pressing challenges in research integrity: improving multi-national communication; exchanging information on managing misconduct investigations; and sharing best practices to promote research integrity. To create a sustainable, robust international partnership to promote research integrity in the region, the purpose of this 2017 meeting was to foster multi-national awareness, understanding, and opportunities for collaboration. The meeting was defined by four objectives that emerged from the previous meetings: (1) Articulate differences as well as areas of common ground; (2) Identify best or recommended practices; (3) Identify opportunities for research or collaboration; and (4) Set an APRI network agenda for coming years. The key anticipated outcome was to advance the conversation surrounding research integrity among academic institutions and regulators in Asian and Pacific Rim nations. This outcome was evidenced by meeting participation, participant satisfaction, and articulation of next steps for the APRI network.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/08989621.2020.1715220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7041487PMC
February 2020

An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data.

Infect Genet Evol 2020 04 24;79:104152. Epub 2019 Dec 24.

Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand.

Whole-genome sequencing (WGS) data allow for an inference of Mycobacterium tuberculosis (Mtb) clusters by using a pairwise genetic distance of ≤12 single nucleotide polymorphisms (SNPs) as a threshold. However, a problem of discrepancies in numbers of SNPs and genetic distance measurement is a great concern when combining WGS data from different next generation sequencing (NGS) platforms. We performed SNP variant calling on WGS data of 9 multidrug-resistant (MDR-TB), 3 extensively drug-resistant tuberculosis (XDR-TB) and a standard M. tuberculosis strain H37Rv from an Illumina/NextSeq500 and an Ion Torrent PGM. Variant calls were obtained using four different common variant calling tools, including Genome Analysis Toolkit (GATK) HaplotypeCaller (GATK-VCF workflow), GATK HaplotypeCaller and GenotypeGVCFs (GATK-GVCF workflow), SAMtools, and VarScan 2. Cross-platform pairwise SNP differences, minimum spanning networks and average nucleotide identity (ANI) were analysed to measure performance of the variant calling tools. Minimum pairwise SNP differences ranged from 2 to 14 SNPs when using GVCF workflow while maximum pairwise SNP differences ranged from 7 to 158 SNPs when using VarScan 2. ANI comparison between SNPs data from NextSeq500 and PGM of MDR-TB and XDR-TB showed maximum ANI of 99.7% and 99.0%, respectively, with GVCF workflow while the other SNP calling results showed lower ANI in a range of 98.6% to 95.1%. In this study, we suggest that the GVCF workflow showed the best performing variant caller to avoid cross-platform pairwise SNP differences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2019.104152DOI Listing
April 2020

Effects of the proportion of high-risk patients and control strategies on the prevalence of methicillin-resistant Staphylococcus aureus in an intensive care unit.

BMC Infect Dis 2019 Dec 3;19(1):1026. Epub 2019 Dec 3.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.

Background: The presence of nosocomial pathogens in many intensive care units poses a threat to patients and public health worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen endemic in many hospital settings. Patients who are colonized with MRSA may develop an infection that can complicate their prior illness.

Methods: A mathematical model to describe transmission dynamics of MRSA among high-risk and low-risk patients in an intensive care unit (ICU) via hands of health care workers is developed. We aim to explore the effects of the proportion of high-risk patients, the admission proportions of colonized and infected patients, the probability of developing an MRSA infection, and control strategies on MRSA prevalence among patients.

Results: The increasing proportion of colonized and infected patients at admission, along with the higher proportion of high-risk patients in an ICU, may significantly increase MRSA prevalence. In addition, the prevalence becomes higher if patients in the high-risk group are more likely to develop an MRSA infection. Our results also suggest that additional infection prevention and control measures targeting high-risk patients may considerably help reduce MRSA prevalence as compared to those targeting low-risk patients.

Conclusions: The proportion of high-risk patients and the proportion of colonized and infected patients in the high-risk group at admission may play an important role on MRSA prevalence. Control strategies targeting high-risk patients may help reduce MRSA prevalence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12879-019-4632-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889565PMC
December 2019

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.

Sci Rep 2019 09 23;9(1):13718. Epub 2019 Sep 23.

Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.

Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1-4 (L1-L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-50078-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6757101PMC
September 2019

Genetic Polymorphisms of CXCL8 (-251) Are Associated with the Susceptibility of Helicobacter pylori Infection Increased the Risk of Inflammation and Gastric Cancer in Thai Gastroduodenal Patients.

