Enteroaggregative Escherichia coli quantification in children stool samples using quantitative PCR

Enteroaggregative Escherichia coli (EAEC) is a common cause of infectious diarrhea, especially in children living in poor‐resource countries. In this article, we present a SYBR Green‐based real‐time polymerase chain reaction (qPCR) method for quantitative detection of EAEC in DNA directly extracted from human stool samples. To test the proposed qPCR system, we examined specificity, sensitivity, repeatability, and also the degree of DNA extraction efficiency using EAEC strain 042 spiked into EAEC‐free stool sample. The specificity of this assay was proved using six strains of EAEC, seven strains of other E. coli types, and one strain of Shigella. The detection limit of qPCR was 67 CFU/reaction. In naturally infected stool samples, we found EAEC in quantities varying from 6.7 × 10⁵ to 2 × 10⁹ CFU/g of feces. We could not detect any reduction after stool DNA extraction for the amounts of 10⁷ and 10⁶ CFU/mL of spiked EAEC. This qPCR assay is simple, rapid, reproducible, sensitive, specific, and allows rapid EAEC quantification to be used in a variety of further EAEC studies. This new quantitative method provides a relatively simple means to quantify EAEC, which will likely be key to understanding the pathophysiology and impact of EAEC infection.     

Direct detection of Vibrio cholerae in stool samples.

A direct method to detect Vibrio cholerae in stool samples was developed by using a PCR procedure that did not require a DNA purification step. Dilution (1/100) of stool samples prevented inhibition of the reaction by contaminants, and two consecutive PCRs, the second one with a nested primer, achieved the desired sensitivity. Comparison of the results obtained from stool swab samples processed by the two-step PCR and by an enzyme-linked immunosorbent assay using GM1 as the capture molecule showed that the former is more sensitive and gave positive results even when V. cholerae was not culturable or dead.     

Detection of enterotoxigenic Escherichia coli in stool samples by using nonradioactively labeled oligonucleotide DNA probes and PCR.

The detection of heat-labile enterotoxin LT-A and heat-stable enterotoxin ST Ia and ST Ib genes from enterotoxigenic Escherichia coli (ETEC) by using oligonucleotide DNA probes and the PCR was evaluated in reconstruction experiments and by testing stool specimens from 29 healthy subjects and from 50 patients with diarrhea who had returned from the (sub)tropics. ETEC strains were detected in concentrations ranging from 10(6) to 10(8) CFU/g of feces when oligonucleotide probes were applied to colony blots from five randomly picked E. coli-like colonies from CLED (cystine lactose electrolyte deficient) agar plates inoculated with the feces. When these probes were applied to blots from whole stool cultures collected from the agar plates (sweep blot), the detection limit was 10(6) CFU/g of feces. PCR of the sweep material could detect toxin genes when the concentration of ETEC strains was 10(2) CFU/g of feces. Results obtained with stool specimens from 29 healthy control subjects were negative. Testing stool specimens from 50 patients confirmed the observation that the number of samples containing ETEC enterotoxin genes was higher when PCR of sweeps was used than when oligonucleotide DNA probe hybridization of either sweep blots or colony blots was used. Furthermore, PCR of sweeps is an easy and rapid method which does not require DNA extraction and purification from fecal specimens.     

Rapid detection of Mycobacterium avium in stool samples from AIDS patients by immunomagnetic PCR.

Direct PCR detection of bacteria in clinical samples is often hindered by the presence of compounds that inhibit the PCR. To improve and accelerate the diagnosis of Mycobacterium avium-M. intracellulare complex infections, an immunomagnetic PCR (IM-PCR) assay was developed. This IM-PCR procedure combines the separation of mycobacteria by antimycobacterial monoclonal antibody coupled to magnetic beads with an M. avium-M. intracellulare complex-specific PCR protocol based on 16S rRNA gene sequences. As few as 10 M. avium bacilli were detected in spiked human stool samples, a clinical specimen usually refractory to conventional PCR analysis, by the IM-PCR method. Moreover, M. avium organisms were detected in about 24 h in 18 of 22 culture-confirmed fecal samples from AIDS patients. This IM-PCR protocol should allow for the rapid and sensitive detection of M. avium isolates in clinical specimens.     

