Objectives In this study, we performed comparative genomic and transcriptomic analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with drug-susceptible tuberculosis (DS-TB). The clinical isolates were categorized based on treatment duration: standard 6 months or >6 months.
Methods Study participants were recruited from a 2016 to 2018 tuberculosis cohort, and clinical M. tuberculosis isolates were collected from the sputum of patients with tuberculosis. We analyzed the genome and transcriptome of the isolated M. tuberculosis.
Results Genomic analysis revealed a specific non-synonymous single-nucleotide polymorphism in pe_pgrs9 and ppe34, exclusive to the group treated for >6 months. Transcriptomic analysis revealed increased expression of various virulence-associated protein family genes and decreased expression of ribosomal protein genes and ppe38 genes in the group treated for >6 months.
Conclusion The identified genetic variation and gene expression patterns may influence treatment outcomes by modulating host immune responses, increasing virulence, and potentially contributing to persister cell formation in M. tuberculosis. This study provides insights into the genetic and transcriptomic factors associated with prolonged DS-TB treatment. However, our study identified molecular characteristics using a small sample size, and further detailed studies are warranted.
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<sec><title>Objectives</title><p>The objectives of this study were to evaluate the long-term effect of anti-platelet treatment on the radiological progression of collagen-induced arthritis in rats.</p></sec><sec><title>Methods</title><p>Female Lewis rats with collagen-induced arthritis were divided into three experimental groups: saline, aspirin monotherapy (n = 12), and aspirin–clopidogrel dual therapy (n = 12). Drugs were administered daily and continued up to 70 days after the induction of arthritis. The clinical arthritis index (weight, morphology score, and paw thickness) and radiological scores were evaluated.</p></sec><sec><title>Results</title><p>The clinical arthritis index peaked on day 20, while the radiological scores peaked on day 35. No intergroup difference was observed in the clinical arthritis index throughout the experiment. The aspirin–clopidogrel dual therapy group had a significantly higher mean radiological score than the other groups (<italic>p</italic> = 0.045) on day 35. Further treatments resulted in significantly improved radiological findings in the aspirin monotherapy and aspirin–clopidogrel dual therapy groups on day 70 but no significant improvement in the saline group.</p></sec><sec><title>Conclusion</title><p>Anti-platelet agent treatment improved radiological findings on day 70. These observations emphasize the importance of a future long-term study of the effects of anti-platelet agent treatment on arthritis.</p></sec>
Objectives
A fast and accurate diagnosis is necessary to control and eliminate tuberculosis (TB). In Korea, TB continues to be a serious public health problem. In this study, diagnostic tests on clinical samples from patients suspected to have TB were performed and the sensitivity and specificity of the various techniques were compared. The main objective of the study was to compare various diagnostic tests and evaluate their sensitivity and specificity for detecting tuberculosis. Methods
From January 2013 to December 2013, 170,240 clinical samples from patients suspected to have TB were tested with smear microscopy, acid-fast bacilli culture, and real-time polymerase chain reaction (PCR). The test results were compared and data were analyzed. Results
A total of 8216 cultures tested positive for TB (positive detection rate, 4.8%). The contamination rate in the culture was 0.6% and the isolation rate of nontuberculous mycobacteria was 1.0%. The sensitivity and specificity of smear microscopy were 56.8% and 99.6%, respectively. The concordance rate between the solid and liquid cultures was 92.8%. <i>Mycobacterium</i> isolates were not detected in 0.4% of the cases in the liquid culture, whereas no <i>Mycobacterium</i> isolates were detected in 6.8% of the cases in the solid culture. The sensitivity and specificity of real-time PCR for the solid culture were 97.2% and 72.4%, respectively, whereas the corresponding data for the liquid culture were 93.5% and 97.2%. Conclusion
The study results can be used to improve existing TB diagnosis procedure as well as for comparing the effectiveness of the assay tests used for detecting <i>Mycobacterium tuberculosis</i> isolates.
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Objectives
<i>Mycobacterium intracellulare</i> is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of <i>M. intracellulare</i> is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. Methods
Antibiotic susceptibility testing, <i>hsp65</i> and <i>rpoB</i> sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 <i>M. intracellulare</i> isolates obtained from patients with pulmonary infections were performed. Results
All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR. Conclusion
The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types.
