Harsh Vardhan Batra

Multiplex PCR‐based strategy to detect contamination with mycotoxigenic Fusarium species in rice and fingermillet collected from southern India

BACKGROUNDnThe genus Fusarium comprises a diverse group of fungi including several species that produce mycotoxins in food commodities. In the present study, a multiplex PCR was standardised for the group-specific detection of fumonisin-producing and trichothecene-producing strains of Fusarium species. Primers for genus-level recognition of Fusarium spp. were designed from the internal transcribed spacer regions 1 and 2 of rDNA. Primers for group-specific detection were designed from the tri5 and tri6 genes involved in trichothecene biosynthesis and the fum1 and fum13 genes involved in fumonisin biosynthesis.nnnRESULTSnAmong the various genera and their strains tested, all the 85 confirmed Fusarium strains were positive for rDNA gene and the rest stayed negative. From among the Fusarium strains, 15 had amplification for trichothecene- and 20 for fumonisin-encoding genes. All PCR positive trichothecene chemotypes of Fusarium species tested were positive for chemical analysis but in the case of fumonisins, of the 20 PCR positive cultures, only 13 showed positive for chemical analysis by HPTLC.nnnCONCLUSIONnThe assay described here provided a rapid and reliable detection of trichothecene- and fumonisin-producing Fusarium directly from natural food grains and the results were always comparable with a conventional HPTLC detection method. It can, therefore, be used by the food industry to monitor quality and safety.

Genotyping of Indian Yersinia pestis strains by MLVA and repetitive DNA sequence based PCRs.

India experienced two plague outbreaks in Gujarat and Maharastra during 1994 and then in the Shimla district of Himachal Pradesh during 2002. Yersinia pestis strains recovered from rodents and pneumonic patients during the 1994 outbreaks, pneumonic patients from the 2002 Shimla outbreak and rodents trapped on the Deccan Plateau during a surveillance activity carried out in 1998 were characterized by MLVA, ERIC-PCR and ERIC-BOX-PCR. MLVA genotyping of Indian Y. pestis strains revealed strains of 2 Orientalis, 1 Mediaevalis and 1 Antiqua genotypes distributed in three distinct branches corresponding to their biovar. The Orientalis genotype strains recovered from the 1994 outbreaks and 1998 surveillance activity clustered in one branch while the Antiqua biovar strains from the Shimla outbreak and the Mediaevalis strain recovered from a rodent trapped on the Deccan Plateau region during surveillance formed the other branches. The Orientalis Y. pestis strains recovered from rodents and patients from the 1994 plague outbreaks exhibited similar MLVA, ERIC-PCR and ERIC-BOX-PCR profiles and these were closely related to the Orientalis strains recovered from the rodents trapped on the Deccan Plateau. These data provide evidence for the possible linkage between the Y. pestis strains resident in the endemic region and those that were associated with the 1994 plague outbreaks. Mediaevalis and Antiqua biovars also were recovered from the environmental reservoir on the Deccan Plateau and from the pneumonic patients of 2002 plague outbreak. Therefore, as in Central Asian and African regions, Antiqua and Mediaevalis biovars seem to be well established in the Indian subcontinent as well. ERIC-PCR DNA fingerprinting delineated genotypes similar to those defined by MLVA. Thus ERIC-PCR appears to have the potential to be used as a molecular marker in the molecular epidemiological investigations of plague.

A novel PCR–DNA probe for the detection of fumonisin-producing Fusarium species from major food crops grown in southern India

Fumonisins are a group of 20 chemically related toxic fungal metabolites mainly produced by Fusarium verticillioides and Fusarium proliferatum. In this study, attempt has been made to develop rapid detection of fumonisin-producing Fusarium species from freshly harvested rice and finger millet by novel and sensitive polymerase chain reaction–deoxyribonucleic acid (PCR–DNA) probe. One set of oligonucleotide primers was designed targeting FUM13 gene involved in fumonisin biosynthesis and PCR–DNA probe was developed for dot-blot hybridization assay. The sensitivity of developed PCR–DNA probe was determined; it could detect 10 pg genomic DNA and 1 pg of purified PCR product. To determine the practical usefulness, the developed PCR–DNA probe was evaluated onto the rice grains that were artificially inoculated with toxigenic fungal spores. Sensitivity of the developed probe was found to be 1u2009×u2009106 CFU per gram of the rice sample using dot-blot hybridization assay. The specificity of the DNA probe was validated by testing against an array of Fusarium, including Gibberella zeae clade and other fungal strains. All PCR–DNA probe results were further cross-checked with conventional high performance thin layer chromatography (HPTLC) method. PCR–DNA probe results were equivocally matched with the HPTLC method. The novel PCR–DNA probe developed in this study may find application in rapid detection of fumonisin-producing Fusarium isolates from contaminated cereal grains.

Selection and Characterization of Aptamers Using a Modified Whole Cell Bacterium SELEX for the Detection of Salmonella enterica Serovar Typhimurium.

