Variable-number Tandem-repeat Patterns Research Articles

Molecular Analysis of Enterococcus Faecalis Isolates in a 4-year Period.

In the present research, we aimed to determine the characteristics of E. faecalis strains collected from an Iranian Children's Hospital for four years. Sixty-seven E. faecalis isolates with virulence genes detection, variable-number tandem repeat (VNTR), and multiple-locus variable-number tandem repeat analysis (MLVA) typing were investigated. A high frequency of virulence genes belonged to gelatinase (73%) and Enterococcus faecalis (62%). The MLVA of 67 E. faecalis isolates revealed 52 VNTR patterns and 38 MLVA types (MTs). Furthermore, genetic diversities with the majority of the MT1 as a major MT in different Wards of the Children's Hospital were found.

Genotyping of Equine Lawsonia intracellularis Sampled in Japan by Using Multilocus Variable-Number Tandem Repeat Analysis

The incidence of equine proliferative enteropathy, caused by Lawsonia intracellularis, is increasing around the world. To investigate the relationships of variable-number tandem repeat (VNTR) patterns with host species and clinical status in horses, multilocus VNTR analysis (MLVA) was applied to 98 L. intracellularis samples collected from horses, seven from pigs, seven from wildlife, one vaccine strain, and 17 public strains. The VNTR patterns were highly diverse: a total of 130 samples identified 99 distinct patterns, and the 98 horses were classified into 71 different patterns. A phylogenetic tree based on the MLVA showed three clusters: porcine, equine, and miscellaneous cluster. The equine cluster contained 46 horse samples, of which 42 (91.3%) were collected from two sampling areas. The MLVA could discriminate horse samples from pig, but the horse samples in the miscellaneous cluster could not be distinguished from wildlife samples. As for clinical data of the horses, the VNTR patterns were unrelated to horse age, clinical signs, and clinical outcomes. This study shows that VNTR patterns had no clear connection with equine clinical status, but the MLVA could be useful to investigate its epidemiological relationships, and interspecific transmission of L. intracellularis between horse and wildlife cannot be ruled out.

A tuberculosis outbreak in a psychiatric hospital: Kanagawa, Japan, 2012.

In January 2012, an inpatient in a ward of a psychiatric hospital with nearly 300 beds in Kanagawa, Japan, was diagnosed with sputum smear-positive pulmonary tuberculosis (TB). Here we characterise the TB outbreak cases and identify the population at risk. TB was diagnosed when a person tested bacteriologically positive for TB or was determined to have TB by a physician. A latent TB infection (LTBI) case was defined as a person tested positive by interferon-gamma release assay (IGRA). A total of 125 contacts were screened via IGRA and chest X-ray. In all, 15 TB and 15 LTBI cases were found by the end of October 2012, and thereafter no additional TB case was found. Of the 15 TB cases, eight were culture-positive and all the isolates had identical variable number tandem repeat patterns. Twenty-four of the 56 (42.9%, 95% confidence interval (CI) 29.7-56.8) inpatients in the ward had either TB or LTBI with a relative risk of 8.6 (95% CI 1.2-59.3), compared to the staff members who did not work full-time in the ward (one of 20 (5.0%, 95% CI 0.0-24.9)). We recommend that psychiatric hospitals conduct periodic screening of staff members and inpatients for TB to prevent nosocomial TB outbreaks.

Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable Resistant Mycobacterium tuberculosis Complex Isolates in the Netherlands from 2004 to 2016.

The variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering of Mycobacterium tuberculosis isolates with identical VNTR patterns is assumed to reflect recent transmission. Hence, clusters are thought to be homogeneous regarding antibiotic resistance. In practice, however, heterogeneous clusters are also identified. This study investigates the prevalence and characteristics of heterogeneous VNTR clusters and assesses whether isolates in these clusters remain clustered when subjected to whole-genome sequencing (WGS). In the period from 2004 to 2016, 9,072 isolates were included. Demographic and epidemiological linkage data were obtained from the Netherlands Tuberculosis Register. VNTR clusters were defined as homogeneous when isolates shared identical resistance profiles or as heterogeneous if both susceptible and (variable) resistant isolates were found. Multivariate logistic regression analysis was performed to identify factors associated with heterogeneous clustering. Isolates from 2016 were subjected to WGS, and a genetic distance of 12 single nucleotide polymorphisms (SNPs) was used as the cutoff for WGS clustering. In total, 4,661/9,072 (51%) isolates were clustered into 985 different VNTR clusters, of which 217 (22%) were heterogeneous. Patient characteristics associated with heterogeneous clustering were non-Dutch ethnicity (odds ratio [OR], 1.46 [95% confidence interval {CI}, 1.22 to 1.75]), asylum seeker (OR, 1.51 [95% CI, 1.24 to 1.85]), extrapulmonary TB (OR, 1.26 [95% CI, 1.09 to 1.46]), previous TB diagnosis (OR, 1.38 [95% CI, 1.04 to 1.82]), and not being a contact of a TB patient (OR, 1.35 [95% CI, 1.08 to 1.69]). With WGS, 34% of heterogeneous and 78% of homogeneous isolates from 2016 remained clustered. Heterogeneous VNTR clusters are common but seem to be explained by a substantial degree of false clustering by VNTR typing compared to WGS.

VNTR analysis demonstrates new patterns and high genetic diversity of Leptospira sp. of animal origin in Brazil.

Animal leptospirosis is an important cause of reproductive failure in livestock and economic losses to producing countries. This study describes several novel variable-number tandem repeats patterns and points out the high genetic diversity of Brazilian strains. Understanding the circulation of strains between animals is essential for the control of leptospirosis in livestock.

Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis

Massive internal migration from rural to urban areas poses new challenges for tuberculosis control in China. We aimed to combine genomic, spatial, and epidemiological data to describe the dynamics of tuberculosis in an urban setting with large numbers of migrants. We did a population-based study of culture-positive Mycobacterium tuberculosis isolates in Songjiang, Shanghai. We used whole-genome sequencing to discriminate apparent genetic clusters of M tuberculosis sharing identical variable-number-tandem-repeat (VNTR) patterns, and analysed the relations between proximity of residence and the risk of genomically clustered M tuberculosis. Finally, we used genomic, spatial, and epidemiological data to estimate time of infection and transmission links among migrants and residents. Between Jan 1, 2009, and Dec 31, 2015, 1620 cases of culture-positive tuberculosis were recorded, 1211 (75%) of which occurred among internal migrants. 150 (69%) of 218 people sharing identical VNTR patterns had isolates within ten single-nucleotide polymorphisms (SNPs) of at least one other strain, consistent with recent transmission of M tuberculosis. Pairs of strains collected from individuals living in close proximity were more likely to be genetically similar than those from individuals who lived far away-for every additional km of distance between patients' homes, the odds that genotypically matched strains were within ten SNPs of each other decreased by about 10% (OR 0·89 [95% CI 0·87-0·91]; p<0·0001). We inferred that transmission from residents to migrants occurs as commonly as transmission from migrants to residents, and we estimated that more than two-thirds of migrants in genomic clusters were infected locally after migration. The primary mechanism driving local incidence of tuberculosis in urban centres is local transmission between both migrants and residents. Combined analysis of epidemiological, genomic, and spatial data contributes to a richer understanding of local transmission dynamics and should inform the design of more effective interventions. National Natural Science Foundation of China, National Science and Technology Major Project of China, and US National Institutes of Health.

Mycobacterium tuberculosis Diversity by Exact Tandem Repeats-Variable Number Tandem Repeat Method in Azerbaijan, Iran

Background Tuberculosis (TB) is the leading cause of adult deaths among infectious agents. One of the genetic fingerprinting techniques to study the epidemiology of TB is variable number tandem repeat (VNTR). The purpose of this study was to determine the diversity of Mycobacterium tuberculosis isolated from patients in Azerbaijan, Iran by exact tandem repeats (ETR)-VNTR method. Methods We used the ETR-VNTR method to analyze the genotypes of M. tuberculosis isolates. Forty-seven isolates were collected from pulmonary and extra pulmonary Tuberculosis patients associated with epidemiological data such as human immunodeficiency virus, anti-TB drugs use, cigarette smoking, diabetes mellitus, lung cancer, contact with TB patients, Bacillus Calmette–Guérin vaccine use, cough, housekeeping, fever, and other risk factors from April 2013 to February 2015 in Tabriz Research Center of Tuberculosis and Lung Disease. Three loci ETR-A, ETR-B, and ETR-C of VNTR patterns were studied. The patients' data were checked to determine the relationships between the epidemiological data and M. tuberculosis diversities. Results Among the 47 isolates, 45 separate ETR-VNTR patterns consist of 9 clusters, 24 nonclusters (unique patterns) were found. No locus was observed in 2 samples. Diabetes and close household contacts were identified as important risk factors for TB in our subjects with unique patterns. Conclusions Thirty-three distinct patterns were distinguished. In the case of respiratory symptoms in patients with diabetes and close household contact patients, TB can be considered as the important differential diagnosis with unique patterns.

Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands

ABSTRACTSince 2004, variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084; P = 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386; P = 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants.

Association between sequevar and antibiotic treatment outcome in patients with Mycobacterium abscessus complex infections in Japan

Macrolide susceptibility differs between subspecies in the Mycobacterium abscessus complex, likely due to differences in erm(41) sequevars. Patients with M. abscessus complex infection generally show poor clinical outcomes in response to antibiotic treatment. Here, the association between genotype and treatment outcome was investigated. We collected 69 isolates from 35 patients with non-cystic fibrosis bronchiectasis: 24 had M. abscessus complex lung disease and non-cystic fibrosis bronchiectasis, and 11 were colonized. Outcome analysis was performed in the 24 infected patients. Molecular analyses, including erm(41) and rrl sequencing, and variable-number tandem-repeat (VNTR) analysis of 69 isolates, from 24 infected and 11 colonized patients, were performed to elucidate the influence of genotype on antibiotic susceptibility. Among the 24 patients, 18 (14 infected with M. abscessus subsp. abscessus and 4 with M. abscessus subsp. massiliense) showed unfavourable outcomes; six (three infected with M. abscessus subsp. abscessus and three with M. abscessus subsp. massiliense) exhibited favourable outcomes. Patients with unfavourable outcomes showed acquired clarithromycin resistance (33.3 vs 0 %), mixed sequevars (38.9 vs 16.7 %) and differing VNTR patterns between initial and serial isolates (33.3 vs 16.7 %). In contrast, in the 11 colonized patients, M. abscessus subsp. abscessus C28 (sequevar 02) and M. abscessus subsp. massiliense were the most prevalent subspecies. Patients infected with multiple sequevars and genotypes were more likely to exhibit treatment failure and/or recurrence. The precise identification of subspecies and analyses of mycobacterial characteristics may help to predict treatment outcomes in patients with M. abscessus complex lung disease.

Transmission is a Noticeable Cause of Resistance Among Treated Tuberculosis Patients in Shanghai, China

It is generally believed that drug resistance among treated tuberculosis (TB) patients is as a result of acquired drug resistance due to inappropriate treatment. Previous studies have shown that primary drug resistance caused by transmission also plays a role among treated cases. Differentiating the two types of drug resistance will help in developing appropriate strategies for control of drug resistant tuberculosis. In this study, we tested the hypothesis that drug resistance among treated TB patients is mainly caused by primary resistance rather than acquired resistance. Defining resistance profiles by molecular drug susceptibility test, we used Unit Variable Number Tandem Repeats (VNTR) to genotype and Whole Genome Sequencing (WGS) to confirm the accordance of the first and last Mycobacterium tuberculosis isolates from treated pulmonary TB patients in Shanghai from 2009–2015. Among 81 patients with increasing drug resistance, out of 390 patients enrolled, paired isolates from 59.3% (48/81) had different VNTR patterns indicating primary drug resistance. Our results have demonstrated that primary resistance due to exogenous reinfection is the major cause of drug resistance among treated TB patients in Shanghai; thus, strategies aimed at preventing and interrupting transmission are urgently needed to effectively reduce the epidemic of drug resistant tuberculosis.

Variable-number tandem-repeat analysis of leptospiral DNA isolated from canine urine samples molecularly confirmed to contain pathogenic leptospires

