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Aung YW, Faksri K, Sangka A, Tomanakan K, Namwat W. Heteroresistance of Mycobacterium tuberculosis in the Sputum Detected by Droplet Digital PCR. Biology 2023; 12:biology12040525. [PMID: 37106726 PMCID: PMC10136199 DOI: 10.3390/biology12040525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Heteroresistance in MTB refers to the presence of distinct subpopulations of bacteria with varying levels of antibiotic susceptibility within a population. Multidrug-resistant and rifampicin-resistant TB are serious global health concerns. In this study, we aimed to determine the prevalence of heteroresistance in MTB from sputum samples of new TB cases using Droplet Digital PCR mutation detection assays for katG and rpoB genes, which are commonly associated with resistance to isoniazid and rifampicin, respectively. We found that out of 79 samples, 9 (11.4%) exhibited mutations in katG and rpoB genes. INH mono-resistant TB, RIF mono-resistant TB, and MDR-TB samples constituted 1.3%, 6.3%, and 3.8% of new TB cases, respectively. Heteroresistance in katG, rpoB, and both genes were found in 2.5%, 5%, and 2.5% of total cases, respectively. Our results suggest that these mutations may have arisen spontaneously, as the patients had not yet received anti-TB drugs. ddPCR is a valuable tool for the early detection and management of DR-TB, as it can detect both mutant and wild-type strains in a population, enabling the detection of heteroresistance and MDR-TB. Overall, our findings highlight the importance of early detection and management of DR-TB for effective TB control (in katG, rpoB, and katG/rpoB).
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Affiliation(s)
- Ye Win Aung
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Arunnee Sangka
- Faculty of Associated Medical Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kanchana Tomanakan
- Department of Medical Laboratory, Khon Kaen Hospital, Khon Kaen 40000, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Poosari A, Nutravong T, Namwat W, Sa-Ngiamwibool P, Ungareewittaya P, Boonyanugomol W. Relationship between Helicobacter Pylori Infection and the Risk of Esophageal Cancer in Thailand. Asian Pac J Cancer Prev 2023; 24:1073-1080. [PMID: 36974563 DOI: 10.31557/apjcp.2023.24.3.1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Indexed: 03/29/2023] Open
Abstract
OBJECTIVE Esophageal cancer (EC) is a multifactorial disease and a leading cause of mortality. Epidemiological and molecular studies have provided evidence that Helicobacter pylori (H. pylori) infection is an important cause of gastric carcinogenesis and thus, may be related to EC. However, esophagus H. pylori infection in Thai patients with newly diagnosed EC has not been reported. Moreover, the evidence of the association with H. pylori to EC is controversial. This study investigated the possible association between H. pylori infection with a virulence gene and EC in Thailand. METHODS A case-control study was conducted that involved 105 newly diagnosed EC patients and 108 healthy controls. The prevalence of H. pylori infection detected in formalin-fixed, paraffin-embedded EC tissue in esophageal biopsy specimens from the subjects was measured using real-time PCR. All the data were collected in face to face interviews using a structured questionnaire. Multivariable unconditional logistic regression was used to calculate and analyses the odds ratios (ORs) of the data. RESULTS A significant association was found between H. pylori infection and EC (p < 0.001, 95% CI:3.11-10.48). H. pylori-positive subjects had a 2.76 times higher risk of developing ESCC. Moreover, the H. pylori-positive subjects who were CagA-positive had slightly higher ORs and statistically significant risk factors. CONCLUSIONS H. pylori infection was found to be associated with a risk of EC in Thailand, and among the H. pylori-positive subjects who were CagA-positive had a higher risk factor of ESCC but not of EAC.
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Affiliation(s)
- Arisara Poosari
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thitima Nutravong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Piti Ungareewittaya
- Department of Pathology, Faculty of Medicine, Khon Kaen Universtity, Khon Kaen, Thailand
| | - Wongwarut Boonyanugomol
- Department of Medical Science, Amnatcharoen Campus, Mahidol University, Amnatcharoen, Thailand
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Poosari A, Nutravong T, Sa-Ngiamwibool P, Namwat W, Chatrchaiwiwatana S, Ungareewittaya P. Association between infection with Campylobacter species, poor oral health and environmental risk factors on esophageal cancer: a hospital-based case-control study in Thailand. Eur J Med Res 2021; 26:82. [PMID: 34332608 PMCID: PMC8325836 DOI: 10.1186/s40001-021-00561-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Background Previous studies have shown the association between Campylobacter species infection and that environmental factors, poor oral hygiene in particular, are linked to an increased risk of esophageal cancer (EC). However, no study has reported on these factors in Thailand. Thus, this study’s objective was to evaluate the impact of the relationship between Campylobacter infection and environmental factors on EC incidence in the population of Thailand. Methods Data from a case–control study were collected from 105 newly diagnosed EC cases and 105 controls recruited from 2007 to 2017. Infection with Campylobacter spp. was detected in the formalin-fixed paraffin-embedded (FFPE) tissue of EC taken from gastroesophageal biopsy specimens obtained from the participants, and evaluated using TaqMan® real-time PCR. Multivariable logistic regression was performed to calculate the odds ratios (ORs) and perform data analysis. Results Smoking, alcohol use, a family history of cancer, history of gastroesophageal reflux disease, poor oral hygiene and Campylobacter spp. infection were shown to be significant risk factors for EC (p < 0.05). The combination of poor oral hygiene and infection with Campylobacter spp. constituted significant risk for EC (p < 0.001). In addition, the risk of EC in subjects co-infected with C. rectus and C. concisus that practiced poor oral hygiene was even higher and was significant (ORadj = 4.7; 95% CI 2.41–9.98; p = 0.003). Conclusions In Thailand, the major risk factors for EC are smoking status, alcohol drinking, family history of cancer, GERD, poor oral hygiene and Campylobacter spp. infection. This study found Campylobacter spp. prevalence to be associated with EC and appears to be enhanced by poor oral hygiene, suggesting that a combination of poor oral hygiene and Campylobacter species infection may together act as an important etiological risk factor for EC. Supplementary Information The online version contains supplementary material available at 10.1186/s40001-021-00561-3.
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Affiliation(s)
- Arisara Poosari
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Thitima Nutravong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Prakasit Sa-Ngiamwibool
- Department of Pathology, Faculty of Medicine, Khon Kaen Universtity, Khon Kaen, 40002, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Piti Ungareewittaya
- Department of Pathology, Faculty of Medicine, Khon Kaen Universtity, Khon Kaen, 40002, Thailand
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Saiboonjan B, Roytrakul S, Sangka A, Lulitanond V, Faksri K, Namwat W. Proteomic analysis of drug-susceptible and multidrug-resistant nonreplicating Beijing strains of Mycobacterium tuberculosis cultured in vitro. Biochem Biophys Rep 2021; 26:100960. [PMID: 33748436 PMCID: PMC7960788 DOI: 10.1016/j.bbrep.2021.100960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/16/2023] Open
Abstract
The existence of latent tuberculosis infection (LTBI) is one of the main obstacles hindering eradication of tuberculosis (TB). To better understand molecular mechanisms and explore biomarkers for the pathogen during LTBI, we cultured strains of Mycobacterium tuberculosis (Mtb) under stress conditions, mimicking those in the host granuloma intracellular environment, to induce entry into the non-replicating persistence stage. The stresses included hypoxia, low pH (5.0), iron deprivation (100 μM of 2, 2’˗dipyridyl) and nutrient starvation (10% M7H9 medium). Three Mtb strains were studied: two clinical isolates (drug-susceptible Beijing (BJ) and multidrug-resistant Beijing (MDR-BJ) strains) and the reference laboratory strain, H37Rv. We investigated the proteomics profiles of these strains cultured in stressful conditions and then validated the findings by transcriptional analysis. NarJ (respiratory nitrate reductase delta chain) was significantly up-regulated at the protein level and the mRNA level in all three Mtb strains. The narJ gene is a member of the narGHJI operon encoding all nitrate reductase subunits, which play a role in nitrate metabolism during the adaptation of Mtb to stressful intracellular environments and the subsequent establishment of latent TB. The identification of up-regulated mRNAs and proteins of Mtb under stress conditions could assist development of biomarkers, drug targets and vaccine antigens. The proteomics profiles between BJ and MDR-BJ strains of M. tuberculosis (Mtb) cultured in vitro in stressful conditions. NarJ is a common protein and significantly up-regulated protein of BJ and MDR-BJ Mtb strains. The unique proteins found on BJ and MDR-BJ Mtb strain were of “Rv3764c/tcrY” and “Rv1356c and Rv1420/uvrC”, respectively.