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Objectives
Our previous longitudinal multicenter-based carriage study showed that the average carriage rate of <i>Streptococcus pneumoniae</i> was 16.8% in 582 healthy children attending kindergarten or elementary school in Seoul, Korea. We assessed serotype-specific prevalence and antimicrobial resistance among colonizing pneumococcal isolates from young children in the era of low use of the seven-valent pneumococcal conjugate vaccine (PCV7). Methods
Serotypes were determined by an agglutination test with specific antisera or by a multiplex polymerase chain reaction (PCR) assay. An antimicrobial susceptibility test was performed with broth microdilution in Korean 96-well panels from Dade-MicroScan (Sacramento, CA, USA). Results
Pneumococcal colonization patterns were dynamic and longterm persistent carriage was rare, which indicated a sequential turnover of pneumococcal strains. Of the 369 pneumococci (except for 23 killed isolates), 129 (34.9%) isolates were PCV7 vaccine serotypes (VTs); 213 (57.8%) isolates were nonvaccine serotypes (NVTs); and the remaining 27 (7.2%) isolates were nontypable (NT). The highest rates of multidrug resistance (MDR) were observed in VTs (86.0%; 111/129 isolates) and NVTs (70.0%; 149/213 isolates). Conclusion
This study overall showed the frequent carriage of VTs and NVTs with MDR in healthy children attending kindergarten or elementary school. Efforts should be directed toward reducing the extensive prescription of antibiotics and using new broader vaccines to reduce the expansion of MDR strains of NVTs in our community.
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Objectives
This study aims to develop a method for calculating infection time lines for disease outbreaks on farms was developed using the 2010/2011 foot-and-mouth disease (FMD) epidemic in the Republic of Korea. Methods
Data on farm demography, the detection date of FMD, the clinical history for the manifestation of lesions, the presence of antibodies against FMD virus (including antibodies against the structural and nonstructural proteins of serotype O), vaccination status (O1 Manisa strain), the number of reactors and information on the slaughter of infected animals were utilized in this method. Results
Based on estimates of the most likely infection date, a cumulative detection probability that an infected farm would be identified on a specific day was determined. Peak infection was observed between late December and early January, but peak detection occurred in mid-January. The early detection probability was highest for pigs, followed by cattle (dairy, then beef) and small ruminants. Nearly 90% of the infected pig farms were detected by Day 11 post-infection while 13 days were required for detection for both dairy and beef cattle farms, and 21 days were necessary for small ruminant (goat and deer) farms. On average, 8.1 ± 3.1 days passed prior to detecting the presence of FMD virus on a farm. The interval between infection and detection of FMD was inversely associated with the intensity of farming. Conclusion
The results of our study emphasize the importance of intensive clinical inspection, which is the quickest method of detecting FMD infection and minimizing the damage caused by an epidemic.
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Objectives
A multiplex real-time polymerase chain reaction (RT-PCR) method was developed for the identification of three <i>Vibrio</i> species: <i>Vibrio cholerae</i>, <i>Vibrio parahaemolyticus</i>, and <i>Vibrio vulnificus</i>. Methods
Specific primers and probes targeting the <i>hlyA</i>, <i>tlh</i>, and <i>vvhA</i> genes were selected and used for multiplex real-time PCR to confirm the identification of <i>V. cholerae</i>, <i>V. parahaemolyticus</i>, and <i>V. vulnificus</i>, respectively. This method was applied to screen <i>Vibrio</i> species from environmental samples and combining it with a culture-based method, its effectiveness was evaluated in comparison with culture-based methods alone. Results
Specific PCR fragments were obtained from isolates belonging to the target species, indicating a high specificity of this multiplex real-time PCR. No cross-reactivity with the assay was observed between the tested bacteria. The sensitivity of the multiplex real-time PCR was found to have a lower limit of 10<sup>4</sup> colony-forming units/reaction for all three <i>Vibrio</i> species. The combination strategy raised the isolation ratio of all three <i>Vibrio</i> species 1.26- to 2.75-fold. Conclusion
This assay provides a rapid, sensitive, and specific technique to detect these three <i>Vibrio</i> species in the environment.
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Objective
In this study, the factors that induced a decrease in the incidence of typhoid fever were analyzed. Based on the study results, we propose a quantitative and concrete solution to reduce the incidence of typhoid fever. Methods
We analyzed the incidence and fatality rate of typhoid fever in Korea. Tap water service rate and the number of pharmacies, which affect the incidence rate of typhoid fever, were used as environmental factors. Results
To prevent typhoid fever in the community, it is necessary to provide clean tap water service to 35.5% of the population, with an individual requiring 173 L of clean water daily. Appropriate access to clean water (51% service coverage, 307 L) helped the population to maintain individual hygiene and food safety practices, which brought about a decrease in the incidence of typhoid fever, and subsequently a decrease in fatality rate, which was achieved twice. During the 8-year study period, the fatality rate decreased to 1% when the population has access to proper medical service. Conclusion
The fatality rate was primarily affected by the availability of medical services as well as by the incidence of typhoid fever. However, an analysis of the study results showed that the incidence of typhoid fever was affected only by the availability of clean water through the tap water system.