OBJECTIVE To use variable-number tandem-repeat (VNTR) analysis to determine the infecting serovar and strain for leptospiral DNA isolated from canine urine samples confirmed through PCR testing to contain pathogenic leptospires and to evaluate the sensitivity and specificity of microscopic agglutination testing (MAT) for identifying the infecting serogroup. DESIGN Diagnostic survey and test evaluation. SAMPLE Leptospiral DNA isolated from urine samples from 98 dogs confirmed through PCR testing to have pathogenic leptospires in their urine. PROCEDURES VNTR analysis of DNA isolates was performed to identify the infecting leptospiral serovar and strain by use of primer pairs for the loci 4, 7, 10, and Lb5. Eighteen pathogenic and 2 saprophytic leptospiral serovars were used as reference strains for VNTR analysis. Results of MAT were compared with those of the PCR assay and VNTR analysis to determine the sensitivity and specificity of MAT for diagnosing leptospirosis and identifying the infecting serovar at various reciprocal titers. RESULTS VNTR analysis identified Leptospira kirschneri serovar Grippotyphosa strain DF as the most common infecting serovar in dogs (78/98 [80%]). Thirteen unique VNTR patterns could not be identified by comparison with the Leptospira reference strains used. The MAT had a maximum sensitivity of 41% and a specificity of 100% for identifying Grippotyphosa as the infecting serogroup. CONCLUSIONS AND CLINICAL RELEVANCE Findings confirmed the importance of Leptospira serovar Grippotyphosa among dogs in the United States. Serologic testing had poor sensitivity for identifying the infecting serogroup, and conclusions about emerging serogroups should be cautiously interpreted when serologic data are reported.

Determination of circulating Mycobacterium tuberculosis strains and transmission patterns among TB patients in Iran, using 15 loci MIRU-VNTR

Aims and objectivesTuberculosis (TB) is considered one of the most important pathogens in the world. Iran has a moderate TB incidence, but borders two high-burden TB countries to the east and one high-burden multidrug-resistant (MDR)-TB country to the north. Limited information is available on the genetic diversity and transmission dynamics of MTB in Iran.To determine the MTB genotypes and their transmission patterns among patients, a collection of isolates from different parts of Iran were genotyped. MethodsGenotypes were generated by means of standard 15-locus variable number tandem repeat (VNTR) for 121 MTB clinical isolates collected from three provinces of Iran, including Sistan–Baluchestan (southeast province of Iran, with the highest rate of TB), Kermanshah (western part of Iran with high TB/human immunodeficiency virus [HIV] cases) and Tehran (the capital of Iran). ResultsSixty-six distinct mycobacterial interspersed repetitive unit (MIRU)-VNTR patterns were detected among 121 isolates. Seventy-five strains were grouped into 20 clusters, and 46 isolates were unique. The genetic diversity of strains from Sistan–Baluchestan was higher than that in the other province. All isolates from Tehran or Kermanshah that were grouped into clusters shared more identical patterns with Sistan–Baluchestan. The Hunter-Gaston discriminatory index (HGDI) was 0.972, indicating a high power of discrimination for MIRU-VNTR typing. The MIRU 16, ETR-A, ETR-E, MTUB04 loci were designated as highly discriminative. ConclusionsMIRU-VNTR typing showed a high genetic diversity and suggests the possibility of transmission from Sistan–Baluchestan to other provinces of Iran. This method could be considered a suitable tool for studying the transmission routes of TB and leading to more appropriate measures for TB control. MIRU-VNTR typing leads to a much better understanding of the bacterial population structure and phylogenetic relationships between strains of MTB in different regions of Iran.

Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands

The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns.

MIRU-VNTR analysis of the Mycobacterium tuberculosis isolates from three provinces of Iran

Iran borders 2 high-burden tuberculosis (TB) countries to the east, and has the highest rates of TB in one of its eastern provinces. Limited information is available on the genetic diversity and transmission dynamics of Mycobacterium tuberculosis (MTB) in Iran. To examine the genetic diversity and transmission dynamics of MTB strains we genotyped a collection of isolates from different parts of Iran. Standard 15-locus variable number tandem repeat (VNTR) typing was applied to genotype 121 MTB clinical isolates collected from 3 provinces of Iran, including Tehran (the capital of Iran), Sistan-Baluchestan (southeast province of Iran, with the highest rate of TB), and Kermanshah (western part of Iran with high TB/human immunodeficiency virus cases). Antibiotic susceptibility for all isolates was determined using the proportion method. Sixty-six distinct mycobacterial interspersed repetitive unit (MIRU)-VNTR patterns were detected among 121 isolates. Seventy-five strains grouped into 20 clusters, and 46 isolates were unique. The genetic diversity of strains from Sistan-Baluchestan was higher than that in the other provinces. All isolates from Tehran or Kermanshah that grouped into clusters shared identical patterns with Sistan-Baluchestan. The Hunter-Gaston discriminatory index (HGDI) was 0.972, indicating a high power of discrimination for MIRU-VNTR typing. The MIRU 16 and ETRA loci were designated as highly discriminative. The rates of monoresistance and multidrug resistance were 9.9% and 2.4%, respectively. MIRU-VNTR typing revealed high genetic diversity and suggests the possibility of transmission from Sistan-Baluchestan to other provinces of Iran. This method has potential for genetic analysis and for studying the transmission routes of TB.