Shiga-toxigenic Escherichia coli detection in stool samples screened for viral gastroenteritis in Alberta, Canada

Shiga-toxigenic Escherichia coli (STEC) is an important cause of diarrheal disease. The most notorious STEC serotype is O157:H7, which is associated with hemorrhagic colitis and hemolytic-uremic syndrome (HUS). As a result, this serotype is routinely screened for in clinical microbiology laboratories. With the bias toward the identification of the O157 serogroup in routine diagnostic processes, non-O157 STEC has been largely underrepresented in the epidemiology of STEC infections. This diagnostic bias is further complicated by the fact that many non-O157 STEC infections cause nonspecific gastroenteritis symptoms reminiscent of enteric viral infections. In this study, real-time PCR was used to amplify Shiga toxin genetic determinants (stx(1) and stx(2)) from enriched stool samples that were initially submitted for the testing of enteric viruses in patients with suspected viral gastroenteritis between May and September of 2006, 2007, and 2008 (n = 2,702). Samples were submitted from the province of Alberta, Yukon, the Northwest Territories, and Nunavut, Canada. A total of 38 samples (1.4%) tested positive for Shiga toxin genes, and 15 isolates were cultured for further characterization. Several of the serotypes identified (O157:H7, O26:HNM, O26:H11, O103:H25, O121:H19, and O145:HNM) have been previously associated with outbreaks and HUS. This study outlines the importance of combining molecular methods with classical culture techniques to enhance the detection of emerging non-O157 as well as O157 serotypes in diarrheal stool samples. Furthermore, atypical diarrhea disease caused by non-O157 STEC can be routinely missed due to screening only for viral agents.     

Improved detection of Shigella using Escherichia coli medium enrichment: Polymerase chain reaction from stool samples

Laboratory diagnosis of shigellosis using conventional culture technique is limited by lower sensitivity and higher turnaround time. Here, we have evaluated the role of polymerase chain reaction from stool samples after enrichment in Escherichia coli medium for detection of Shigellae. The technique not only increased the sensitivity but also decreased the turnaround time.     

Unusual verotoxin-producing Escherichia coli associated with hemorrhagic colitis.

All strains of Escherichia coli isolated from cases of hemorrhagic colitis and sent to the Centers for Disease Control, Atlanta, Ga., over a 3-year period were assayed for toxicity in Vero cell cultures. Strains that produced moderate or high levels of verotoxin were characterized by serotype, biotype, antimicrobial resistance, plasmid profile, and adherence to HeLa cells. Over 200 isolates were typical O157:H7 strains. Six isolates were atypical O157:H7 strains; two were resistant to antimicrobial agents; one was indole negative, two were citrate positive, and one was urea positive. Six isolates were nonmotile O157 strains. All of these isolates were similar to typical O157:H7 strains by plasmid profile and negative or slow sorbitol fermentation. Eleven other verotoxigenic isolates did not possess the O157 antigen, had a variety of plasmid profiles, and were sorbitol positive. Two of the eleven were enteropathogenic serotypes (O111:NM and O26:H11), yet none were adherent to HeLa cells. We conclude that verotoxigenic E. coli associated with hemorrhagic colitis includes atypical O157 strains and other serotypes. Hence, investigators should use current screening methods with caution.     

Experimental infection of infant rabbits with verotoxin-producing Escherichia coli.