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Affiliation(s)
- Bhanubong Saiboonjan
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Rama VI Rd., Pathumthani, Thailand
| | - Arunnee Sangka
- Department of Clinical Microbiology, Faculty of Associated Medical Science, Khon Kaen University, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Corresponding author.
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Moe Sann WW, Namwat W, Faksri K, Swe TL, Swe KK, Thwin T, Sangka A. Genetic diversity of Mycobacterium tuberculosis using 24-locus MIRU-VNTR typing and Spoligotyping in Upper Myanmar. J Infect Dev Ctries 2020; 14:1296-1305. [PMID: 33296343 DOI: 10.3855/jidc.12998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/30/2020] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION MIRU-VNTR typing and Spoligotyping are the useful molecular tools for TB epidemiology study. Information regarding genetic diversity and tuberculosis (TB) transmission in Upper Myanmar only is scares. METHODOLOGY We determined the genetic diversity of Mycobacterium tuberculosis (Mtb) and TB transmission from Upper Myanmar TB Reference Laboratory, Mandalay Region, including Mandalay (72), Shan (22), Magway (15), Sagaing (13), Nay Pyi Taw (8), Kachin (7), Chin (2) and Kayah (1). One hundred and forty Mtb isolates were genotyped using 24-locus MIRU-VNTR typing and spoligotyping. Lineage classification and TB transmission analysis were performed. RESULTS 24-locus MIRU-VNTR typing identified 135 unique profiles and two clusters compared to 35 spoligotyping profiles which contained 12 clusters and 23 unique isolates, Beijing (n=100, 71.4%) was found to be prominent lineage by combine two methods. The expected proportion attributable to recent transmission based on clustering rate was 2.1%. One cluster case was more likely to be in MDR patient. CONCLUSIONS Our findings showed Beijing genotypes were dominant in Upper Myanmar. The usage and analysis of 24-locus MIRU-VNTR typing might prove useful for our broader understanding of TB outbreaks and epidemiology than spoligotyping. The genotypic pattern of this combined method suggests that the lower transmission rate may be due to a higher possibility of reactivation cases in Upper Myanmar.
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Affiliation(s)
- Waing Waing Moe Sann
- Medical Technology Program, Faculty of Associated medical Sciences, Khon Kaen University, Khon Kaen,Thailand.
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
| | | | - Kyi Kyi Swe
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Thandar Thwin
- National TB Control Program, Upper Myanmar TB Reference Laboratory, Mandalay Region, Myanmar.
| | - Arunnee Sangka
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.
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Sirichoat A, Sankuntaw N, Engchanil C, Buppasiri P, Faksri K, Namwat W, Chantratita W, Lulitanond V. Comparison of different hypervariable regions of 16S rRNA for taxonomic profiling of vaginal microbiota using next-generation sequencing. Arch Microbiol 2020; 203:1159-1166. [PMID: 33221964 DOI: 10.1007/s00203-020-02114-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 12/20/2022]
Abstract
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.
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Affiliation(s)
- Auttawit Sirichoat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Nipaporn Sankuntaw
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
| | - Chulapan Engchanil
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pranom Buppasiri
- Department of Obstetrics and Gynecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wises Namwat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wasun Chantratita
- Medical Genome Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Kham-Ngam I, Chetchotisakd P, Ananta P, Chaimanee P, Reechaipichitkul W, Lulitanond V, Namwat W, Faksri K. Differentiation between persistent infection/colonization and re-infection/re-colonization of Mycobacterium abscessus isolated from patients in Northeast Thailand. Infect Genet Evol 2018; 68:35-42. [PMID: 30521865 DOI: 10.1016/j.meegid.2018.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/20/2018] [Accepted: 12/01/2018] [Indexed: 01/15/2023]
Abstract
Mycobacterium abscessus can cause true infection or be present in the host as a harmless colonist. The ability of M. abscessus to cause disease and develop drug resistance is known to have a genetic basis. We aimed to differentiate between persistent infection and reinfection using multilocus sequence typing (MLST) and to study the genetic diversity of M. abscessus relative to multi-organ infection and drug resistance in Northeast Thailand. DNA was extracted from 62 M. abscessus isolates (24 cases). The following genes were sequenced: argH, cya, glpK, gnd, murC, pta, purH and rpoB. Drug susceptibility tests were performed using broth microdilution. Subspecies classification and phylogeny were determined. Among the 24 cases (62 isolates), 19 cases (49 isolates) were of true NTM infection and 5 cases (13 isolates) examples of colonization. Two subspecies, M. abscessus subsp. massiliense (12 cases, 32 isolates) and M. abscessus subsp. abscessus (12 cases, 30 isolates) were identified. The major sequence type (ST) was ST227. Two clonal groups among patients were found; clonal cluster I (5 cases, 8 isolates) and clonal cluster II (2 cases, 4 isolates) but no epidemiological link was apparent. Reinfection (2 cases with different clones of M. abscessus strains; >9 SNPs different) and persistent infection (14 cases with the same clone; <6 SNPs) were distinguished based on a phylogeny. Based on these SNP cutoff values, 3 cases of persistent colonization (same strain through time) and 2 cases of re-colonization (different strains through time) were identified. M. abscessus subsp. abscessus was significantly associated with clarithromycin resistance (p < .001) and multi-organ infection (p = .03). Molecular epidemiology based on MLST can be used to differentiate between reinfection vs persistent infection, persistent colonization vs re-colonization. ST227 was the main epidemic strain in Northeast Thailand.
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Affiliation(s)
- Irin Kham-Ngam
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | | | - Pimjai Ananta
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Clinical Microbiology Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Prajaub Chaimanee
- Clinical Microbiology Unit, Srinagarind Hospital, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wipa Reechaipichitkul
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand.
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Sirichoat A, Buppasiri P, Engchanil C, Namwat W, Faksri K, Sankuntaw N, Pasomsub E, Chantratita W, Lulitanond V. Characterization of vaginal microbiota in Thai women. PeerJ 2018; 6:e5977. [PMID: 30498641 PMCID: PMC6252066 DOI: 10.7717/peerj.5977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background The vaginal microbiota (VMB) plays a key role in women’s reproductive health. VMB composition varies with ethnicity, making it necessary to characterize the VMB of the target population before interventions to maintain and/or improve the vaginal health are undertaken. Information on the VMB of Thai women is currently unavailable. We therefore characterized the VMB in normal Thai women. Methods Vaginal samples derived from 25 Thai women were subjected to 16S rRNA gene next-generation sequencing (NGS) on the Ion Torrent PGM platform. Results Two groups of VMB were detected, lactobacilli-dominated (LD) and non-lactobacilli dominated (NLD) groups. Lactobacillus iners was the most common species found in the LD group while Gardnerella vaginalis followed by Atopobium vaginae and Pseudumonas stutzeri were commonly found in the NLD group. Conclusions The VMB patterns present in normal Thai women is essential information to further determine the factors associated with VMB patterns in vaginal health and disease and to develop proper management of reproductive health of Thai women.
