Development of a rapid quantitative PCR assay for direct detection and quantification of culturable and non-culturable Escherichia coli from agriculture watersheds

A cross comparison of QPCR to agar-based or defined substrate test methods for the determination of Escherichia coli and enterococci in municipal water quality monitoring programs

Molecular methods such as quantitative, real-time polymerase chain reaction (QPCR) are intended to shorten the period between sampling and publicly available results. Cross comparison studies in Racine, WI, USA evaluated QPCR against agar-based (US EPA Method 1600) and defined substrate (IDEXX Colilert-18) methods for the detection and quantification of Escherichia coli and enterococci in a variety of aqueous environments (wastewater, stormwater, and surface water). Regulatory outcomes were also compared based on choice of indicator and method. Positive correlation was seen between QPCR cell equivalents and viable cells through the wastewater treatment process and in all surface water samples (river or freshwater bathing beach) but not in direct stormwater discharge. For surface water samples, correlation improved with the application of a site-specific corrective factor, with regulatory action correctly predicted 98% of the time at bathing beaches. This study suggests the potential utility of QPCR for certain water quality monitoring applications.

Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade

Specific SYBR green-based quantitative-PCR assays targeting conserved regions in the 16S-23S rRNA internal transcribed spacer regions were developed for five subgroups of the environmentally abundant and biogeochemically active Roseobacter clade of marine bacteria. The assays were applied to field samples demonstrating their utility in investigations of abundant Roseobacter group phylotypes in the environment.

Enterotoxigenic Escherichia coli in sewage-impacted waters and aquatic weeds: quantitative PCR for culture-independent enumeration

AIM

To develop quantitative PCR for culture-independent enumeration of enterotoxigenic Escherichia coli (ETEC) in sewage-impacted waters and aquatic weeds.

METHODS AND RESULTS

Two fluorescent probes (TaqMan and FRET) based on two different real-time PCR chemistries were designed in highly conserved region of LT1 gene encoding heat labile enterotoxin. Both the assays could detect 2 CFU ml(-1) from serially diluted (two-fold and ten-fold) culture of reference strain (E. coli MTCC 723). FRET performed better in terms of CT value and PCR efficiency than TaqMan. The presence of 10(6) CFU ml(-1) of nonpathogenic E. coli reduced the detection limit two-fold with both the probes. However, the performance for two chemistries in various environmental samples was significantly (student's t-test, P<0.05) different.

CONCLUSION

It could be inferred from this study that real-time PCR chemistries (TaqMan and FRET) could detect very few copies of target DNA in pure cultures, but may give varied response in the presence of nonspecific DNA and natural inhibitors present in environmental sample matrices.

SIGNIFICANCE AND IMPACT OF THE STUDY

The assays can be used for pre-emptive monitoring of aquatic weeds (a potential nonpoint source), surface and potable waters to prevent waterborne outbreaks caused by ETEC.

Characterization of cefoxitin-resistant Escherichia coli isolates from recreational beaches and private drinking water in Canada between 2004 and 2006

A total of 142 cefoxitin-resistant Escherichia coli isolates from water sources were collected across Canada. Multidrug resistance was observed in 65/142 (45.8%) isolates. The bla(CMY-2) gene was identified in 110/142 (77.5%) isolates. Sequencing of the chromosomal ampC promoter region showed mutations from the wild type, previously shown to hyperproduce AmpC. CMY-2-producing plasmids predominantly belonged to replicon groups I1-Igamma, A/C, and K/B. The majority of the E. coli isolates belonged to the nonvirulent phylogenetic groups A and B1.

Screening for residual disease in pediatric burkitt lymphoma using consensus primer pools

Assessing molecular persistent or minimal residual disease (PD/MRD) in childhood Burkitt lymphoma (BL) is challenging because access to original tumor is usually needed to design patient-specific primers (PSPs). Because BL is characterized by rearranged immunoglobulin heavy chain (IgV_H) genes, IgV_H primer pools from IgV_H1–IgV_H7 regions were tested to detect PD/MRD, thus eliminating the need for original tumor. The focus of the current study was to assess the feasibility of using IgV_H primer pools to detect disease in clinical specimens. Fourteen children diagnosed with B-NHL had follow-up repository specimens available to assess PD/MRD. Of the 14 patients, 12 were PD/MRD negative after 2 months of therapy and remained in remission at the end of therapy; 2/14 patients were PD/MRD positive at 2-3 months and later relapsed. PSP-based assays from these 14 patients showed 100% concordance with the current assay. This feasibility study warrants further investigation to assess PD/MRD using IgV_H primer pools, which could have clinical significance as a real-time assessment tool to monitor pediatric BL and possibly other B-cell non-Hodgkin lymphoma therapy.