This study describes the selection of single-stranded DNA (ssDNA) aptamers against Salmonella enterica serovar Typhimurium using a modified whole cell systematic evolution of ligands by exponential enrichment (whole cell SELEX). For evolving specific aptamers, ten rounds of selection to live Salmonella cells, alternating with negative selection against a cocktail of related pathogens, were performed. The resulting highly enriched oligonucleotide pools were sequenced and clustered into eight groups based on primary sequence homology and predicted secondary structure similarity. Fifteen sequences from different groups were selected for further characterization. The binding affinity and specificity of aptamers were determined by fluorescence binding assays. Aptamers (SAL 28, SAL 11, and SAL 26) with dissociation constants of 195 ± 46, 184 ± 43, and 123 ± 23 nM were used to develop a nanogold-based colorimetric detection method and a sedimentation assay. The former showed a better sensitivity limit of 10(2) CFU/mL using aptamer SAL 26. This approach should enable further refinement of diagnostic methods for the detection of Salmonella enterica serovar Typhimurium and of other microbial pathogens.

Involvement of c-Jun N-terminal kinase in rF1 mediated activation of murine peritoneal macrophages in vitro.

Fraction 1 (F1) protein forms a capsule on the surface of Yersinia pestis. Recently, we reported rF1-induced activation of macrophages. In current investigation, we studied the role of JNK MAPK signal transduction pathway in rF1-induced activation of macrophages in vitro. SP600125, a specific inhibitor of JNK, inhibited JNK MAPK phosphorylation, indicating the specificity of the above response. Though, the rF1-induced phosphorylation of JNK MAPK was also inhibited by upstream protein kinase C inhibitor H7, tyrosine kinase inhibitor genestein and PI3-K inhibitor wotmannin. Activation of the transcription factor NF-kB (phosphorylation of IkB) and c-Jun was observed in response to rF1 treatment. The rF1-induced JNK MAPK activity was correlated to the functional activation of macrophages by demonstrating the inhibition of NO, TNF-α production and microtubule polymerization caused by SP600125. Taken together, the data suggests the involvement of JNK MAPK/NF-kB pathway in rF1-induced activation of macrophages.

Virulence markers of LCR plasmid in Indian isolates of Yersinia pestis

Presence of 10 important yop genes in Yersinia pestis isolates (18 in number) of Indian origin from 1994 plague outbreak regions of Maharashtra (6 Rattus rattus & Tetera indica rodents) and Gujarat (11 from human patients, 1 from R. rattus) and from plague endemic regions of the Deccan plateau (8 from T. indica) was located by PCR and specific enzyme immunoassay. PCRs were standardized for six effector yops (YopE, YopH, YopJ, YopM, YopO and YopT), three translocator yops (YopB, YopD and YopK) and a regulator LcrV gene. Amplification of all the 10 yop genes was observed in isolates recovered from pneumonic patients and in 5 of 7 rodents from outbreak regions. Among these, amplification of the yopD gene was absent in all eight isolates, and that of yopM in all except one (10R). One of the isolates from rodents of the Deccan plateau (24H) was consistently negative for all the yops. Cloning and expression of truncated yopM (780 bp), yopB (700 bp) and lcrV (796 bp) genes in pQE vectors with SG13009 host cells yielded recombinant proteins for generation of monoclonal antibodies for further use in enzyme immunoassay. Ten stable reactive clones for YopB, nine for YopM and six for LcrV were obtained, all of them exhibiting specific reactions only to Y. pestis. Testing of 26 Y. pestis isolates by monoclonal antibody dot‐ELISA and Western blotting provided results identical to PCR, suggesting that the isolates that failed to show PCR amplification also had no expression of their respective proteins. The Y. pestis isolates of outbreak regions had their virulence factors intact in the LCR plasmid. Yersinia pestis isolates recovered from rodents of the Deccan plateau were relatively heterogeneous. It appears that a long residency of Y. pestis of nearly 100 years in the enzootic plague foci has resulted in shedding of virulence genes in the LCR plasmid region in a fairly large proportion of the organisms, possibly due to natural recombination.

Monoclonal Antibodies Against Recombinant Hemolysin BL Complex of Bacillus cereus

A three component complex system, designated hemolysin BL (HBL), is believed to be the major diarrheal toxin of Bacillus cereus. Identification of HBL toxin by immunoassay is advantageous over PCR as it detects the expressed form of the gene, thereby differentiating pathogenic strains from nonpathogenic strains. However, most of the immunoassays, like the BCET RPLA kit, are based on the utilization of polyclonal antisera, which show cross-reactivity at times with other Bacillus species. The use of monoclonal antibodies (MAbs) binding specifically to the B. cereus HBL toxin epitopes could be advantageous. To address the problems of non-specificity of the reported detection systems and toxicity of L(1) and L(2) components during expression, we made use of recombinant chimeric rHBL protein to generate murine monoclonal antibodies. From among the L(2) MAbs stabilized, immunoblotting analyses on B. cereus strains revealed nine MAbs to be directed against the hbl D encoded L(1) protein, two to the hbl A encoded B protein, and one with the hbl C encoded L(2) protein. When tested on a large number of B. cereus standard and other related Bacillus species, there was no cross-reactivity observed among the group of MAbs. The presence of HBL component toxins among the strains recovered from food and environmental sources was evaluated by these sets of MAbs and the results compared with that of PCRs for the individual HBL toxin gene components. The HBL toxin profile characterization of the strains by Western blot using MAbs almost matched with the PCR profiles. The MAbs reported here, therefore, can be of immense help in providing the B. cereus identification/detection reliably, rapidly, and at a relatively low cost.