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Affiliation(s)
- Auttawit Sirichoat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Pranom Buppasiri
- Department of Obstetrics and Gynecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chulapan Engchanil
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nipaporn Sankuntaw
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
| | - Ekawat Pasomsub
- Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wasun Chantratita
- Medical Genome Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Nonghanphithak D, Reechaipichitkul W, Namwat W, Lulitanond V, Naranbhai V, Faksri K. Genetic polymorphisms of CCL2 associated with susceptibility to latent tuberculous infection in Thailand. Int J Tuberc Lung Dis 2018; 20:1242-8. [PMID: 27510253 DOI: 10.5588/ijtld.16.0017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extent to which individuals exhibit genetic susceptibility to tuberculosis (TB) is still unclear. Genetic variations in chemokine genes might influence the early clearance of Mycobacterium tuberculosis, affecting TB susceptibility. OBJECTIVES To study single nucleotide polymorphisms (SNPs) of chemokine genes CCL2, CXCL9, CXCL10 and CXCL11, and their association with TB susceptibility. DESIGN Of 248 participants enrolled, 49 had active TB, 43 had latent tuberculous infection (LTBI) and 156 were non-infected, including 24 healthy controls with no known TB exposure. These populations were divided into two groups based on TB exposure: susceptible (n = 92) and resistant (early clearance) (n = 132). RESULTS Only CCL2 SNPs (-2518A/G) were significantly associated with increased TB susceptibility. Based on adjusted multivariate analysis, persons with the GG genotype at this SNP were twice as susceptible to TB as those with the AA genotype (P = 0.018, OR 2.880, 95%CI 1.201-6.903). Risk of LTBI was three times higher among those with GG (P = 0.003, OR 3.358, 95%CI 1.525-7.396 for AA+AG vs. GG and P = 0.012, OR 3.706, 95%CI 1.340-10.254 for AA vs. GG). Persons with the GG genotype produced significantly lower CCL2 levels in response to M. tuberculosis antigen stimulation (AA+AG vs. GG, P = 0.038). CONCLUSION The CCL2 polymorphism (-2518A/G) was associated with susceptibility to LTBI in a North-East Thai populations.
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Affiliation(s)
- D Nonghanphithak
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
| | - W Reechaipichitkul
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - W Namwat
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - V Lulitanond
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand; Department of Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
| | - V Naranbhai
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K Faksri
- Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand; Department of Research and Diagnostic Centre for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, Thailand
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Wongphutorn P, Chomvarin C, Sripa B, Namwat W, Faksri K. 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. BMC Microbiol 2018; 18:10. [PMID: 29378521 PMCID: PMC5789744 DOI: 10.1186/s12866-018-1150-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 01/21/2018] [Indexed: 12/21/2022] Open
Abstract
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.
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Affiliation(s)
- Phattharaphon Wongphutorn
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Liver Fluke and Cholangiocarcinoma Research Center, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Liver Fluke and Cholangiocarcinoma Research Center, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Banchob Sripa
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, 40002, Thailand.
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Nonghanphithak D, Reechaipichitkul W, Namwat W, Naranbhai V, Faksri K. Chemokines additional to IFN-γ can be used to differentiate among Mycobacterium tuberculosis infection possibilities and provide evidence of an early clearance phenotype. Tuberculosis (Edinb) 2017; 105:28-34. [PMID: 28610785 DOI: 10.1016/j.tube.2017.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 02/07/2023]
Abstract
Current diagnostic tests for tuberculosis (TB) remain limited in their ability to discriminate between active TB (ATB) and latent TB infection (LTBI). Early clearance (EC) of TB by individuals exposed to Mycobacterium tuberculosis is a debated phenomenon for which evidence is lacking. We measured and compared secreted chemokines in the plasma fraction from 48 ATB, 38 LTBI, 162 presumed EC and 39 healthy controls (HC) using the QuantiFERON®-TB Gold In-Tube assay. Single chemokine markers were limited in their ability to discriminate between ATB and LTBI: IFN-γ showed 16.7% sensitivity; CCL2 showed moderate sensitivity (70.8%) and specificity (74.4%); CXCL10 showed high sensitivity (87.5%) and specificity (78.9%). Compared to IFN-γ alone, IFN-γ combined with CXCL10 significantly improved (p < 0.001) the sensitivity and specificity to discriminate between ATB and HC (97.9% sensitivity and 94.9% specificity) and between ATB and LTBI (89.6% sensitivity and 71.1% specificity). Levels of CCL2 were very significantly lower (p < 0.0001) in EC compared to HC groups and hence CCL2 is a useful marker for EC. This study demonstrated the potential application of profiling using multiple chemokines for differentiating among the various M. tuberculosis infection possibilities. We also present evidence to support the EC phenomenon based on the decrease of CCL2 levels.
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Affiliation(s)
| | - Wipa Reechaipichitkul
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Vivek Naranbhai
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Centre for the AIDS Program of Research in South Africa, Nelson R Mandela School of Medicine, University of KwaZulu Natal, South Africa
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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Tirapattanun A, Namwat W, Kanthawong S, Wongboot W, Wongwajana S, Wongphutorn P, Chomvarin C. DETECTION OF HELICOBACTER PYLORI AND VIRULENCE-ASSOCIATED GENES IN SALIVA SAMPLES OF ASYMPTOMATIC PERSONS IN NORTHEAST THAILAND. Southeast Asian J Trop Med Public Health 2016; 47:1246-1256. [PMID: 29634191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aims of the study were to develop nested-PCR (targeting vacA and cagA), SYBR green quantitative PCR (targeting 16S rDNA) tests and compared them with indirect fluorescent-monoclonal antibody (IFA) method for determination of the prevalence of Helicobacter pylori in 118 saliva samples from asymptomatic individuals in Khon Kaen, Thailand. Detection limit of both PCR-based assays was one cell. Prevalence of H. pylori in saliva samples was 55% based on the criterion of positivity of IFA test and one of the PCR-based methods or positivity of both PCR assays. Forty-nine percent of H. pylori detected carried cagA, encoding a cytotoxin associated with severe clinical outcomes. These results imply that the mouth may be an important reservoir for H. pylori, with nearly 50% of the virulent type that could possibly lead to gastroduodenal disease.
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Faksri K, Hanchaina R, Sangka A, Namwat W, Lulitanond V. Development and application of single-tube multiplex real-time PCR for lineage classification of Mycobacterium tuberculosis based on large sequence polymorphism in Northeast Thailand. Tuberculosis (Edinb) 2015; 95:404-10. [PMID: 26025596 DOI: 10.1016/j.tube.2015.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/16/2015] [Accepted: 04/19/2015] [Indexed: 12/21/2022]
Abstract
An appreciation of the genetic diversity of Mycobacterium tuberculosis (Mtb) is needed for effective planning of strategies in tuberculosis (TB) control. Large sequence polymorphisms (LSPs) are the molecular epidemiological and evolutionary markers for classification of Mtb into East Asian (EA) or Beijing, Indo-Oceanic (IO), Euro-American (EuA) and East African-Indian (EAI) lineages. We aimed to develop a single-tube multiplex real-time PCR assay using melting curve analysis for lineage classification of Mtb based on LSPs. The technique was optimized and tested with well-characterized strains (n = 89). The developed technique was then applied to classify Mtb isolates from TB patients (n = 256) randomly recruited from 19 provinces covering Northeast Thailand in 2013-2014. The technique demonstrated 100% sensitivity and specificity based on well-characterized strains compared to conventional techniques. The detection limit of the technique is 0.05 ng of genomic DNA of Mtb. The 256 Mtb isolates represented IO (n = 178, 70%), Beijing (n = 60, 23%) and EuA (n = 18, 7%) lineages. Significant associations of the Beijing lineage with drug resistance (p < 0.001) and younger average age of TB patients (p < 0.001) compared to other lineages were shown. The single-tube multiplex real-time PCR technique provides a simple, rapid and high performance tool for characterizing Mtb based on LSPs.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Rattanavinan Hanchaina
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen 40002, Thailand
| | - Arunnee Sangka
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wises Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen 40002, Thailand
| | - Viraphong Lulitanond
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen 40002, Thailand
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Kasa S, Faksri K, Kaewkes W, Lulitanond V, Namwat W. DOUBLE-STEP MULTIPLEX REAL TIME PCR WITH MELTING CURVE ANALYSIS FOR DETECTION AND DIFFERENTIATION OF MYCOBACTERIA IN SPUTUM. Southeast Asian J Trop Med Public Health 2015; 46:63-70. [PMID: 26513906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
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.