Iran J Allergy Asthma Immunol 2019 Aug 17;18(4):393-401. Epub 2019 Aug 17.

College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani, Thailand.

CXC Chemokine Ligand 8 (CXCL8) plays an important role in gastric inflammation and in the progression of gastric cancer induced by Helicobacter pylori (H. pylori) infection. The association of CXCL8, CXC Chemokine Receptor 1 (CXCR1), and CXC Chemokine Receptor 2 (CXCR2) polymorphisms with H. pylori infection and gastric cancer progression needs to be investigated in a population within an enigma area consisting of multiple ethnicities, such as Thailand. To analyze the relative risk of H. pylori infection and gastric cancer among Thai gastroduodenal patients, gene polymorphisms in CXCL8 (promoter region -251) and in CXCR1 and CXCR2 (receptors for CXCL8) were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and allele specific-PCR (AS-PCR). We also determined the presence of cytotoxin-associated gene A (cagA) in Thai patients with H. pylori infection. Correlation between the CXCL8 (-251) polymorphism and CXCL8 gene expression was evaluated by quantitative reverse transcriptase-PCR (qRT-PCR). We found a significant association between the T/A and A/A genotypes of CXCL8 (-251) with H. pylori infection. However, no significant correlation was found between the CXCR1 (+2607) and CXCR2 (+1208) gene polymorphisms with H. pylori infection among Thai gastroduodenal subjects. Within the H. pylori-infected group of Thai gastroduodenal patients, no significant differences in cagA were observed. In addition, the A/A genotype of CXCL8 (-251) significantly correlated with the risk of gastric cancer and correlated with higher CXCL8 gene expression levels in Thai gastroduodenal patients. These results suggest that CXCL8 (-251) polymorphisms are associated with H. pylori infection, an increased risk of stronger inflammatory responses, and gastric cancer in Thai gastroduodenal patients.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18502/ijaai.v18i4.1417DOI Listing
August 2019

Hot and Cold Spot Areas of Household Tuberculosis Transmission in Southern China: Effects of Socio-Economic Status and Genotypes.

Int J Environ Res Public Health 2019 05 27;16(10). Epub 2019 May 27.

Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.

The aims of the study were: (1) compare sociodemographic characteristics among active tuberculosis (TB) cases and their household contacts in cold and hot spot transmission areas, and (2) quantify the influence of locality, genotype and potential determinants on the rates of latent tuberculosis infection (LTBI) among household contacts of index TB cases. Parallel case-contact studies were conducted in two geographic areas classified as "cold" and "hot" spots based on TB notification and spatial clustering between January and June 2018 in Guangxi, China, using data from field contact investigations, whole genome sequencing, tuberculin skin tests (TSTs), and chest radiographs. Beijing family strains accounted for 64.6% of (Mtb) strains transmitted in hot spots, and 50.7% in cold spots (-value = 0.02). The positive TST rate in hot spot areas was significantly higher than that observed in cold spot areas (-value < 0.01). Living in hot spots (adjusted odds ratio (aOR) = 1.75, 95%, confidence interval (CI): 1.22, 2.50), Beijing family genotype (aOR = 1.83, 95% CI: 1.19, 2.81), living in the same room with an index case (aOR = 2.29, 95% CI: 1.5, 3.49), travelling time from home to a medical facility (aOR = 4.78, 95% CI: 2.96, 7.72), history of Bacillus Calmette-Guérin vaccination (aOR = 2.02, 95% CI: 1.13 3.62), and delay in diagnosis (aOR = 2.56, 95% CI: 1.13, 5.80) were significantly associated with positive TST results among household contacts of TB cases. The findings of this study confirmed the strong transmissibility of the Beijing genotype family strains and this genotype's important role in household transmission. We found that an extended traveling time from home to the medical facility was an important socioeconomic factor for Mtb transmission in the family. It is still necessary to improve the medical facility infrastructure and management, especially in areas with a high TB prevalence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijerph16101863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6572207PMC
May 2019

Infectivity of Genotypes and Outcome of Contact Investigation in Classroom in Guangxi, China.

Biomed Res Int 2019 14;2019:3980658. Epub 2019 Apr 14.

Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand.

Objective: To evaluate the infectivity of () genotypes of index cases in the classroom of adolescent schools in Guangxi, China.

