Genomic analysis of local isolate of Mycobacterium avium subspecies paratuberculosis.

Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne's disease (JD or paratuberculosis) in animals and has also been implicated in Crohn's disease of humans. It has been shown that MAP is endemic in animal population of India. Understanding of heterogeneity among MAP strains is important both for diagnosis and design control measures. Genotyping and epidemiological investigations revealed that MAP 'Bison type' was the predominant strain infecting domestic ruminant population in India. MAP 'Bison type' has also been reported from USA. A number of comparative genomics studies have been conducted to understand 'Cattle type' and 'Sheep type' strains. However, present study was the first attempt to characterize MAP 'Bison type' S5 using different markers including IS900, ISMAP02, IS1311, LSPs and SSRs. Study showed that MAP S5 is similar to MAP K10 in terms of number of IS900, IS1311 and ISMAP02 elements. There was high sequence similarity for IS900 and ISMAP02 between MAP K10 and MAP S5. However, this study also reported genetic differences between two strains. In some IS1311 loci, TG gap at 64th and 65th position was observed in MAP S5. Further sequencing of few more MAP isolates confirmed that this gap was specific to indigenous MAP 'Bison type' and can be further used as molecular signature. ISMAP02 locus 1 was observed at polymorphic position in MAP S5 compared to MAP K10. MAP 'Bison type' S5 also showed polymorphic profile for LSP(P)4. Polymorphism was also observed in SSRs. This pilot study may form the basis for future epidemiological investigations.

Non-chemical method of DNA recovery and characterization of Mycobacterium avium subspecies paratuberculosis using IS 900 PCR.

In the present study, two methods of DNA isolation-routine, traditional and standard DNA isolation protocol for Mycobacteria (Method 1) and a new non-chemicals and non-enzymes (physical) method (Method 2) of DNA recovery have been compared and evaluated in IS900 PCR for the specific detection of pathogen. Using the new Method 2, DNA has been recovered from few (1 - 3 colonies), extremely minute and stunted colonies. DNA, thus, isolated from these colonies (colonies PCR) and cultured for the first time from the cases of Crohn's disease in human beings, dairy cattle, raw milk and pasteurized commercial milk samples has been characterized in the present study. It is the first report from India.

Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression.

BACKGROUND AND AIMS: Crohn's disease (CD) and intestinal tuberculosis (ITB) are both chronic granulomatous conditions with similar phenotypic presentations. Hence, there is need for a biomarker to differentiate between both these two diseases. This study aimed at genome-wide gene expression analysis of colonic biopsies from confirmed cases of ITB and CD in comparison with controls. To evaluate the role of T regulatory cells, forkhead box P3 (FOXP3) mRNA expression was quantified in serum as well as in colonic biopsies from patients with ITB and with the controls. METHODS: Paired samples, including serum and colonic biopsies, were taken from 33 study subjects (CD, ITB and controls), and total RNA was extracted. Human whole genome gene expression microarray analysis was performed using the Illumina HumanWG-6 BeadChip Kit with six total RNA samples of the three groups in duplicates. Real-time PCR for FOXP3 mRNA expression was analyzed in serum samples and colonic biopsy samples (4-CD, 5-ITB, 4-controls). RESULTS: In CD and ITB there was 1.5-fold upregulation of 92 and 382 genes and 1.5-fold downregulation of 91 and 256 genes, respectively. Peroxisome proliferators via the PPARγ pathway were most significantly downregulated (P < 0.005) in CD. Additionally, the IL4/5/6 signaling pathways and Toll-like receptor signaling pathway were identified as significantly differentially regulated (P < 0.005) at > 2-fold change. In ITB, the complement activation pathway, specifically the classical pathway, was the most significantly upregulated. FOXP3 mRNA expression was significantly elevated in colonic biopsies obtained from ITB patients as compared with CD cases (4.70 ± 2.21 vs 1.48 ± 0.31, P = 0.016). CONCLUSIONS: FOXP3 mRNA expression in colonic mucosa could be a discriminatory marker between ITB and CD. Upregulation of the complement activation pathway in ITB suggests that pathogenetic mechanisms for ITB are similar to those of pulmonary tuberculosis. In CD, downregulation of PPARγ was seen in colonic tissue, suggesting that restoration of PPARγ-dependent anti-microbial barrier function may be a therapeutic target.