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Wongboot W, Chomvarin C, Namwat W. PHENOTYPIC AND GENOTYPIC DETECTION OF ENTEROTOXINS, TOXIC SHOCK SYNDROME TOXIN-1 AND OF METHICILLIN RESISTANCE IN STAPHYLOCOCCUS AUREUS ISOLATED FROM RETAIL READY-TO-EAT FOODS IN NORTHEASTERN THAILAND. Southeast Asian J Trop Med Public Health 2015; 46:97-104. [PMID: 26513910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Toxigenic Staphylococcus aureus contamination of ready-to-eat (RTE) foods is a leading cause of foodborne illness in Thailand. From 151 RTE food samples randomly collected from food vendors and food shops in Khon Kaen municipality, Thailand and after culture-based identification of S. aureus isolates, pentaplex PCR was used for simultaneous detection of super-antigenic toxin (SE) genes (sea, seb, sec, sed and tst-1) and presence of their toxins by reversed passive latex agglutination assay. S. aureus was identified in 57 isolates, of which 60% and 25% was positive for presence of super-antigenic toxin genes and toxins, respectively; and among the former isolates sea was the most common (46%), as well as its product (SEA) (14%) among the latter group. Methicillin resistance S. aureus mecA was not found in any of the isolates using both PCR and disk diffusion methods. These results showed that pentaplex PCR is a useful tool for detection of SE-encoding genes in S. aureus isolates from RTE food.
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Tabunhan S, Wongratanacheewin S, Wongwajana S, Welbat TU, Faksri K, Namwat W. Characterization of a novel two-component system response regulator involved in biofilm formation and a low-iron response of Burkholderia pseudomallei. Southeast Asian J Trop Med Public Health 2014; 45:1065-1079. [PMID: 25417508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
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.
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Namwat W, Somnate B, Maleehual D, Chareonsudjai S, Lulitanond V, Faksri K. Cloning, expression and characterization of Mycobacterium tuberculosis sirR. Southeast Asian J Trop Med Public Health 2014; 45:689-699. [PMID: 24974654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
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.
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Sutantangjai M, Faksri K, Chaicumpar K, Chaimanee P, Lulitanond V, Namwat W. Evaluation of an immunochromatographic test kit for detecting Mycobacterium tuberculosis complex in sputum samples and on solid and in liquid cultures. Southeast Asian J Trop Med Public Health 2014; 45:357-364. [PMID: 24968676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A rapid, cheap and effective method for diagnosing tuberculosis (TB) is essential for TB control. We evaluated the performance of an immunochromatographic assay (ICA) kit (SD Bioline TB Ag MPT64 rapid test) designed for detecting Mycobacterium tuberculosis complex (MTC) in liquid and solid cultures to determine its ability to detect and differentiate MTC directly in sputum samples. We attempted to optimize antigen extraction using several sputum solvents under various conditions. Adding the sputum solvent prior to using the ICA kit gave a sensitivity of 71.7% (43/60) for all acid-fast bacillus (AFB) stain positive specimens and a 100% specificity (20/20) among AFB negative specimens. Without sputum solvent, the ICA kit had 0% sensitivity for detecting MTC in sputum. We also evaluated the ICA test kit for its designed purpose of detecting MTC in 80 solid and liquid culture specimens positive for MTC using the niacin accumulation test or polymerase chain reaction (PCR) (16s-23s ITS). The ICA kit gave 100% sensitivity and specificity. We also evaluated the ICA test kit on 3 reference specimens of MTC, 15 nontuberculous mycobacteria (NTM) species, 7 bacterial species and 5 Candida albicans specimens. The tested ICA kit gave 100% specificity. The tested ICA kit was useful for detecting and differentiating MTC in solid and liquid cultures, but not useful for detecting MTC in sputum samples even treated with sputum solvent. The tested ICA kit should be used only for liquid and solid culture specimens. Therefore, the tested kit is inappropriate for use in evaluating sputum samples.
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Hanchaina R, Lulitanond V, Namwat W, Faksri K. Development of single-tube multiplex PCR for classification of Mycobacterium tuberculosis lineages based on large sequence polymorphisms. Southeast Asian J Trop Med Public Health 2014; 45:365-374. [PMID: 24968677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
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.
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Neamnak J, Tabunhan S, Wongwajana S, Wongratanacheewin S, Chamgramol Y, Pairojkul C, Faksri K, Namwat W. Comparison of stress adaptation and survival rate between Burkholderia pseudomallei with mutant and wild type bfmR. Southeast Asian J Trop Med Public Health 2014; 45:346-351. [PMID: 24968674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Burkholderia pseudomallei (Bp) is highly adaptable to a wide range of environmental changes for survival and pathogenesis. However, the underlying mechanisms of such adaptability are still unclear. Two-component system (TCS) is a common signal transduction used by bacteria in response to environmental changes. A gene designated as bfmR (locus tag of BPSL2024) has been proposed to encode a response regulator, a member of the TCS, and was studied by mutagenesis and comparison of its phenotypic changes compared with those of the wild type. The growth rates of the mutant Bp at temperatures of 37 degrees-39 degrees C and pH 5-8 were significantly lower than the wild type strain (p < 0.05), especially at 39 degrees C (p = 0.01) and pH 7 (p = 0.01). The survival rate of the mice infected with the mutant strain is not significantly different from mice infected with wild type strain. The defective phenotypes were recovered in the complemented strain. These results indicated that bfmR is involved in adaptation of Bp to thermal- and pH-induced stress conditions.
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Suebwongsa N, Panya M, Namwat W, Sookprasert S, Redruello B, Mayo B, Alvarez MA, Lulitanond V. Cloning and expression of a codon-optimized gene encoding the influenza A virus nucleocapsid protein in Lactobacillus casei. Int Microbiol 2014; 16:93-101. [PMID: 24400527 DOI: 10.2436/20.1501.01.184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Lactic acid bacteria (LAB) species are envisioned as promising vehicles for the mucosal delivery of therapeutic and prophylactic molecules, including the development of oral vaccines. In this study, we report on the expression of a synthetic nucleocapsid (NP) gene of influenza A virus in Lactobacillus casei. The NP gene was re-designed based on the tRNA pool and the codon usage preference of L. casei BL23. The codon-optimized NP gene was then cloned and expressed in L. casei RCEID02 under the control of a constitutive promoter, that of the lactate dehydrogenase (ldh) gene. The synthetic NP gene was further expressed in L. casei EM116 under the control of an inducible promoter, that of the structural gene of nisin (nisA) from Lactococcus lactis. Based on Western blot analysis, the specific protein band of NP, with a molecular mass of 56.0 kDa, was clearly detected in both expression systems. Thus, our study demonstrates the success of expressing a codon-optimized influenza A viral gene in L. casei. The suitability of the recombinant LAB strains for immunization purposes is currently under evaluation.