Methods: Adolescent school tuberculosis (TB) contact investigations were conducted for all reported index TB cases from November 2016 to December 2017 in Guangxi, China. Genotypes of index cases and contact cases were identified by 15-loci mycobacterial interspersed repetitive units-variable number tandem repeat and spoligotyping. Outcome variable was 5 levels' order of tuberculin skin test (TST) results to new active TB [0-5 mm, 6-9 mm, 10-14 mm, ≥ 15 mm (without TB), and ≥15 mm (with TB)]. Multivariate ordered logistic regression analysis was performed to evaluate the independent effect of genotypes of index case on contact screening outcome.

Results: Beijing genotype occurred more commonly in female index patients. One genotypic cluster of two index cases and one cluster of two contact cases were detected. The association between infectivity of Beijing genotype of index cases and outcome of contact investigation was statistically significant in univariate analysis but no so after adjustment for characteristics of contacts and sex of index cases (=0.057). Female index cases increased the chance for TB infection/being active TB among contacts (ordinal odds ratio = 1.39, 95% confidence interval: 1.21, 1.60). Contacts who studied in the middle school, who with non-Han ethnicity and who without BCG scar had increased risk for TB infection/being active TB.

Conclusion: There was not enough evidence from our data to support that Beijing strains were more infective than non-Beijing strains in TB transmission in school setting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1155/2019/3980658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487147PMC
November 2019

Modeling Clostridium difficile in a hospital setting: control and admissions of colonized and symptomatic patients.

Theor Biol Med Model 2019 01 31;16(1). Epub 2019 Jan 31.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.

Background: Clostridium difficile (C. difficile) infection is an important cause of healthcare-associated diarrhea. Several factors such as admission of colonized patients, levels of serum antibodies in patients, and control strategies may involve in determining the prevalence and the persistence of C. difficile in a hospital unit.

Methods: We develop mathematical models based on deterministic and stochastic frameworks to investigate the effects of control strategies for colonized and symptomatic patients and admissions of colonized and symptomatic patients on the prevalence and the persistence of C. difficile.

Results: Our findings suggest that control strategies and admissions of colonized and symptomatic patients play important roles in determining the prevalence and the persistence of C. difficile. Improving control of C. difficile in colonized and symptomatic patients may generally help reduce the prevalence and the persistence of C. difficile. However, if admission rates of colonized and symptomatic patients are high, the prevalence of C. difficile may remain high in a patient population even though strict control policies are applied.

Conclusion: Control strategies and admissions of colonized and symptomatic patients are important determinants of the prevalence and the persistence of C. difficile.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12976-019-0098-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357410PMC
January 2019

Infection of multiple strains among tuberculosis/human immunodeficiency virus co-infected patients: A molecular study in Myanmar.

Int J Mycobacteriol 2018 Oct-Dec;7(4):375-379

Department of Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.

Background: Appearance of Mycobacterium tuberculosis (MTB) in the sputum of a tuberculosis (TB)/human immunodeficiency virus (HIV) co-infected patient under treatment may indicate either failure or new infection. This study aims to evaluate whether TB treatment failure among TB/HIV co-infected patients is a real failure.

Methods: A prospective cohort study was conducted among 566 TB/HIV co-infected patients who started TB treatment in 12 townships in the upper Myanmar. Among the 566 participants, 16 (2.8%) resulted in treatment failure. We performed a molecular study using mycobacterial interspersed repetitive-unit-variable number of tandem repeat (MIRU-VNTR) genotyping for them. The MIRU-VNTR profiles were analyzed using the web server, MIRU-VNTRplus. All data were entered into EpiData version 3.1 and analyzed using R version 3.4.3.

Results: Among 16 failure patients, seven had incomplete laboratory results. Of the nine remaining patients, nobody had exactly the same MIRU-VNTR pattern between the initial and final isolates. Four patients had persistent East-African Indian (EAI) lineages and one each had persistent Beijing lineage, changing from EAI to Beijing, from Beijing to EAI, NEW-1 to Beijing, and NEW-1 to X strains. Female patients have significantly larger genetic difference between MTB of the paired isolates than male patients (t-test, P = 0.04).

Conclusion: Thus, in our study patients, infection of multiple MTB strains is a possible cause of TB treatment failure. Explanation for the association between gender and distance of genotypes from the initial to subsequent MTB infection needs further studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4103/ijmy.ijmy_108_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341994PMC
June 2019

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

Sci Rep 2018 08 2;8(1):11597. Epub 2018 Aug 2.

Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.

Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-29986-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6072702PMC
August 2018

Melioidosis in Thailand: Present and Future.

Trop Med Infect Dis 2018 8;3(2):38. Epub 2018 Apr 8.

The Office of Disease Prevention and Control 12, Songkla 90000, Thailand.

A recent modelling study estimated that there are 2800 deaths due to melioidosis in Thailand yearly. The Thailand Melioidosis Network (formed in 2012) has been working closely with the Ministry of Public Health (MoPH) to investigate and reduce the burden of this disease. Based on updated data, the incidence of melioidosis is still high in Northeast Thailand. More than 2000 culture-confirmed cases of melioidosis are diagnosed in general hospitals with microbiology laboratories in this region each year. The mortality rate is around 35%. Melioidosis is endemic throughout Thailand, but it is still not uncommon that microbiological facilities misidentify as a contaminant or another organism. Disease awareness is low, and people in rural areas neither wear boots nor boil water before drinking to protect themselves from acquiring . Previously, about 10 melioidosis deaths were formally reported to the National Notifiable Disease Surveillance System (Report 506) each year, thus limiting priority setting by the MoPH. In 2015, the formally reported number of melioidosis deaths rose to 112, solely because Sunpasithiprasong Hospital, Ubon Ratchathani province, reported its own data ( = 107). Melioidosis is truly an important cause of death in Thailand, and currently reported cases (Report 506) and cases diagnosed at research centers reflect the tip of the iceberg. Laboratory training and communication between clinicians and laboratory personnel are required to improve diagnosis and treatment of melioidosis countrywide. Implementation of rapid diagnostic tests, such as a lateral flow antigen detection assay, with high accuracy even in melioidosis-endemic countries such as Thailand, is critically needed. Reporting of all culture-confirmed melioidosis cases from every hospital with a microbiology laboratory, together with final outcome data, is mandated under the Communicable Diseases Act B.E.2558. By enforcing this legislation, the MoPH could raise the priority of this disease, and should consider implementing a campaign to raise awareness and melioidosis prevention countrywide.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/tropicalmed3020038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928800PMC
April 2018

In Vitro Activities of Enantiopure and Racemic 1'-Acetoxychavicol Acetate against Clinical Isolates of Mycobacterium tuberculosis.

Sci Pharm 2017 Sep 18;85(3). Epub 2017 Sep 18.

Tuberculosis Research Laboratory, Medical Molecular Biology Research Unit, BIOTEC, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand.

In the process of evaluating the effect of several plant extracts against using the Microplate Alamar Blue Assay (MABA), an extract of Thai herb rhizome and its major component, 1'-acetoxychavicol acetate (ACA), exhibited marked anti-tuberculosis activity. The minimal inhibition concentrations (MICs) of the -enantiomer of ACA (-ACA) against H37R ATCC 25177 and H37R ATCC 27294 strains were 0.2 µg/mL and 0.7 µg/mL, respectively. More than 95% of 100 drug-sensitive and 50 drug-resistant mycobacterial clinical isolates were inhibited by extracted -ACA at 1.0 µg/mL. All of the remaining isolates were inhibited at 2.0 µg/mL. In contrast to the -enantiomer, synthetic racemic 1'--ACA (-ACA) showed MICs of 0.5 µg/mL and 2.7 µg/mL for H37R ATCC 25177 and H37R ATCC 27294, respectively, suggesting that the anti-tuberculosis effect might be primarily due to the -form. These observations were in line with the MICs of -ACA against 98% of 93 drug-resistant clinical isolates, which showed the effective inhibitory dose at 2.0 µg/mL. After exposure to 2.7 µg/mL of -ACA for at least 3 h, the tubercle bacilli were completely killed. These demonstrated that ACA had potent anti-TB activity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/scipharm85030032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620519PMC
September 2017

Pathogen lineage-based genome-wide association study identified CD53 as susceptible locus in tuberculosis.

J Hum Genet 2017 Dec 7;62(12):1015-1022. Epub 2017 Sep 7.

Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand.