To study the pathogenesis of diarrheal disease due to verotoxin (VT)-producing Escherichia coli, 3-day-old rabbits were inoculated intragastrically with live E. coli O157:H7 (high VT producer), E. coli O113:K75:H21 (low VT producer), or O157:H45 (VT negative) and were examined for clinical symptoms, bacterial colonization, presence of detectable free VT in the intestines, and histological changes. Diarrhea developed consistently with 10(8) bacteria of E. coli O157:H7 but was observed only infrequently with even a higher dose of E. coli O113:K75:H21. VT-negative strains failed to cause diarrhea under the same experimental conditions. E. coli O157:H7 was recovered from the colon of infected animals in a significantly higher concentration than from the small intestine, and the clinical symptoms correlated with the presence of detectable free VT in the colon. Histological changes were seen mainly in the mid- and distal colon; these changes were characterized by a vast increase in apoptosis in the surface epithelium, increased mitotic activity in the crypts, mucin depletion, and a mild to moderate infiltration of neutrophils in the lamina propria and epithelium. Multiple foci of attached bacteria were seen on the surface epithelium of the gut-associated lymphoid tissue, cecum, and colon. Bacteria were never seen in epithelial cells or the lamina propria. These mucosal abnormalities as well as clinical symptoms were reproduced in infant rabbits by the intragastric administration of VT alone. These results are consistent with the hypothesis that VT plays a major role in the pathogenesis of diarrhea caused by E. coli O157:H7 and other VT-producing E. coli.     

Improvement of PCR for detection of Opisthorchis viverrini DNA in human stool samples

Opisthorchis viverrini is an important food-borne trematode in Southeast Asia. The infection causes significant morbidity in terms of hepatobiliary diseases and cholangiocarcinoma. The aim of this study was to improve the sensitivity of the PCR-based diagnosis of O. viverrini infection. A new fecal DNA extraction protocol for the detection of O. viverrini DNA using cetyltrimethyl-ammoniumbromide to remove PCR inhibitor was used and compared with the commercial stool kit method. The sensitivity of the new test was 79.3%, compared with the 44.8% of the previous method (P < 0.01). PCR-positive tests identified several cases judged parasite negative by the parasitological method (28.6%), indicating the new test's advantage in the diagnosis of individuals with light infections.     

Colorimetric detection of heat-labile toxin-encoding gene of enterotoxigenic Escherichia coli by PCR.

In the developing world, enterotoxigenic Escherichia coli (ETEC) strains which produce enterotoxins are a significant cause of morbidity and mortality. Heat-labile (LT) toxin PCR detection methods have been described, but they have limited applications in a routine laboratory setting. A colorimetric DNA method for the rapid amplification and detection of the LT toxin gene in ETEC strains is described. Target amplification together with colorimetric detection would overcome many of the limitations of conventional PCR. This paper describes a colorimetric PCR detection method specific for LT-gene-encoding ETEC strains. DNA was extracted from two representative colonies from each bacterial isolate and amplified by PCR. Digoxigenin was incorporated into the amplification product, permitting a one-step direct detection using anti-digoxigenin alkaline phosphatase-conjugated antibody. This technique was applied to the investigation of 70 E. coli isolates derived from clinical fecal samples obtained from an Irish population. Eleven percent of the samples were LT positive, confirming the applicability of this method. All LT-positive ETEC strains (controls and clinical isolates) were detected, and no false-positive results occurred.     

Rapid Immunoassay for detection of Escherichia coli O157 directly from stool specimens.

A new and rapid ( < 1 h) enzyme-linked immunosorbent assay (ELISA) was compared with conventional sorbitol-MacConkey agar (SMAC) culture for the detection of Escherichia coli O157 from stool specimens. Among 34 positive specimens, confirmed by colony-sweeping and immunofluorescence stain methods, 6 did not exhibit visible sorbitol-negative colonies on SMAC. These six specimens would have been considered to be negative if SMAC alone had been used. The ELISA detected 31 of the 34 positive samples, including 5 of the above-mentioned 6 false-negative samples, resulting in a sensitivity and specificity of 91.2 and 99.5%, respectively. Cross-reactivity with other enteric pathogens was not noted by ELISA. The SMAC method had a sensitivity and specificity of 82.4 and 100%, respectively. The ELISA-negative specimens do not require culture confirmation, whereas positive results must be considered to be presumptive until confirmed by culture. The test is accurate and is easy to perform, making it a very efficient method for screening stool specimens for E. coli O157.     