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Affiliation(s)
- Namfon Suebwongsa
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Marutpong Panya
- College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani, Thailand
| | - Wises Namwat
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Saovaluk Sookprasert
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Senachai P, Chomvarin C, Namwat W, Wongboot W, Wongwajana S, Tangkanakul W. Application of tetraplex PCR for detection of Vibrio cholerae, V. parahaemolyticus, V. vulnificus and V. mimicus in cockle. Southeast Asian J Trop Med Public Health 2013; 44:249-258. [PMID: 23691635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A tetraplex PCR method was developed for simultaneous detection of Vibrio cholerae, V. parahaemolyticus, V. vulnificus and V. mimicus in cockle samples in comparison with conventional culture method. Specific primers targeting ompW of V. cholerae, tl of V. parahaemolyticus, hsp60 of V. vulnificus and sodB of V. mimicus were employed in the same PCR. Detection limit of the tetraplex PCR assay was 104 cfu/ml (400 cfu/PCR reaction) for pure cultures of all four species of Vibrio. In Vibrio spiked cockle samples, the limit of detection after 6 hours enrichment in alkaline peptone water was 1 cfu/10 g of cockle tissue for three Vibrio spp, except for V. mimicus that was 102 cfu/10 g of cockle tissue. When the tetraplex PCR and culture methods were applied to 100 cockle samples, V. parahaemolyticus, V. vulnificus, V. cholerae and V. mimicus were detected in 100, 98, 80 and 9% of the samples by tetraplex PCR and in 76, 42, 0 and 0% by the culture method, respectively. This developed tetraplex PCR method should be suitable for simultaneous and rapid detection of Vibrio species in food samples and for food safety assessment.
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Affiliation(s)
- Pachara Senachai
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Boonyanugomol W, Chomvarin C, Sripa B, Chau-in S, Pugkhem A, Namwat W, Wongboot W, Khampoosa B. Molecular analysis of Helicobacter pylori virulent-associated genes in hepatobiliary patients. HPB (Oxford) 2012; 14:754-63. [PMID: 23043664 PMCID: PMC3482671 DOI: 10.1111/j.1477-2574.2012.00533.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The Helicobacter pylori virulence-associated genes in hepatobiliary patients, including vacA, iceA, babA2, cagA and cagE, have not been reported. The aim of this study was to investigate these genes and the association of those and the clinical outcomes in hepatobiliary diseases. METHODS Eighty H. pylori-PCR-positive cases were obtained from hepatobiliary patients, representing both cholangiocarcinoma (CCA) (n= 58) and cholelithiasis (n= 22). The diversity of virulence genes was examined by polymerase chain reaction and DNA sequencing. Phylogenetic analysis of cagA was determined using the maximum parsimony method. RESULTS The vacAs1a + c/m1, iceA1 and babA2 genes were the most predominant genotypes in both CCA and cholelithiasis patients. The cagA and cagE genes were found significantly more frequently in patients with CCA than those with cholelithiasis (P < 0.05). The cagA positive samples were the Western-type cagA and showed that almost all of the detected sequences in Thai hepatobiliary and Thai gastric cancer patients were classified in the same cluster but separated from the cluster of Japan and other countries. CONCLUSIONS The cagA and cagE genes may be associated in the pathogenesis of hepatobiliary diseases, especially of CCA. Besides the bacterial variation, other host factors may be involved in the pathogenesis of hepatobiliary cancer.
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Affiliation(s)
- Wongwarut Boonyanugomol
- Department of MicrobiologyKhon Kaen,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen UniversityKhon Kaen
| | - Chariya Chomvarin
- Department of MicrobiologyKhon Kaen,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen UniversityKhon Kaen
| | - Banchob Sripa
- Department of PathologyKhon Kaen,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen UniversityKhon Kaen
| | - Siri Chau-in
- Department of SurgeryKhon Kaen,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen UniversityKhon Kaen
| | - Ake Pugkhem
- Department of SurgeryKhon Kaen,Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen UniversityKhon Kaen
| | | | | | - Bandit Khampoosa
- School of Bioinformatics and Systems Biology, King Mongkut's University of Technology ThonburiBangkok, Thailand
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Kulsantiwong P, Chomvarin C, Mairiang P, Sangchan A, Chanlertrith K, Chaicumpar K, Namwat W, Kularbkaew C. PCR-RFLP and antimicrobial susceptibility profiles of Helicobacter pylori isolated from antrum and corpus of dyspeptic patients in Thailand. Southeast Asian J Trop Med Public Health 2012; 43:933-942. [PMID: 23077816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The study determined the genetic heterogeneity of Helicobacter pylori isolates from antrum and corpus of the same dyspeptic patients in a Thai population and determined the relationship between the antimicrobial susceptibility (AS) profile (antibiogram) and PCR-restriction fragment length polymorphism (PCR-RFLP) pattern. One hundred and nineteen H. pylori isolates comprising 7 single and 56 paired antrum and corpus isolates obtained by gastric biopsy from 160 dyspeptic patients were analyzed. For PCR-RFLP, the 820 bp amplicon of ureC was digested with Sau3AI and HhaI, which revealed 16 (A-Q) and 19 (a- s) different PCR-RFLP patterns after Sau3AI and HhaI digestion, respectively. Combination of the restriction enzyme digestion patterns resulted in 35 distinct RFLP types. Among the 56 paired isolates, 47 were infected with H. pylori having the same AS and PCR-RFLP profiles, 7 with different AS profiles but the same PCR-RFLP profiles and 2 with different PCR-RFLP profiles but the same AS profiles. No patient was infected with H. pylori different in both PCR-RFLP and AS profiles. The results indicate that the majority of the paired H. pylori isolates displayed identical AS profile and PCR-RFLP patterns suggesting that most patients were infected with a single strain. Some patients could have been infected with single strains that were different in the AS profiles.
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Affiliation(s)
- Panthong Kulsantiwong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Chomvarin C, Phusri K, Sawadpanich K, Mairiang P, Namwat W, Wongkham C, Hahnvajanawong C. Prevalence of cagA EPIYA motifs in Helicobacter pylori among dyspeptic patients in northeast Thailand. Southeast Asian J Trop Med Public Health 2012; 43:105-115. [PMID: 23082560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The aims of this study were to determine the prevalence of cagA type in Helicobacter pylori isolated from dyspeptic patients in northeastern Thailand and to determine whether the pattern of cagA EPIYA motifs were associated with clinical outcomes. One hundred and forty-seven H. pylori-infected dyspeptic patients were enrolled, of whom 68 had non-ulcer dyspepsia (NUD), 57 peptic ulcer disease (PUD), 18 gastric cancer (GCA), and 4 other gastroduodenal diseases. PCR and DNA sequence analysis were used to determine the cagA genotype and the pattern of EPIYA motifs. cagA-positive H. pylori were identified in 138 (94%) of H. pylori-infected dyspeptic patients of whom 75 (54%) were of the Western-type, 44 (32%) the East Asian type and 19 (14%) of the other types. The Western type is significantly found in PUD patients (p = 0.0175). The majority of cagA EPIYA was EPIYA-ABC (43%) and EPIYA-ABD (28%). There is no significant correlation between the increase in number of EPIYA-C motifs and clinical outcomes. Thus, the most frequent cagA type found among northeastern Thai dyspeptic patients was the Western cagA type, which is significantly associated with PUD indicating a possible predictive parameter for clinical outcome.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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Panya M, Lulitanond V, Tangphatsornruang S, Namwat W, Wannasutta R, Suebwongsa N, Mayo B. Sequencing and analysis of three plasmids from Lactobacillus casei TISTR1341 and development of plasmid-derived Escherichia coli-L. casei shuttle vectors. Appl Microbiol Biotechnol 2011; 93:261-72. [PMID: 21822904 DOI: 10.1007/s00253-011-3503-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/12/2011] [Accepted: 07/19/2011] [Indexed: 11/26/2022]
Abstract
Pyrosequencing followed by conventional PCR and sequencing was used to determine the complete nucleotide sequence of three plasmids (pRCEID2.9, pRCEID3.2, and pRCEID13.9) from the Lactobacillus casei strain TISTR1341. The plasmid sequences were found to be almost identical, respectively, to those of pLA106, pLA105, and pLA103 from Lactobacillus acidophilus strain TK8912, suggesting that these strains may be related. Sequence analysis and comparison indicated that pRCEID2.9 replicates by a rolling circle (RC) mechanism, while pRCEID3.2 and pRCEID13.9 probably follow a theta-type mode of replication. Replicons of pRCEID2.9 and pRCEID13.9 were used to develop Escherichia coli/L. casei compatible shuttle vectors, which were stably maintained in different genetic backgrounds. Real-time quantitative PCR analysis showed copy numbers of around 4 and 15, respectively, for the pRCEID13.9- and pRCEID2.9-derived shuttle vectors per chromosome equivalent. The functionality of vector pRCEID-LC13.9 was proved by cloning and expressing in L. casei of a green fluorescent protein gene variant from Aequorea victoria under the control of the promoter from a homologous lactate dehydrogenase gene. The new vectors might complement those currently in use for the exploitation of L. casei as a cellular factory and in other biotechnological applications.