Ecological characterization of the colonic microbiota of normal and diarrheic dogs

We used terminal restriction fragment polymorphism (T-RFLP) analysis to assess (1) stability of the fecal microbiota in dogs living in environments characterized by varying degrees of exposure to factors that might alter the microbiota and (2) changes in the microbiota associated with acute episodes of diarrhea. Results showed that the healthy canine GI tract harbors potential enteric pathogens. Dogs living in an environment providing minimal exposure to factors that might alter the microbiota had similar microbiotas; the microbiotas of dogs kept in more variable environments were more variable. Substantial changes in the microbiota occurred during diarrheic episodes, including increased levels of Clostridium perfringens, Enterococcus faecalis, and Enterococcus faecium. When diet and medications of a dog having a previously stable microbiota were changed repeatedly, the microbiota also changed repeatedly. Temporal trend analysis showed directional changes in the microbiota after perturbation, a return to the starting condition, and then fluctuating changes over time.

Rapid culture-independent quantitative detection of enterotoxigenic Escherichia coli in surface waters by real-time PCR with molecular beacon

Rapid and reliable detection of enterotoxigenic Escherichia coli (ETEC) is critical for the management of the waterborne diseases threatening human lives worldwide. In this study, a culture-independent real-time PCR assay, in molecular beacon format was designed and validated for detection and quantitative enumeration of ETEC harboring LT1 gene (encoding heat labile toxin) in surface waters contaminated by fecal pollutants of human and animal origin. It was observed that the assay was able to detect 2 CFU/mL of ETEC (r = 0.997; PCR efficiency = 99.8%) from water samples spiked by a reference organism (E. coli MTCC 723). In the presence of 10(6) CFU/mL of nonpathogenic E. coli(E. coli DH5alpha), the lowest detection limit from spiked water samples was 4 CFU/mL. The assay was 500 times more sensitive than conventional PCR using the same oligomers (Student's t test p < 0.05). The assay could specifically detect and quantify ETEC (1.2 x 10(3) to 1.4 x 10(6) CFU/100 mL) in polluted surface waters of river Gomti. The rapid culture-independent assay developed in this study for detection and quantitative enumeration of ETEC can be used for preliminary monitoring of surface waters to prevent waterborne outbreaks.

Genetic background of IL-10(-/-) mice alters host-pathogen interactions with Campylobacter jejuni and influences disease phenotype

We hypothesized that particular genetic backgrounds enhance rates of colonization, increase severity of enteritis, and allow for extraintestinal spread when inbred IL-10(-/-) mice are infected with pathogenic C. jejuni. Campylobacter jejuni stably colonized C57BL/6 and NOD mice, while congenic strains lacking IL-10 developed typhlocolitis following colonization that mimicked human campylobacteriosis. However, IL-10 deficiency alone was not necessary for the presence of C. jejuni in extraintestinal sites. C3H/HeJ tlr4(-/-) mice that specifically express the Cdcs1 allele showed colonization and limited extraintestinal spread without enteritis implicating this interval in the clinical presentation of C. jejuni infection. Furthermore, when the IL-10 gene is inactivated as in C3Bir tlr4(-/-) IL-10(-/-) mice, enteritis and intensive extraintestinal spread were observed, suggesting that clinical presentations of C. jejuni infection are controlled by a complex interplay of factors. These data demonstrate that lack of IL-10 had a greater effect on C. jejuni induced colitis than other immune elements such as TLR4 (C3H/HeJ, C3Bir IL-10(-/-)), MHC H-2g7, diabetogenic genes, and CTLA-4 (NOD) and that host genetic background is in part responsible for disease phenotype. C3Bir IL-10(-/-) mice where Cdcs1 impairs gut barrier function provide a new murine model of C. jejuni and can serve as surrogates for immunocompromised patients with extraintestinal spread.