Tuberculosis (TB) is known to be affected by host genetic factors. We reported a specific genetic risk factor through a genome-wide association study (GWAS) that focused on young age onset TB. In this study, we further focused on the heterogeneity of Mycobacterium tuberculosis (M. tb) lineages and assessed its possible interaction with age at onset on host genetic factors. We identified the pathogen lineage in 686 Thai TB cases and GWAS stratified by both infected pathogen lineage information and age at onset revealed a genome-wide significant association of one single-nucleotide polymorphism (SNP) on chromosome 1p13, which was specifically associated with non-Beijing lineage-infected old age onset cases (P=2.54E-08, OR=1.74 (95% CI=1.43-2.12)), when we compared them to the population-matched healthy controls. This SNP locates near the CD53 gene, which encodes a leukocyte surface glycoprotein. Interestingly, the expression of CD53 was also correlated with the patients' active TB status. This is the first report of a pathogen lineage-based genome-wide association study. The results suggested that host genetic risk in TB is depended upon the pathogen genetic background and demonstrate the importance of analyzing the interaction between host and pathogen genomes in TB.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/jhg.2017.82DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709719PMC
December 2017

Genetic characterisation of a whiB7 mutant of a Mycobacterium tuberculosis clinical strain.

J Glob Antimicrob Resist 2015 Dec 11;3(4):262-266. Epub 2015 Aug 11.

Tuberculosis Research Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani 12120, Thailand. Electronic address:

Mycobacterium tuberculosis is naturally resistant to clarithromycin (CLR). The genes Rv3197A (whiB7) and Rv1988 (ermMT) have been shown to be involved in the resistant phenotype. In this study, a CLR-susceptible M. tuberculosis clinical strain was identified, designated as DS3214, and the nucleotide sequences and expression profiles of whiB7 and ermMT were investigated. The results revealed that strain DS3214 contained a one nucleotide deletion in whiB7, leading to a truncated peptide. Expression of whiB7 was low, whereas comparable expression of ermMT was determined compared with the reference strain M. tuberculosis H37Rv. Overexpression of the mutant whiB7 in M. tuberculosis H37Ra did not increase the minimum inhibitory concentration (MIC) to CLR or kanamycin, indicating the defect of the mutant WhiB7. The CLR-susceptible M. tuberculosis clinical strain, whose whiB7 is naturally mutated, was first described in this study and whiB7 has been shown to play a role in the CLR-susceptible phenotype.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2015.07.004DOI Listing
December 2015

Mutations in rrs, rpsL and gidB in streptomycin-resistant Mycobacterium tuberculosis isolates from Thailand.

J Glob Antimicrob Resist 2016 03 15;4:5-10. Epub 2015 Dec 15.

Tuberculosis Research Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand; Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.

The objectives of this study were to characterise mutations in rrs, rpsL and gidB genes in Mycobacterium tuberculosis isolates from Thailand and to examine possible associations between mutations and strain genotypes. In total, 110 streptomycin (STR)-resistant M. tuberculosis isolates and 51 STR-susceptible isolates obtained from a sample collection in Thailand during 1999-2011 were sequenced for mutation analysis in rrs, rpsL and gidB. Genotypes of the isolates were identified using spoligotyping and large sequence polymorphisms. Mutations at codons 43 and 88 in rpsL represented 63.6% of the STR-resistant isolates and were mostly associated with Beijing strains. Mutations in rrs existed in 17.3% of the STR-resistant isolates; only 8.2% harboured resistance-associated mutations. Twenty-five different mutations were found in gidB, twelve of which are new. Eight gidB mutations were likely to contribute to STR resistance in ca. 14% of the resistant isolates; about one-half of the isolates also had a mutation in rrs or rpsL. Nearly all of the double mutants belonged to Beijing strains, whereas isolates carrying only STR-associated gidB mutation were non-Beijing strains. Three different alleles in gidB were also found, each specific to Beijing, East-African Indian and Euro-American lineages, respectively. Most of the STR-resistant isolates (80.9%) carried putative resistance-associated mutations in the analysed genes. Beijing strains were related not only to single resistance-associated mutations in rpsL or rrs but usually harboured a second mutation in gidB. Strains harbouring resistance-associated gidB mutations without rrs or rpsL mutations were more associated with non-Beijing isolates. Certain gidB mutations were also potential lineage markers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jgar.2015.11.009DOI Listing
March 2016

Cloning, expression and characterization of histidine-tagged biotin synthase of Mycobacterium tuberculosis.

Tuberculosis (Edinb) 2016 05 4;98:42-9. Epub 2016 Mar 4.

Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand; National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand. Electronic address:

The emergence of Mycobacterium tuberculosis strains that are resistant to the current anti-tuberculosis (TB) drugs necessitates a need to develop a new class of drugs whose targets are different from the current ones. M. tuberculosis biotin synthase (MtbBS) is one such target that is essential for the survival of the bacteria. In this study, MtbBS was cloned, overexpressed and purified to homogeneity for biochemical characterization. It is likely to be a dimer in its native form. Its pH and temperature optima are 8.0 and 37 °C, respectively. Km for DTB and SAM was 2.81 ± 0.35 and 9.95 ± 0.98 μM, respectively. The enzyme had a maximum velocity of 0.575 ± 0.015 μM min(-1), and a turn-over of 0.0935 min(-1). 5'-deoxyadenosine (dAH), S-(5'-Adenosyl)-l-cysteine (AdoCy) and S-(5'-Adenosyl)-l-homocysteine (AdoHcy) were competitive inhibitors of MtbBS with the following inactivation parameters: Ki = 24.2 μM, IC50 = 267.4 μM; Ki = 0.84 μM, IC50 = 9.28 μM; and Ki = 0.592 μM, IC50 = 6.54 μM for dAH, AdoCy and AdoHcy respectively. dAH could inhibit the growth of M. tuberculosis H37Ra with an MIC of 392.6 μg/ml. This information should be useful for the discovery of inhibitors of MtbBS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tube.2016.02.006DOI Listing
May 2016

Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand.

PeerJ 2016 12;4:e1905. Epub 2016 Apr 12.

Department of Microbiology, Faculty of Science, Mahidol University , Bangkok , Thailand.

Genome sequencing plays a key role in understanding the genetic diversity of Mycobacterium tuberculosis (M.tb). The genotype-specific character of M. tb contributes to tuberculosis severity and emergence of drug resistance. Strains of M. tb complex can be classified into seven lineages. The Nonthaburi (NB) genotype, belonging to the Indo-Oceanic lineage (lineage 1), has a unique spoligotype and IS6110-RFLP pattern but has not previously undergone a detailed whole genome analysis. In addition, there is not much information available on the whole genome analysis of M. tb isolates from tuberculous meningitis (TBM) patients in public databases. Isolates CSF3053, 46-5069 and 43-13838 of NB genotype were obtained from the cerebrospinal fluids of TBM Thai patients in Siriraj Hospital, Bangkok. The whole genomes were subjected to high throughput sequencing. The sequence data of each isolate were assembled into draft genome. The sequences were also aligned to reference genome, to determine genomic variations. Single nucleotide polymorphisms (SNPs) were obtained and grouped according to the functions of the genes containing them. They were compared with SNPs from 1,601 genomes, representing the seven lineages of M. tb complex, to determine the uniqueness of NB genotype. Susceptibility to first-line, second-line and other antituberculosis drugs were determined and related to the SNPs previously reported in drug-resistant related genes. The assembled genomes have an average size of 4,364,461 bp, 4,154 genes, 48 RNAs and 64 pseudogenes. A 500 base pairs deletion, which includes ppe50, was found in all isolates. RD239, specific for members of Indo Oceanic lineage, and RD147c were identified. A total of 2,202 SNPs were common to the isolates and used to classify the NB strains as members of sublineage 1.2.1. Compared with 1,601 genomes from the seven lineages of M. tb complex, mutation G2342203C was found novel to the isolates in this study. Three mutations (T28910C, C1180580T and C152178T) were found only in Thai NB isolates, including isolates from previous study. Although drug susceptibility tests indicated pan-susceptibility, non-synonymous SNPs previously reported to be associated with resistance to anti-tuberculous drugs; isoniazid, ethambutol, and ethionamide were identified in all the isolates. Non-synonymous SNPs were found in virulence genes such as the genes playing roles in apoptosis inhibition and phagosome arrest. We also report polymorphisms in essential genes, efflux pumps associated genes and genes with known epitopes. The analysis of the TBM isolates and the availability of the variations obtained will provide additional resources for global comparison of isolates from pulmonary tuberculosis and TBM. It will also contribute to the richness of genomic databases towards the prediction of antibiotic resistance, level of virulence and of origin of infection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.7717/peerj.1905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841212PMC
April 2016

Resistance to cellular autophagy by Mycobacterium tuberculosis Beijing strains.