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Affiliation(s)
- Marutpong Panya
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Ottiwet O, Chomvarin C, Chaicumpar K, Namwat W, Mairiang P. Nested polymerase chain reaction for detection of Helicobacter pylori in gastric biopsy specimens. Southeast Asian J Trop Med Public Health 2010; 41:1423-1431. [PMID: 21329319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Sensitivity and specificity are important for tests used to defect Helicobacter pylori infection from gastric biopsy specimens. Molecular methods, such as PCR and nested PCR, are sensitive methods for H. pylori detection. The objective of this study was to evaluate the performance of PCR and nested PCR compared to culture, the rapid urease test (RUT) and histology for the diagnosis of H. pylori in 130 gastric biopsy specimens from symptomatic dyspeptic patients. Sensitivity and specificity with PCR were 91 and 100% and with nested PCR were 95 and 97%, respectively. H. pylori was detected by PCR and nested PCR at levels as low as 125 fg (70 cells) and 25 fg (14 cells), respectively. These results suggest nested PCR is a highly sensitive direct method to detect H. pylori infection from biopsy specimens.
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Affiliation(s)
- Orawan Ottiwet
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Hahnvajanawong C, Boonyanugomol W, Nasomyon T, Loilome W, Namwat N, Anantachoke N, Tassaneeyakul W, Sripa B, Namwat W, Reutrakul V. Apoptotic activity of caged xanthones from Garcinia hanburyi in cholangiocarcinoma cell lines. World J Gastroenterol 2010; 16:2235-43. [PMID: 20458760 PMCID: PMC2868216 DOI: 10.3748/wjg.v16.i18.2235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the growth inhibitory mechanism of four caged xanthones from Garcinia hanburyi in cholangiocarcinoma (CCA) KKU-100 and KKU-M156 cells.
METHODS: Four caged xanthones, selected on the basis of their anticancer potency and chemical structure diversities (i.e. isomorellin, isomorellinol, forbesione and gambogic acid) were used in this study. Growth inhibition of these caged xanthones was determined using the sulforhodamine B assay. Induction of apoptosis was assessed by observing cell morphology, ethidium bromide and acridine orange staining and DNA fragmentation assay. Levels of apoptotic-related gene and protein expressions were determined by a real-time reverse transcriptase polymerase chain reaction and Western blotting analysis, respectively.
RESULTS: The compounds were found to inhibit growth of both cell lines in a dose-dependent manner and also showed selective cytotoxicity against the cancer cells when compared with normal peripheral blood mononuclear cells. Growth suppression by these compounds was due to apoptosis, as evidenced by the cell morphological changes, chromatin condensation, nuclear fragmentation, and DNA ladder formation. At the molecular level, these compounds induced down-regulation of Bcl-2 and survivin proteins with up-regulation of Bax and apoptosis-inducing factor proteins, leading to the activation of caspase-9 and -3 and DNA fragmentation. The functional group variations did not appear to affect the anticancer activity with regard to the two CCA cell lines; however, at a mechanistic level, isomorellinol exhibited the highest potency in increasing the Bax/Bcl-2 protein expression ratio (120 and 41.4 for KKU-100 and KKU-M156, respectively) and in decreasing survivin protein expression (0.01 fold as compared to control cells in both cell lines). Other activities at the molecular level indicate that functional groups on the prenyl side chain may be important.
CONCLUSION: Our findings for the first time demonstrate that four caged xanthones induce apoptosis in CCA cells which is mediated through a mitochondria-dependent signaling pathway.
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Kulsuntiwong P, Chomvarin C, Chaicumpar K, Namwat W, Kaewkes W, Mairiang P, Sangchan A. Antimicrobial susceptibility of Helicobacter pylori isolated from gastric biopsies in dyspeptic patients. Southeast Asian J Trop Med Public Health 2008; 39:1102-1109. [PMID: 19062703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The objective of this study was to evaluate the prevalence of antimicrobial resistance in Helicobacter pylori isolated from the antrum and corpus of dyspeptic patients in Khon Kaen, Thailand, and to compare the antimicrobial susceptibility patterns of H. pylori isolated from the antrum and corpus in individual patients. Antimicrobial susceptibility was determined by disk diffusion, studying susceptibility to metronidazole, clarithromycin, amoxicillin, erythromycin, ciprofloxacin, and tetracycline. The H. pylori resistant rate to at least one of the six antimicrobial agents tested was 37%. The resistance rates were 30.2% for metronidazole, 9.2% for ciprofloxacin, 5% for clarithromycin, 2.4% for amoxicillin, and 1.7% for erythromycin and tetracycline. Single, double, and more than double antimicrobial resistances were found in 27.7, 6.7 and 2.5%, respectively. Antimicrobial susceptibility testing revealed 11 antibiotypes. The most common antimicrobial susceptibility pattern found was sensitivity to 6 antimicrobial agents (63%). H. pylori antimicrobial resistance in specimens isolated from the antrum and corpus were nearly equivalent, 37.3% (22/59) and 36.7% (22/60), respectively. Most of the H. pylori specimens isolated from the antrum and corpus in individual patients were identical (87.7%).
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Affiliation(s)
- Panthong Kulsuntiwong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Chomvarin C, Jumroenjit W, Chaicumpar K, Namwat W. Association of ompU gene in Vibrio cholerae from patients and environment with bile resistance. Southeast Asian J Trop Med Public Health 2008; 39:876-881. [PMID: 19058583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The objective of this study was to determine whether Vibrio cholerae, possessing ompU isolated from patients and the environment, conferred bile resistance and whether other virulence genes were also related to bile resistance. Fifty-two V cholerae O1 and non-O1 isolates were examined by PCR for the presence of the virulence-associated and regulatory genes, ctxA, tcpA, zot, ace, ompU, toxR, hlyA and stn/sto. V. cholerae possessing ompU resistant to equal or greater than 10% sodium deoxycholate were found in 93% of isolates but only in 9% of V. cholerae isolates not possessing ompU. The effects of other virulence genes on bile resistance could not be ascertained in this study. Thus V cholerae non-O1 with ompU and possibly other virulence genes isolated from the environment have the potential of affecting public health.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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Chomvarin C, Namwat W, Wongwajana S, Alam M, Thaew-Nonngiew K, Sinchaturus A, Engchanil C. Application of duplex-PCR in rapid and reliable detection of toxigenic Vibrio cholerae in water samples in Thailand. J GEN APPL MICROBIOL 2007; 53:229-37. [PMID: 17878662 DOI: 10.2323/jgam.53.229] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Toxigenic Vibrio cholerae, the cause of cholera, is a native flora of the aquatic environment which is transmitted through drinking water and still remains the leading cause of morbidity and mortality in many developing countries including Thailand. The culture method (CM), which is routinely used for assessing water quality, has not proven as efficient as molecular methods because the notorious pathogen survives in water mostly in a non-culturable state. We employed duplex-polymerase chain reaction (duplex-PCR) for detection of tcpA and ctxA genes in toxigenic V. cholerae, and compared PCR detection with CM in various waters of Khon Kaen Municipality, Thailand. We also evaluated the effect of different pre-PCR conditions on the results of ctxA and tcpA detection including: 1) water filtered and enriched in alkaline peptone water (APW) for 3 h before PCR, 2) water filtered without enrichment before PCR, and 3) use of only enrichment in APW for 6 h before PCR. Of the 96 water samples (taken from waste-water, potable and waste-water from patients' houses, and from rivers) tested, 48 (50%) were positive for ctxA and tcpA by duplex-PCR, whereas only 29 (30%) were positive for V. cholerae by CM. Of the 29 V. cholerae isolated by CM, 2 (7%) were toxigenic V. cholerae belonging to serovar O1, while the rests were non-O1/ non-O139. Results revealed, therefore, that ctxA and tcpA-targeted duplex PCR is more sensitive than CM for detection of toxigenic V. cholerae from water samples because CM detected much less toxigenic V. cholerae than the non-toxigenic V. cholerae. Template DNA as low as 100 fg or 23 cells of V. cholerae in the water sample was detected in duplex PCR. Pre-PCR filtration followed by enrichment for 3 h significantly increase in the efficiency of duplex-PCR detection of toxigenic V. cholerae.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand.