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Objectives
Enteroaggregative <i>Escherichia coli</i> (EAEC) was recently reported as a major diarrheagenic pathogen in infant and adult travelers, both in developing and developed countries. EAEC strains are known to be highly resistant to antibiotics including quinolones. Therefore in this study we have determined the various mechanisms of quinolone resistance in EAEC strains isolated in Korea. Methods
For 26 EAEC strains highly resistant to fluoroquinolone, minimal inhibitory concentrations for fluoroquinolones were determined, mutations in the quinolone target genes were identified by PCR and sequencing, the presence of transferable quinolone resistance mechanism were identified by PCR, and the contribution of the efflux pump was determined by synergy tests using a proton pump inhibitor. The expression levels of efflux pump-related genes were identified by relative quantification using real-time PCR. Results
Apart from two, all tested isolates had common mutations on GyrA (Ser83Leu and Ser87Gly) and ParC (Ser80Gln). Isolates EACR24 and EACR39 had mutations that have not been reported previously: Ala81Pro in ParC and Arg157Gly in GyrA, respectively. Increased susceptibility of all the tested isolates to ciprofloxacin and norfloxacin in the presence of the pump inhibitor implies that efflux pumps contributed to the resistance against fluoroquinolones. Expression of the efflux pump-related genes, <i>tolC</i>, <i>mdfA</i>, and <i>ydhE</i>, were induced in isolates EACR 07, EACR 29, and EACR 33 in the presence of ciprofloxacin. Conclusion
These results indicate that quinolone resistance of EAEC strains mainly results from the combination of mutations in the target enzyme and an increased expression of efflux pump-related genes. The mutations Ala81Pro in ParC and Arg157Gly in GyrA have not been reported previously the exact influence of these mutations should be investigated further.
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Evaluating the efficacy of an algae-based treatment to mitigate elicitation of antibiotic resistance Kassandra L. Grimes, Laura J. Dunphy, Erica M. Loudermilk, A. Jasmin Melara, Glynis L. Kolling, Jason A. Papin, Lisa M. Colosi Chemosphere.2019; 237: 124421. CrossRef
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Objectives
We aimed at evaluating the virulence of atypical <i>Shigella flexneri</i> II:(3)4,7(8) by DNA microarray and invasion assay. Methods
We used a customized <i>S. flexneri</i> DNA microarray to analyze an atypical <i>S. flexneri</i> II:(3)4,7(8) gene expression profile and compared it with that of the <i>S. flexneri</i> 2b strain. Results
Approximately one-quarter of the atypical <i>S. flexneri</i> II:(3)4,7(8) strain genes showed significantly altered expression profiles; 344 genes were more than two-fold upregulated, and 442 genes were more than 0.5-fold downregulated. The upregulated genes were divided into the category of 21 clusters of orthologous groups (COGs), and the “not in COGs” category included 170 genes. This category had virulence plasmid genes, including the <i>ipa-mxi-spa</i> genes required for invasion of colorectal epithelium (type III secretion system). Quantitative reverse-transcription polymerase chain reaction results also showed the same pattern in two more atypical <i>S. flexneri</i> II:(3)4,7(8) strains. Atypical <i>S. flexneri</i> II:(3)4,7(8) showed four times increased invasion activity in Caco-2 cells than that of typical strains. Conclusion
Our results provide the intracellularly regulated genes that may be important for adaptation and growth strategies of this atypical <i>S. flexneri</i>.
Two real-time polymerase chain reaction assays were developed to detect mutations in codons 83 and 87 in <i>gyrA</i> and in codons 80 and 91 in <i>parC</i>, the main sites that causes quinolone resistance in pathogenic <i>Escherichia coli </i>and <i>Shigella</i> spp. isolates. These assays can be employed as a useful method for controlling infections caused by quinolone-resistant <i>E coli </i>and <i>Shigella</i> isolates.
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In this study, we measured the drug resistance conferred by <i>mdfA</i> mutations in two <i>Shigella flexneri</i> strains. A mutant in <i>mdfA</i> genes was constructed by polymerase chain reaction–based, one-step inactivation of chromosomal genes. The antimicrobial susceptibility of parent and mutant strains to fluoroquinolones was determined by minimal inhibitory concentration (MICs). The <i>△mdfA</i> mutants were somewhat more susceptible to fluoroquinolones than the parent strains. The low level changes in MICs of the <i>△mdfA</i> mutants suggest that <i>mdfA</i> contributed the fluoroquinolone resistance in <i>S flexneri</i>. This finding found that the increased expression level of an MdfA efflux pump mediated fluoroquinolone resistance, but it is not likely a major effecter of higher resistance levels.