Recombinant Bivalent Fusion Protein rVE Induces CD4+ and CD8+ T-Cell Mediated Memory Immune Response for Protection Against Yersinia enterocolitica Infection.

Studies investigating the correlates of immune protection against Yersinia infection have established that both humoral and cell mediated immune responses are required for the comprehensive protection. In our previous study, we established that the bivalent fusion protein (rVE) comprising immunologically active regions of Y. pestis LcrV (100–270 aa) and YopE (50–213 aa) proteins conferred complete passive and active protection against lethal Y. enterocolitica 8081 challenge. In the present study, cohort of BALB/c mice immunized with rVE or its component proteins rV, rE were assessed for cell mediated immune responses and memory immune protection against Y. enterocolitica 8081. rVE immunization resulted in extensive proliferation of both CD4 and CD8 T cell subsets; significantly high antibody titer with balanced IgG1: IgG2a/IgG2b isotypes (1:1 ratio) and up-regulation of both Th1 (TNF-α, IFN-γ, IL-2, and IL-12) and Th2 (IL-4) cytokines. On the other hand, rV immunization resulted in Th2 biased IgG response (11:1 ratio) and proliferation of CD4+ T-cell; rE group of mice exhibited considerably lower serum antibody titer with predominant Th1 response (1:3 ratio) and CD8+ T-cell proliferation. Comprehensive protection with superior survival (100%) was observed among rVE immunized mice when compared to the significantly lower survival rates among rE (37.5%) and rV (25%) groups when IP challenged with Y. enterocolitica 8081 after 120 days of immunization. Findings in this and our earlier studies define the bivalent fusion protein rVE as a potent candidate vaccine molecule with the capability to concurrently stimulate humoral and cell mediated immune responses and a proof of concept for developing efficient subunit vaccines against Gram negative facultative intracellular bacterial pathogens.

Production and characterization of monoclonal antibodies against YopM effector protein of Yersinia pestis.

The YopM is an essential virulence effector produced by the bubonic plague bacterium. Yersinia pestis specific PCR gene was developed using 780 bp fragment of yopM gene. The PCR product was further cloned (in pUC57) an subcloned (pQE32 expression vector) and transformed in SG13009 E. coli host cells. The IPTG-induced recombinant protein was expressed at approximately 32 kDa region by SDS-PAGE. The recombinant protein was with 80% purity and 3mg/mL of concentration. Polyclonal and monoclonal antibodies (MAb) were generated. A total number of nine specific monoclonal antibodies obtained reacted at 43 kDa native protein of Y. pestis. Both the PCR-based assay and immunoassays were evaluated on Indian Y. pestis strains. Isolates recovered from outbreak region were positive, whereas isolates recovered from the surveillance region were negative (except one) by yopM gene PCR- and MAb-based dot-ELISA. The PCR- and ELISA-based systems developed in the present study might be utilized for detection or strain typing of Y. pestis alone or in conjunction with virulence markers such as F1 (fraction 1) and Pla (plasminogen activator).

Generation and Characterization of Monoclonal Antibodies Against Klebsiella pneumoniae

The present work was undertaken with the aim to generate highly specific monoclonal antibodies (MAb) targeted against Klebsiella pneumoniae that could be incorporated into a highly sensitive and simple ELISA (plate and dot) based system for the rapid identification of K. pneumoniae strains. Four murine monoclonal antibodies (KP-1, KP-2, KP-3, and KP-4) reactive to K. pneumoniae were generated and stabilized. Monoclonal antibodies KP-1 and KP-2 were of IgM type and KP-3 and KP-4 were of IgG type. All of the MAbs were found to be specific to K. pneumoniae strain, as they did not show any cross reactivity when tested with 22 different species and stains of members of the Enterobacteriaceae group. In Western blotting with whole cell lysate antigens of K. pneumoniae, KP-3 and KP-4 were found to react with 70 to 110 kDa regions. The nature of the epitope recognized by all four monoclonal antibodies was carbohydrate as determined by periodate and trypsin treatment of antigens. The monoclonal antibodies were further evaluated on 20 biochemical identified K. pneumoniae strains. The KP-3 and KP-4 monoclonal antibodies produced strong reactions with 19 and 18 strains, respectively, by dot-ELISA. KP-1 and KP-2 (IgM) did not show reaction in dot-ELISA but by agglutination test these could detect 11 and 13 strains, respectively.