Prevalence of Ciprofloxacin and Nalidixic Acid Resistant Salmonella enterica serovar Typhi in Bangladesh

A total of 1,059 Salmonella enterica serovar Typhi were isolated from blood samples during January 2006 to October 2007 from urban rural facilities in Dhaka, Bangladesh, of which 980 (92.5%) isolates were nalidixic acid resistant. The minimum inhibitory concentrations (MIC) of ciprofloxacin (CIP) were determined for 127 nalidixic acid resistant Salmonella enterica serovar Typhi (NARST) strains (every fifth) isolated during 2006. Nine isolates were found to be resistant against CIP (3%) with high MIC (12 - &gt;32 ?g/mL). Only four isolates were found to be sensitive (MIC &lt;0.125 ?g/mL), whereas most of the isolates (N=113) showed reduced susceptibility (MIC 0.125 – 2 ?g/mL) to CIP. All these isolates were subjected to molecular typing by multiplex PCR on VNTR (variable number tandem repeats) loci, which revealed eight different VNTR patterns. Almost all CIP resistant strains had similar genetic organization, identical to the most common VNTR type. Restriction fragment length polymorphism (RFLP) analysis of the gyrA gene revealed point mutations at Ser-83 and Asp- 87 in all CIP resistant strains. DOI: http://dx.doi.org/10.3329/bjm.v28i1.11802 Bangladesh J Microbiol, Volume 28, Number 1, June 2011, pp 7-11

Heteroplasmy, Length, and Sequence Characterization of the Mitochondrial Control Region in Tomistoma schlegelii

This study describes the organization of the repetitive pattern in the mtDNA control region of Tomistoma schlegelii. Using newly designed primers, we detected length variations of approximately 50-100bp among individuals, and only one individual showed a heteroplasmic band. Sequencing the region after CSB III revealed two main patterns: a repeat motif and a variable number tandem repeat (VNTR) pattern. The VNTR region, with a core unit of 104bp, consisting of four motifs and a short AT chain, is implicated in the length variation seen among individuals of Tomistoma. A conserved motif seen in a family unit indicated that the repeat pattern was stably inherited from the maternal parent to all offspring. A combination of VNTR patterns specific to different crocodilians was seen in Tomistoma, and the overall secondary structure was shown to be similar to that in Crocodylus and Gavialis.

Different Mycobacterium avium subsp. paratuberculosis MIRU–VNTR patterns coexist within cattle herds

A better understanding of the biodiversity of Mycobacterium avium subsp. paratuberculosis (MAP) offers more insight in the epidemiology of paratuberculosis and therefore may contribute to the control of the disease. The aim of this study was to investigate the genetic diversity in bovine MAP isolates using PCR-based methods detecting genetic elements called Variable-Number Tandem Repeats (VNTRs) and Mycobacterial Interspersed Repetitive Units (MIRUs) to determine if multiple MAP strains can coexist on farms with endemic MAP infection. For 52 temporal isolates originating from infected cattle from 32 commercial dairy herds with known trading history, MIRU–VNTR analysis was applied at 10 loci of which six showed variation. Within the group of 52 isolates, 17 different MIRU–VNTR patterns were detected. One MIRU–VNTR pattern was found in 29 isolates, one pattern in four isolates, one pattern in three isolates, two times one MIRU–VNTR pattern was found occurring in two isolates, and 12 patterns were found only once. Eleven herds provided multiple isolates. In five herds a single MIRU–VNTR pattern was detected among multiple isolates whereas in six herds more than one pattern was found. This study confirms that between dairy farms as well as within dairy farms, infected animals shed MAP with different MIRU–VNTR patterns. Analysis of trading history and age within herds indicated that cows born within the same birth cohort can be infected with MAP strains exhibiting variations in the number of MIRU–VNTR repeats. These data indicate that such multiple genotypes of MAP can coexist within one herd.