Evaluation of performance and potential clinical impact of ProSpecT Shiga toxin Escherichia coli microplate assay for detection of Shiga Toxin-producing E. coli in stool samples

Shiga toxin-producing Escherichia coli bacteria (STEC) are emerging pathogens capable of producing sporadic and epidemic diarrhea, hemorrhagic colitis, and potentially life-threatening hemolytic-uremic syndrome. Although the presence of E. coli O157 can be readily detected in stool by sorbitol-MacConkey agar culture (SMAC), STEC non-O157 serotypes cannot. In contrast to culture, testing for the presence of Shiga toxins 1 and 2 in stool detects both O157 and non-O157 STEC serotypes capable of causing disease. Over two consecutive summers, we evaluated the performance of the ProSpecT Shiga toxin E. coli Microplate assay (Alexon-Trend, Ramsey, Minn.), an enzyme immunoassay for the detection of Shiga toxins 1 and 2, on all stools submitted for culture of enteric pathogens, and the potential clinical impact of Shiga toxin detection. Twenty-nine stool specimens were STEC positive by ProSpecT assay. Twenty-seven of 29 STEC-positive isolates were confirmed by SMAC and serotyping or by a second enzyme immunoassay and PCR (positive predictive value, 93%). Thirteen of 27 confirmed Shiga toxin-producing strains were serotype O157. The remaining 14 strains represented 8 other serotypes. The ProSpecT assay was 100% sensitive and specific for detection of E. coli O157 in stool (7 of 7) compared to SMAC. In addition, the ProSpecT assay detected twice as many STEC as SMAC. Fifty-two percent of confirmed STEC-positive stools were nonbloody. Thus, in our population, screening strategies that test only visibly bloody stools for STEC would miss a majority of cases. Eleven (41%) STEC-positive patients were hospitalized, and eight (30%) developed severe disease (two developed hemolytic-uremic syndrome, and six developed hemorrhagic colitis). Prior to detection of STEC infection, seven (26%) and eight patients (30%) underwent unnecessary diagnostic procedures or received potentially deleterious empirical treatment, respectively. We propose that establishing a specific diagnosis of STEC may have prevented these potentially harmful interventions. We conclude that the ProSpecT assay is sensitive and specific for the detection of Shiga toxins 1 and 2 in stool and has potentially significant clinical impact for the individual patient and public health. Shiga toxin assays should be considered for routine use in settings where prevalence of STEC disease warrants testing.     

Impact of free verotoxin testing on epidemiology of diarrhea caused by verotoxin-producing Escherichia coli.

During a 10-week period in the summer of 1990, an epidemiologic investigation of the prevalence of verotoxin (VT)-producing Escherichia coli infection was conducted in Calgary, Alberta, Canada. Consecutive stool specimens (n = 3,577) were cultured for E. coli O157:H7, and fecal filtrates were tested for free VTs (FVTs). E. coli O157:H7 was recovered from 22 specimens (0.6%), but VT was detected in 74 specimens (2.1%). Sixty-nine stool specimens positive for FVTs or E. coli O157:H7 were probed for VT genes by colony blot hybridization; 22 of 38 VT gene probe-positive isolates were non-O157:H7 E. coli organisms. Fourteen of 22 strains could not be induced to produce VT in vitro, despite the presence of FVTs in the stool sample, positivity on colony blot hybridization, positive PCR probes with the primers described by Pollard et al. (D. R. Pollard, W. M. Johnson, H. Lior, S. D. Tyler, and K. R. Rozee, J. Clin. Microbiol. 28:540-545, 1990) or Gannon et al. (V. P. Gannon, R. K. King, J. Y. Kim, and E. J. Golsteyn-Thomas, Appl. Environ. Microbiol. 58:3809-3815, 1992) (but not those described by Karch and Meyer [H. Karch and T. Meyer, J. Clin. Microbiol. 27:2751-2757, 1989]), and positive Southern blot analysis of isolates in 10 of 14 strains. The patient survey questionnaire showed that E. coli O157:H7 infection was associated with bloody diarrhea of short duration, whereas infection with other serotypes or persistence of FVT only was associated with longer-duration nonbloody diarrheal illness.(ABSTRACT TRUNCATED AT 250 WORDS)     

Rapid detection of Escherichia coli in urine samples by a new chromogenic beta-glucuronidase assay.