Adverse Drug Reactions to Anti-TB Drugs: Pharmacogenomics Perspective for Identification of Host Genetic Markers.

Adverse drug reactions (ADRs) are associated with clinical morbidity and, in severe cases, even mortality. Globally billions of dollars are spent on managing these ADRs for common and uncommon diseases. The developing world suffers from a high burden of tuberculosis, which requires 6-8 months of multi-drug treatment. In spite of most cases being treatable the problem persists mainly due to a high attrition rate associated with ADR mediated complications. Due to these reasons drug resistant strains have emerged and are now a serious challenge to TB eradication. To effectively deliver the available treatment regimen and ensure patient compliance it is important to manage ADRs more efficiently. Recent studies have demonstrated that drug outcomes are patient-specific and can, therefore be predicted. A few of these drugs, including a few administered for TB, have shown excellent correlation with response rates and development of ADRs. In this review, we profile information available in public domain for existing anti-TB drugs to understand the genesis of ADRs and patient response. Additionally, human genome variation databases have been used to correlate the frequency of these markers and their genomic variants in different populations.

GSIT: An integrated web-tool for identification of genomic signatures in highly similar DNA sequences.

UNLABELLED: Accurate identification and characterization of infectious agent and its subtype is essential for efficient treatment of infectious diseases on a target population of patients. Comparative biology of microbial populations in vitro and in vivo can identify signatures that may be used to develop and improve diagnostic procedures. Here we report Genomic Signature Identification Tool (GSIT) a web based tool for identification and validation of genomic signatures in a group of similar DNA sequences of microorganisms. GSIT uses multiple sequence alignment to identify the unique base sites and scores them for inclusion as genomic signature for the particular strain. GSIT is a web based tool where the front-end in designed using HTML/CSS and Javascript, while back-end is run using CGI-Perl. AVAILABILITY: The server is freely available at the http://genome-sign.net/gsit.

Mutation profiling of the hepatitis B virus strains circulating in North Indian population.

AIMS: The aim of this study was to investigate the genomic mutations in the circulating Hepatitis B virus strains causing infection in the Indian population. Further, we wanted to analyze the biological significance of these mutations in HBV mediated disease. METHODS: 222 HBsAg positive patients were enrolled in the study. The genotype and mutation profile was determined for the infecting HBV isolate by sequencing overlapping fragments. These sequences were analyzed by using different tools and compared with previously available HBV sequence information. Mutation Frequency Index (MFI) for the Genes and Diagnosis group was also calculated. RESULTS: HBV Genotype D was found in 55% (n = 121) of the patient group and genotype A was found in 30% (n = 66) of samples. The majority (52%) of the HBV-infected individuals in the present study were HBeAg-negative in all the age groups studied. Spontaneous drug associated mutations implicated in resistance to antiviral therapy were also identified in about quarter of our patients, which is of therapeutic concern. The MFI approach used in the study indicated that Core peptide was the most conserved region in both genotypes and Surface peptide had highest mutation frequency. Few mutations in X gene (T36A and G50R) showed high frequency of association with HCC. A rare recombinant strain of HBV genotype A and D was also identified in the patient group. CONCLUSIONS: HBV genotype D was found out to be most prevalent. More than half of the patients studied had HBeAg negative disease. Core region was found to be most conserved. Drug Associated mutations were detected in 22% of the patient group and T36A and G50R mutations in X gene were found to be associated with HCC.

Mycobacterium avium subspecies paratuberculosis diagnosis and geno-typing: genomic insights.