Innate Immun 2015 Oct 9;21(7):746-58. Epub 2015 Jul 9.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand

Autophagy represents a key pathway in innate immune defense to restrict Mycobacterium tuberculosis growth inside host macrophages. Induction of autophagy has been shown to promote mycobacterial phagosome acidification and acquisition of lysosomal hydrolases, resulting in the elimination of intracellular M. tuberculosis reference strains such as H37Rv. The notorious Beijing genotype has been previously shown to be hyper-virulent and associated with increased survival in host cells and a high mortality rate in animal models, but the underlying mechanism that renders this family to have such advantages remains unclear. We hypothesize that autophagic control against M. tuberculosis Beijing strains may be altered. Here, we discovered that the Beijing strains can resist autophagic killing by host cells compared with that of the reference strain H37Rv and a strain belonging to the East African Indian genotype. Moreover, we have determined a possible underlying mechanism and found that the greater ability to evade autophagic elimination possessed by the Beijing strains stems from their higher capacity to inhibit autophagolysosome biogenesis upon autophagy induction. In summary, a previously unrecognized ability of the M. tuberculosis Beijing strains to evade host autophagy was identified, which may have important implications for tuberculosis treatment, especially in regions prevalent by the Beijing genotype.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/1753425915594245DOI Listing
October 2015

Different behaviours of promoters in Mycobacterium tuberculosis H37Rv and H37Ra.

World J Microbiol Biotechnol 2015 Feb 4;31(2):407-13. Epub 2015 Jan 4.

National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand,

Mycobacterium tuberculosis H37Rv and H37Ra are two closely-related bacterial strains in which the former is virulent whereas the latter is not. Although the genetic differences between these strains are known, our understanding of how they control the difference in virulence characteristics is incomplete. In this work, we tested the activities of different mycobacterium gene promoters in the two strains using a gfp reporter gene. The promoter activities were compared between growth in vitro and growth of bacteria residing in U937 cells (a-macrophage-like cell line). The promoters tested included M. tuberculosis isocitrate lyase (icl), alpha crystalline homolog (hspX) and moeZ, and the M. avium macrophage-induced gene (mig) promoter. Two hspX constructs with different lengths of the promoter sequence were tested. All promoters except the shorter hspX construct were active in the H37Ra strain in both liquid culture and in U937 cells. In the H37Rv strain, the shorter hspX and icl constructs were induced in infected U937 cells relative to liquid culture, whereas the mig construct was active in both conditions. In conclusion, the inducible properties of the shorter hspX and the icl promoters evident in H37Rv appeared to be lost in the H37Ra strain. Furthermore, sequence further upstream of the hspX gene appears to modulate the inducible property of the hspX promoter in a strain-dependent manner.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11274-014-1794-xDOI Listing
February 2015

Genetic diversity and dynamic distribution of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in Thailand.

J Clin Microbiol 2014 Dec 8;52(12):4267-74. Epub 2014 Oct 8.

Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.

This study examined the genetic diversity and dynamicity of circulating Mycobacterium tuberculosis strains in Thailand using nearly neutral molecular markers. The single nucleotide polymorphism (SNP)-based genotypes of 1,414 culture-positive M. tuberculosis isolates from 1,282 pulmonary tuberculosis (PTB) and 132 extrapulmonary TB (EPTB) patients collected from 1995 to 2011 were characterized. Among the eight SNP cluster groups (SCG), SCG2 (44.1%), which included the Beijing (BJ) genotype, and SCG1 (39.4%), an East African Indian genotype, were dominant. Comparisons between the genotypes of M. tuberculosis isolates causing PTB and EPTB in HIV-negative cases revealed similar prevalence trends although genetic diversity was higher in the PTB patients. The identification of 10 reported sequence types (STs) and three novel STs was hypothesized to indicate preferential expansion of the SCG2 genotype, especially the modern BJ ST10 (15.6%) and ancestral BJ ST19 (13.1%). An association between SCG2 and SCG1 genotypes and particular patient age groups implies the existence of different genetic advantages among the bacterial populations. The results revealed that increasing numbers of young patients were infected with M. tuberculosis SCGs 2 and 5, which contrasts with the reduction of the SCG1 genotype. Our results indicate the selection and dissemination of potent M. tuberculosis genotypes in this population. The determination of heterogeneity and dynamic population changes of circulating M. tuberculosis strains in countries using the Mycobacterium bovis BCG (bacillus Calmette-Guérin) vaccine are beneficial for vaccine development and control strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/JCM.01467-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313297PMC
December 2014
-->