A new compound, indoxyl-beta-D-glucuronide, was assessed as a substrate for the rapid detection of Escherichia coli in urine. Incorporation of this compound into MacConkey agar allowed the direct differentiation of E. coli as deep blue colonies distinct from lactose and nonlactose fermenters. The sensitivity was 88 to 90%, and the specificity was 100%.     

Evaluation of an immunoassay for direct detection of Escherichia coli O157 in stool specimens.

An enzyme-linked immunosorbent assay (ELISA) produced by LMD Laboratories, Inc., Carlsbad, Calif., was compared with culture for the detection of Escherichia coli O157. Nine of 185 stool specimens evaluated had positive results by the LMD E. coli O157 ELISA and grew E. coli O157 on culture; 174 had negative by LMD E. coli O157 ELISA results and did not grow E. coli O157 on culture. Of 174 specimens negative by LMD E. coli O157 ELISA, 117 specimens grew other enteric pathogens: Campylobacter spp. (46 isolates), Salmonella spp. (43 isolates), Yersinia spp. (20 isolates), and Shigella spp. (8 isolates). There were two indeterminant results by the LMD E. coli O157 ELISA. One stool specimen did not grow other enteric pathogens on culture, and one grew a Campylobacter sp. on culture. Both had negative LMD E. coli O157 ELISA results upon repeat testing. The LMD E. coli O157 ELISA is an accurate, easy-to-read screening method for the detection of E. coli O157 in fecal specimens.     

Use of modified PCR ribotyping for direct detection of Clostridium difficile ribotypes in stool samples

PCR ribotyping was modified to allow direct detection of Clostridium difficile from stool samples. Direct PCR ribotyping was possible in 86 out of 99 C. difficile-positive stool samples, and in 84 cases (84.8%), the ribotype determined directly from the stool sample was identical to the ribotype of the strain isolated from the same stool sample.     

Detection and characterization of fecal verotoxin-producing Escherichia coli from healthy cattle.

Verotoxin-producing Escherichia coli isolates from feces of healthy cattle were identified by DNA hybridization with verotoxin 1- and verotoxin 2-specific gene probes. Among 259 animals investigated, 28 (10.8%) were found to carry verotoxin-producing E. coli strains. Characterization of the verotoxin-producing isolates revealed a heterogeneous population in terms of serotype and toxin type. Nearly 40% of the strains belonged to serogroups known to be pathogenic for humans, i.e., O22, O39, O82, O91, O113, O116, O126, and O136. Two isolates from different bulls were identified as serotype O157:H7. Results obtained in this study indicate that cattle may be an important source of verotoxigenic E. coli involved in human disease.     

Polymerase chain reaction for detection of adenoviruses in stool samples.

The usefulness of the polymerase chain reaction (PCR) method for diagnosing adenovirus infections was investigated. Several primers, including primers specific for the hexon-coding region and for enteric adenovirus types 40 and 41, were evaluated. The PCR method was validated against cell culturing in routine diagnostic work and against restriction enzyme analysis of viral DNA. Sixty diagnostic specimens were selected for evaluation by the PCR method. Twenty of the 60 specimens were found positive on the basis of cytopathic effects and latex agglutination (Adenolex [Orion Diagnostica, Helsinki, Finland]), and 16 were identified and typed as adenoviruses by polyacrylamide gel electrophoresis. PCR was performed on all 60 specimens in parallel directly on diluted stool samples and on viral DNA extracted from cells inoculated with the same stool samples. When the general hexon primers were used 51 of the 60 specimens from infected cell cultures were found positive by PCR, whereas only 13 specimens were found positive when PCR was performed directly on stool samples. With the use of selective primers for enteric adenoviruses 16 of the 60 cell cultures were found to exhibit amplification products by PCR, whereas 4 were detected in stool samples. None of the 60 specimens were found positive by PCR when an adenovirus type 40-specific primer pair was used. PCR was found to be a fast, sensitive, and reliable method for the detection of adenoviruses in diarrheal disease, provided the amplifications were performed directly on diluted stool samples.