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Chomvarin C, Namwat W, Chaicumpar K, Mairiang P, Sangchan A, Sripa B, Tor-Udom S, Vilaichone RK. Prevalence of Helicobacter pylori vacA, cagA, cagE, iceA and babA2 genotypes in Thai dyspeptic patients. Int J Infect Dis 2007; 12:30-6. [PMID: 17548220 DOI: 10.1016/j.ijid.2007.03.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Revised: 02/28/2007] [Accepted: 03/05/2007] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES To investigate the prevalence of the vacA, cagA, cagE, iceA, and babA2 genotypes in Helicobacter pylori strains isolated from Thai dyspeptic patients, and to determine whether any correlation exists between these genotypes and clinical manifestations. METHODS Helicobacter pylori was examined in 112 patients (62 with non-ulcer dyspepsia (gastritis), 34 with peptic ulcer disease, and 16 with gastric cancer (GCA)), detected by culture or direct detection from gastric biopsies. Allelic variants of the vacA, cagA, cagE, iceA, and babA2 genotypes were identified by using the polymerase chain reaction. RESULTS The positive rates for the vacAs1, vacAs2, cagA, cagE, iceA1, iceA2, and babA2 genes in H. pylori of dyspeptic patients were 100%, 0%, 98.2%, 88.4%, 45.5%, 33.1%, and 92%, respectively. The allelic variant vacAs1m1 was more prevalent (58%) than vacAs1m2 (42%). The cagA and cagE genes were commonly found together (87.5%). The most predominant genotypes were vacAs1m1, cagA, cagE, iceA1, and babA2. The various genes alone or in combination had no statistically significant association with the clinical outcomes (p>0.05). CONCLUSION Neither single gene nor combination of vacA, cagA, cagE, iceA, and babA2 genes was significantly helpful in predicting the clinical outcome of H. pylori infection in Thai patients. The high prevalence of these genes in H. pylori isolated from Thai patient groups suggests that H. pylori strains are geographically dependent.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
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Chomvarin C, Chantarasuk Y, Mairiang P, Kularbkaew C, Sangchan A, Chanlertrith K, Namwat W. Sensitivity and specificity of an in-house rapid urease test for detecting Helicobacter pylori infection on gastric biopsy. Southeast Asian J Trop Med Public Health 2006; 37:312-9. [PMID: 17124992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We developed an in-house rapid urease test (iRUT) and evaluated the efficacy and the agreement of the iRUT and the cRUT compared with culture and histology for the detection of H. pylori infection. Five iRUT media were tested with H. pylori isolates and other bacteria. The most suitable iRUT medium was further evaluated for detection of H. pylori infection. Gastric biopsies from 120 patients were diagnosed by culture, iRUT, cRUT and histology. The results of the iRUT and cRUT were read at 30 minutes, 1 hour and up to 24 hours. A true positive result was either the culture or both the RUT (cRUT or iRUT) and the histological examination being positive. The sensitivity and specificity of the iRUT result at 30 minutes, 1 hour and up to 24 hours were 77.1% and 100%, 77.6% and 100%, and 94.1% and 94.2%, respectively. Values for the same parameters of cRUT were 87.5% and 100%, 89.8% and 100%, and 100% and 94.2%, respectively. The agreement between the iRUT and cRUT was very good (kappa values > or = 0.82). Our results indicate that the iRUT is a-sensitive, specific and cost effective test. It can be appropriately applied for detecting H. pylori infection in gastric biopsy specimens.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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Chomvarin C, Ratchtrachenchai OA, Chantarasuk Y, Srigulbutr S, Chaicumpar K, Namwat W, Kotimanusvanij D. Characterization of diarrheagenic Escherichia coli isolated from food in Khon Kaen, Thailand. Southeast Asian J Trop Med Public Health 2005; 36:931-9. [PMID: 16295548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Four categories of 186 ready-to-eat food samples in Khon Kaen municipality, Thailand, were collected and investigated for fecal contamination by enumeration of Escherichia coli using the most probable number (MPN) method. Then, the E. coli isolates were presumptively identified as diarrheagenic E. coil by agglutinating with polyvalent O-antisera and monovalent O-antisera commonly found in diarrheagenic strains and were subsequently investigated for the presence of the recognized virulence genes for enteroaggregative (EAEC), enteroinvasive (EIEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), and shiga toxin-producing E. coli (STEC or EHEC) by multiplex PCR assays. All E, coli isolates were examined for antimicrobial susceptibilities by the agar disc diffusion method, and the results were compared with those obtained from clinical samples. The percentage of each type of food with E. coli, including no heat food, low heat food, high heat food, and fruit juices and beverages, was higher than accepted standards at 60.4, 46.5, 38.6 and 20%, respectively. Of 140 E. coli isolates obtained from food samples, 11 isolates (7.9%) agglutinated with 6 monovalent O-antisera, including one isolate each of O6, O8, O114 and O159, two isolates of O1, and five isolates of O157. None of the 11 isolates harbored the virulence genes for EPEC, ETEC, EAEC, EIEC and STEC. Although O157 E. coli isolates were found, the most frequent, E. coli O157:H7, was not found in this study. The astA gene, however, was found in 1 E. coli isolate that showed weakly positive agglutination against the polyvalent antisera. Approximately 50% of the 140 E. coli isolates were resistance to at least one antimicrobial agent. The resistant strains showed high resistance to tetracycline (43%), co-trimoxazole (36%), ampicillin (26%) and chloramphenicol (23%), respectively. The resistance of E. coli was high for nearly all antimicrobial agents, particularly ampicillin (76%), tetracycline (70%), co-trimoxazole (69%) and nalidixic acid (44%). The results show that nearly half of the ready-to-eat food samples evaluated in Khon Kaen Municipality had levels of E. coli higher than acceptable standards. Of the diarrheagenic E. coli classified by serogroup, almost none of the isolates had virulence genes. These results indicate the disadvantage of relying on serogrouping alone for the recognition of diarrheagenic E. coli. E. coli isolated from food may not be an enteropathogenic strain. We also found that E. coli antimicrobial resistant strains are widespread in both food and humans.
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Affiliation(s)
- Chariya Chomvarin
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
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Tepsiri N, Chaturat L, Sripa B, Namwat W, Wongkham S, Bhudhisawasdi V, Tassaneeyakul W. Drug sensitivity and drug resistance profiles of human intrahepatic cholangiocarcinoma cell lines. World J Gastroenterol 2005; 11:2748-53. [PMID: 15884115 PMCID: PMC4305909 DOI: 10.3748/wjg.v11.i18.2748] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To study the effect of a number of chemotherapeutic drugs on five human intrahepatic cholangiocarcinoma (CCA) cell lines. The expressions of genes that have been proposed to influence the resistance of chemotherapeutic drugs including thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD), glutathione-S-transferase P1 (GSTP1), multidrug resistance protein (MDR1) and multidrug resistance-associated proteins (MRPs) were also determined.