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Objectives
This study aimed to investigate the prevalence of antibiotic resistance in fecal <i>Escherichia coli</i> isolates from healthy persons and patients with diarrhea. Methods
<i>E. coli</i> isolates (<i>n</i> = 428) were obtained from fecal samples of apparently healthy volunteers and hospitalized patients with diarrhea. Susceptibility patterns of isolates to 16 antimicrobial agents were determined by agar disc diffusion. Results
Most <i>E. coli</i> isolates exhibited less than 10% resistance against imipenem, cefotetan, aztreonam, cefepime, cefoxitin, amikacin and netilamicin, although greater than 65% were resistant to ampicillin and tetracycline. No significant difference in resistance rates for all tested antibiotics was found between isolates from the healthy-and diarrheal-patient groups, including for multi-drug resistance (<i>p</i> = 0.22). The highest number of resistant antibiotics was 12 antibiotics. No significant differences in antibiotic resistance were found among the sex and age strata for isolates from healthy individuals. However, antibiotic resistance rates to cefoxitin, cefotaxime, amikacin, and netilamicin were significantly higher in the isolates of men than those of women (<i>p</i> < 0.05) in isolates from patients with diarrhea. Furthermore, isolates from patients with diarrhea older than 40-years of age showed higher resistance to cefepime and aztreonam (<i>p</i> < 0.05). Conclusion
High resistance to the antibiotics most frequently prescribed for diarrhea was found in isolates from patients with diarrhea and apparently healthy individuals without any significant difference.
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Objectives
<i>Vibrio vunificus</i> is known to cause septicemia and severe wound infections in patients with chronic liver diseases or an immuno-compromised condition. We carried out the molecular characterization of <i>V. vulnificus</i> isolates from human <i>Vibrio</i> septicemia cases based on pulsed-field gel electrophoresis (PFGE) using NotI and SfiI. Methods and Results
PFGE was used to characterize a total of 78 strains from clinical cases after NotI or SfiI digestion. The geographical distribution of PFGE patterns for the strains from the southern part of Korea, a high-risk region for <i>Vibrio</i> septicemia, indicated that the isolates from southeastern Korea showed a comparatively higher degree of homology than those from southwestern Korea. Conclusions
We report the genetic distribution of <i>V. vulnficus</i> isolated from <i>Vibrio</i> septicemia cases during 2000–2004 in Korea. This method has potential use as a subspecies-typing tool for <i>V. vulnificus</i> strains isolated from distant geographic regions.
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Objectives
To characterise the genetic and serological diversity of pathogenic <i>Escherichia coli</i>, we tested 111 <i>E coli</i> strains isolated from diarrhoeal patients in Korea between 2003 and 2006. Methods
The isolates were tested through polymerase chain reaction (PCR) and slide agglutination method for the detection of virulence genes and serotypes, respectively. To compare the expression of Shiga toxin (<i>stx</i>)-1 and <i>stx2</i> genes, real-time quantitative reverse-transcriptase PCR and rapid exprssion assay, reversed-passive latex agglutination, were performed. Results
Forty-nine Shiga toxin-producing <i>E coli</i> (STEC) strains and 62 non-STEC strains, including 20 enteropathogenic <i>E coli</i>, 20 enterotoxigenic <i>E coli</i>, 20 enteroaggregative <i>E coli</i>, and 2 enteroinvasive <i>E coli</i> were randomly chosen from the strains isolated from diarrhoeal patients in Korea between 2003 and 2006. PCR analysis indicated that locus of enterocyte effacement pathogenicity island, that is, <i>eae</i>A, <i>esp</i>ADB, and <i>tir</i> genes were present in STEC, enteropathogenic <i>E coli</i>, and enteroinvasive <i>E coli</i>. Quorum sensing-related gene <i>lux</i>S was detected in most of pathogenic <i>E coli</i> strains. Major serotypes of the STEC strains were O157 (26%) and O26 (20%), whereas the non-STEC strains possessed various serotypes. Especially, all the strains with serotype O157 carried <i>stx</i>2 and the tested virulence factors. Of the STEC strains, the data of real-time quantitative reverse-transcriptase PCR and reversed-passive latex agglutination tests showed that messenger RNA- and protein expression of <i>stx</i>2 gene were higher than those of <i>stx</i>1 gene. Conclusion
Our results provide the epidemiological information regarding the trend of STEC and non-STEC infections in the general population and show the fundamental data in association of serotypes with virulence genes in diarrhoeagenic <i>E coli</i> strains from Korea.
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