Effective control of paratuberculosis and investigations of potential link to Crohn's disease have been hampered by the lack of effective assays for easy and accurate diagnosis of Mycobacterium avium subspecies paratuberculosis (Map). Map is extremely fastidious and depends on iron chelator (Mycobactin). Map strains from humans and sheep are very difficult to isolate and may require years to emerge. Therefore, small numbers of Map isolates have been maintained in available collections. This situation has limited the study of biodiversity of Map. Though, much is known about environmental and host factors that contribute to paratuberculosis disease, but little is known about bacterial genetic mechanism of infection. Diagnostic and strain typing markers still demand improvements. Complete genome sequence of Map K10 strain is available in public domain for comparative genomics with other mycobacteria and clinical isolates of Map. It is anticipated that the genome sequence will help in carrying molecular diagnosis and strain typing with respect to Map forward at rapid pace. This paper reviews the current diagnostic and strain typing markers, which may be useful in typing of clinical isolates in near future.

Genetic characterization of VP3 gene of group A rotaviruses.

We sequenced VP3 gene of four rotavirus strains and examined the diversity of VP3 and its other genetic characteristics in a total of 22 Group A rotaviruses. The 22 rotavirus strains were derived from six different host species (human, avian, bovine, equine, simian and porcine). Comparison of the partial VP3 peptide sequences (aa 141-294) showed identities ranging from 49 to 99% among different species. The phylogenetic analysis of VP3 sequences revealed segregation according to the species origin. This was further confirmed by identification of three host specific domains within the VP3 peptide. Thus, the host range restriction or attenuation previously shown to associate with VP3 may be attributed to the species-specific nature of the gene.

Quantitative evaluation of rotaviral antigenemia in children with acute rotaviral diarrhea.

BACKGROUND: Rotaviral antigen and RNA have recently been identified in the serum of patients with rotaviral gastroenteritis, but the roles they play in disease remains undetermined. METHODS: Rotaviral antigen and RNA were quantified by enzyme-linked immunosorbant assay and by quantitative reverse-transcription polymerase chain reaction in stool and serum specimens from children with rotaviral diarrhea (n=102), children with nonrotaviral diarrhea (n=40), and nondiarrheal control children (n=30). RESULTS: Rotaviral antigenemia was detected in 64%, 3%, and 0% of the children with rotaviral diarrhea, the children with nonrotaviral diarrhea, and the nondiarrheal control children, respectively. The level of rotaviral antigen in serum was approximately 2x10(2) -fold lower than that in stool, and a moderate correlation was observed between the 2 levels. Rotaviral RNA was detected in 93% of the antigen-positive serum specimens. The median number of RNA copies in serum was approximately 1 x 10(5) -fold lower than that in stool, and no correlation was observed between the 2 levels. Serum levels of both antigen and RNA were inversely associated with baseline titers of rotaviral serum immunoglobulin G (P<.01). Antigenemia was also associated with G1 serotype. CONCLUSIONS: Rotaviral antigenemia and viremia were common in children with rotaviral diarrhea, but antigen and RNA levels in serum were substantially lower than those in stool. Antigenemia was associated with infection with G1 strains and with low baseline titers of rotaviral serum antibody.

Incidence of severe rotavirus diarrhea in New Delhi, India, and G and P types of the infecting rotavirus strains.

A total of 62,475 children <5 years old from a defined population of approximately 500,000 children and adults from slums in New Delhi, India, were assessed for 1 year by means of passive surveillance, to identify children who were hospitalized for diarrhea. The incidence of severe rotavirus diarrhea was estimated, and the G and P types of the infecting rotavirus strains were determined and were correlated with the clinical severity of diarrhea. Of 584 children who were hospitalized with diarrhea, 137 (23.5%) had rotavirus detected in stool specimens (incidence of rotavirus diarrhea-associated hospitalizations, 337 hospitalizations/100,000 children <5 years of age). Most cases of diarrhea (98%) occurred during the first 2 years of life, peaking at 9-11 months of age. Rotavirus-associated diarrhea occurred year-round but was predominant in winter. Among the strains that could be G-typed, G1 was the most common serotype, followed by G9 and G2; 10% of cases of diarrhea were due to mixed G-type infections. Common strains identified in the present surveillance study were P[8]G1, P[4]G2, P[8]G9, P[6]G1, P[6]G9, and P[6]G3. Children infected with G1 strains had a greater risk of developing more-severe cases of diarrhea than did children infected with other rotavirus strains (odds ratio, 2.95; 95% confidence interval, 1.3-6.67).