METHODS: Five human CCA cell lines (KKU-100, KKU-M055, KKU-M156, KKU-M214 and KKU-OCA17) were treated with various chemotherapeutic drugs and growth inhibition was determined by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay. Semi-quantitative levels of gene expression were determined by a reverse transcriptase polymerase chain reaction (RT-PCR). Results of IC50 values and the ratios of gene expression were analyzed by linear regression to predict their relationship.
RESULTS: Among five CCA cell lines, KKU-M055 was the most sensitive cell line towards all chemotherapeutic drugs investigated, particularly taxane derivatives with IC50 values of 0.02-3 nmol/L, whereas KKU-100 was apparently the least sensitive cell line. When compared to other chemotherapeutic agents, doxorubicin and pirarubicin showed the lowest IC50 values (<5 μmol/L) in all five CCA cell lines. Results from RT-PCR showed that TS, MRP1, MRP3 and GSTP1 were highly expressed in these five CCA cell lines while DPD and MRP2 were only moderately expressed. It should be noted that MDR1 expression was detected only in KKU-OCA17 cell lines. A strong correlation was only found between the level of MRP3 expression and the IC50 values of etoposide, doxorubicin and pirarubicin (r = 0.86-0.98, P<0.05).
CONCLUSION: Sensitivity to chemotherapeutic agents is not associated with the histological type of CCA. Choosing of the appropriate chemotherapeutic regimen for the treatment of CCA requires knowledge of drug sensitivity. MRP3 was correlated with resistance of CCA cell lines to etoposide, doxorubicin and pirarubicin, whereas other chemotherapeutic drugs showed no association. The role of this multidrug resistance-associated protein, MRP3, in chemotherapeutic resistance in CCA patients needs to be further investigated.
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Affiliation(s)
- Nisana Tepsiri
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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Namwat W, Kinoshita H, Nihira T. Identification by heterologous expression and gene disruption of VisA as L-lysine 2-aminotransferase essential for virginiamycin S biosynthesis in Streptomyces virginiae. J Bacteriol 2002; 184:4811-8. [PMID: 12169606 PMCID: PMC135275 DOI: 10.1128/jb.184.17.4811-4818.2002] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The visA gene of Streptomyces virginiae has been thought to be a part of the virginiamycin S (VS) biosynthetic gene cluster based on its location in the middle of genes that encode enzymes highly similar to those participating in the biosynthesis of streptogramin-type antibiotics. Heterologous expression of the visA gene was achieved in Escherichia coli by an N-terminal fusion with thioredoxin (TrxA), and the intact recombinant VisA protein (rVisA) was purified after cleavage with enterokinase to remove the TrxA moiety. The purified rVisA showed clear L-lysine 2-aminotransferase activity with an optimum pH of around 8.0 and an optimum temperature at 35 degrees C, with 2-oxohexanoate as the best amino acceptor, indicating that VisA converts L-lysine into Delta(1)-piperidine 2-carboxylic acid. A visA deletion mutant of S. virginiae was created by homologous recombination, and the in vivo function of the visA gene was studied by phenotypic comparison between the wild type and the visA deletion mutant. No differences in growth in liquid media or in morphological behavior on solid media were observed, indicating that visA is not involved in primary metabolism or morphological differentiation. However, the visA mutant failed to produce VS while maintaining the production of virginiamycin M(1) at a level comparable to that of the parental wild-type strain, demonstrating that visA is essential to VS biosynthesis. These results, together with the observed recovery of the defect in VS production by the external addition of 3-hydroxypicolinic acid (3-HPA), a starter molecule in VS biosynthesis, suggest that VisA is the first enzyme of the VS biosynthetic pathway and that it supplies 3-HPA from L-lysine.
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Affiliation(s)
- Wises Namwat
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Abstract
Streptomyces virginiae produces -butyrolactone autoregulators (virginiae butanolide, VB), which control the biosynthesis of virginiamycin M1 and S. A 6.3-kb region downstream of the virginiamycin S (VS)-resistance operon in S. virginiae was sequenced, and four plausible open reading frames (ORFs) (visA, 1,260 bp; visB, 1,656 bp; visC, 888 bp; visD, 1209 bp) were identified. Homology analysis revealed significant similarities with enzymes involved in the biosynthesis of cyclopeptolide antibiotics: VisA (53% identity, 65% similarity) to -lysine 2-aminotransferase (NikC) of nikkomycin D biosynthesis, VisB (66% identity, 72% similarity) to 3-hydroxypicolinic acid:AMP ligase of pristinamycin I biosynthesis, VisC (48% identity, 59% similarity) to lysine cyclodeaminase of ascomycin biosynthesis, and VisD (43% identity, 56% similarity) to erythromycin C-22 hydroxylase of erythromycin biosynthesis. Northern blotting as well as high-resolution S1 analysis of the ORFs revealed that they were transcribed as two bicistronic transcripts, namely 3.0-kb visB-visA and another 2.7-kb visC-visD transcript, with promoters locating upstream of visB and visC, respectively. Transcription of the two operons was observed only 1 h after the VB production, which was 2 h before the virginiamycin production. Furthermore, prompt induction of the transcription was observed as a result of external VB addition, suggesting that the expression of the two operons was under the control of VB.
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Affiliation(s)
- Wises Namwat
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Namwat W, Lee CK, Kinoshita H, Yamada Y, Nihira T. Identification of the varR gene as a transcriptional regulator of virginiamycin S resistance in Streptomyces virginiae. J Bacteriol 2001; 183:2025-31. [PMID: 11222601 PMCID: PMC95098 DOI: 10.1128/jb.183.6.2025-2031.2001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene designated varR (for virginiae antibiotic resistance regulator) was identified in Streptomyces virginiae 89 bp downstream of a varS gene encoding a virginiamycin S (VS)-specific transporter. The deduced varR product showed high homology to repressors of the TetR family with a conserved helix-turn-helix DNA binding motif. Purified recombinant VarR protein was present as a dimer in vitro and showed clear DNA binding activity toward the varS promoter region. This binding was abolished by the presence of VS, suggesting that VarR regulates transcription of varS in a VS-dependent manner. Northern blot analysis revealed that varR was cotranscribed with upstream varS as a 2.4-kb transcript and that VS acted as an inducer of bicistronic transcription. Deletion analysis of the varS promoter region clarified two adjacent VarR binding sites in the varS promoter.
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Affiliation(s)
- W Namwat
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Namwat W, Luangsuk P, Palittapongarnpim P. The genetic diversity of Mycobacterium tuberculosis strains in Thailand studied by amplification of DNA segments containing direct repetitive sequences. Int J Tuberc Lung Dis 1998; 2:153-9. [PMID: 9562126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To develop and use a polymerase chain reaction (PCR) method for studying the genetic diversity of Mycobacterium tuberculosis. DESIGN Two polymorphic DNA segments of M. tuberculosis H37Rv were identified and sequenced. Primers were then designed for simultaneous amplification of both polymorphic segments. The method was used for studying 179 clinical isolates of M. tuberculosis that had been previously characterized by Southern hybridization with IS6110. RESULTS Both polymorphic segments contained direct repetitive sequences. In one segment the direct repetitive sequences were within the putative coding sequence of alpha-isopropylmalate synthase gene. After amplifying both segments of the 179 isolates, 40 patterns of PCR products could be identified. The method was able to differentiate 38 IS6110-single-banded isolates into 23 types. Most of the isolates belonging to the Beijing family had PCR products identical to the H37Rv strain. The PCR products of the members of the Nonthaburi group were similar to each other. CONCLUSION These results agree with the hypothesis that the members of the Beijing family and the Nonthaburi group descended from two common ancestors. The PCR method might be useful for differentiating strains of M. tuberculosis that contain a single copy of IS6110.
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Affiliation(s)
- W Namwat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Thailand
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