Variability of Colletotrichum kahawae in Relation to Other Colletotrichum Species from Tropical Perennial Crops and the Development of Diagnostic Techniques

AbstractTwenty‐six isolates of Colletotrichum kahawae, the causal agent of coffee berry disease, from coffee in Africa, and 25 isolates, mostly of Colletotrichum gloeosporioides, from coffee and other tropical perennial crops, were examined for the ability to metabolize citrate and tartrate and their molecular genetic variability was assessed using restriction fragment length polymorphisms (RFLP) and variable number tandem repeats (VNTR). Twenty‐four isolates of C. kahawae were also assessed using amplified fragment length polymorphisms (AFLP). Vegetative compatibility within a collection of nine isolates, including two of C. gloeosporioides was also assessed. All isolates of C. kahawae from across Africa failed to metabolize citrate or tartrate, but all other isolates metabolized one or both. Colletotrichum kahawae isolates also showed minimal variability using the molecular techniques with two isolates from Cameroon showing slightly different banding patterns in RFLP analysis. All other isolates had variable VNTR and RFLP banding patterns. AFLP analysis failed to detect variability within 12 isolates from Kenya, but did detect differences between isolates from other countries. Five isolates from Kenya were vegetatively compatible but differed from two from Cameroon and from two C. gloeosporioides isolates. Results demonstrate some geographic variability within C. kahawae isolates, although this is small, probably due to the relatively young age of C. kahawae populations. The biochemical and molecular techniques used showed clear differences from other Colletotrichum isolates, and can be used to distinguish the species. Lack of citrate and tartrate metabolism provides a readily applicable diagnostic method.

Multiple-locus variable-number of tandem-repeats analysis distinguishes Vibrio parahaemolyticus pandemic O3:K6 strains

A specific serotype of Vibrio parahaemolyticus, O3:K6, has recently been linked to epidemics of gastroenteritis in Southeast Asia, Japan, and North America. These pandemic O3:K6 strains appear to have recently spread across continents from a single origin to reach global coverage, based on profiling of strains by several molecular typing methods. In this study, variable-number tandem repeats (VNTR)-based fingerprinting was applied to clinical and environmental V. parahaemolyticus O3:K6 strains in an attempt to develop a molecular method with increased sensitivity for discriminating strains; the relative discriminatory powers were compared with ribotyping and pulsed-field gel electrophoresis (PFGE). All clinical strains tested were independent human isolates obtained from different outbreaks or from sporadic cases in Tokyo during the period from 1996 to 2003. Multiple-locus VNTR analysis (MLVA) was shown to have high resolution and reproducibility for typing of V. parahaemolyticus clones. MLVA analysis of 28 pandemic V. parahaemolyticus O3:K6 strains isolated from human cases produced 28 distinct VNTR patterns. The VNTR loci displayed between 2 and 15 alleles at each of eight loci with Nei's diversity index ranging from 0.35 and 0.91. These data demonstrated that MLVA is useful for individual strain typing of new O3:K6 strains, which appear to be closely related by other molecular methods.

Identification and distribution of Mycobacterium leprae genotypes in a region of high leprosy prevalence in China: a 3-year molecular epidemiological study.

Multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) has been proposed as a means of strain typing for tracking the transmission of leprosy. However, empirical data for a defined population are lacking. To this end, a study was initiated to assess the diversity and distribution of prevalent Mycobacterium leprae strains in Qiubei County, Yunnan Province, People's Republic of China, where the annual detection rate of leprosy is 10-fold higher than the national average rate. Sixty-eight newly diagnosed leprosy patients were included in the study. MLVA at eight M. leprae loci was applied using DNA extracts from skin biopsies. The number of alleles per locus ranged from 4 to 24, providing adequate strain discrimination. MLVA strain typing identified several clusters of patients whose M. leprae specimens shared similar VNTR profiles. Two of these clusters were comprised of patients who resided predominantly in the north and northwest parts of Qiubei County. Furthermore, it was found that multicase families are common in this county: 23 of the 68 patients were from 11 families. Intrafamilial VNTR profiles closely matched within six families, although they were different between the families. Moreover, VNTR patterns related to those found in some multicase families were also detected in patients in the same or adjacent townships, indicating the utility of VNTR strain typing to identify and detect short-range transmission events. Social contact through village markets is proposed as a means of transmission.