Comparison of Shiga toxin-producing Escherichia coli detection methods using clinical stool samples

Antimicrobial susceptibility and virulence gene analysis of Shigella species causing dysentery in Iranian children: Implications for fluroquinolone resistance

Shigella species significantly impact global health due to their role in diarrheal diseases. A 2019-2022 cross-sectional study on 432 stool samples from pediatric patients in Mashhad, Iran, identified Shigella spp. and tested their susceptibility to 12 antimicrobials by the disk diffusion method. The presence of virulence factors, namely ipaH, virA, stx1, and stx2, as well as plasmid-mediated quinolone resistance (PMQR) genes, including qnrA, qnrB, qnrC, qnrD, and qnrS, were ascertained through the utilization of polymerase chain reaction techniques. Sequencing of 15 isolates detected mutations within quinolone resistance-determining regions (QRDRs) at the gyrA and parC genes, indicating fluoroquinolone (FQ) resistance. 19.2 % (83/432) of stool samples contained Shigella, primarily S. sonnei (77.1 %), followed by S. flexneri (21.6 %) and S. boydii (1.2 %). Most isolates were from children under five (55.4 %). All strains had the ipaH gene, lacked stx1 and stx2, and 86.7 % had virA. High resistance was noted for ampicillin and tetracycline (84.3 % each), trimethoprim-sulfamethoxazole (81.9 %), and azithromycin (60.2 %). 87.1 % of isolates were multidrug-resistant (MDR). The most common PMQR genes were qnrA and qnrS (41 % each). The qnrD gene, prevalent in 36.1 % of cases, is reported in Iran for the first time. The most common PMQR profile was qnrADS (15.7 %). Resistance to nalidixic acid and ciprofloxacin was 45.8 % and 12 %, respectively. The Shigella isolates exhibited mutations in the gyrA (at codons 83, 87, and 211) and parC (at codons 80, 84, 93, 126, 128, 129, and 132) genes. The D87Y mutation in the gyrA gene was the most common in Shigella isolates, occurring in 73 % of cases. The F93S and L132T mutations in the parC gene were unique to this study. Empirical FQ therapy in patients infected with MDR Shigella, possessing PMQR determinants and/or mutations in the QRDRs of gyrA and parC, may escalate the risks of secondary diseases, extended treatment duration, therapeutic failure, and resistance spread. Consequently, the necessity for continuous surveillance and genetic testing to detect FQ-resistant Shigella strains is of paramount importance.

Infectious agents present in monk parakeet (Myiopsitta monachus) and rose-ringed parakeet (Psittacula krameri) invasive species in the parks of Madrid and Seville, Spain

Introduction

The introduction of invasive species into an ecosystem could result in biodiversity loss and the spread of infectious agents that could cause re-emergent or emergent zoonotic diseases. Monk parakeets (Myiopsitta monachus) and rose-ringed parakeets (Psittacula krameri) are considered widespread invasive exotic species in urban habitats from the Iberian Peninsula. The aim of this study was to assess the presence of relevant infectious agents in wild parakeets captured in urban parks in Madrid and Seville (Spain).

Methods

A total of 81 cloacal samples were collected and analysed using molecular techniques.

Results

The prevalence of infectious agents varied between parakeet species: 9.5% of monk parakeets and 15% of rose-ringed parakeets were positive for enteropathogenic E. coli (EPEC), 13.3% of rose-ringed parakeets for avian influenza virus (AIV), 3.3% of rose-ringed parakeets for Newcastle disease virus (NDV), and a 23.8% of monk parakeets for Chlamydia psittaci.

Discussion

All C. psittaci-identified isolates were classified as B, E, or E/B genotypes, indicating transmission from wild urban pigeons to parakeets. These results highlight the need for monitoring parakeet populations due to the implications for human and animal health.

Virulence Determinants and Multidrug Resistance of Escherichia coli Isolated from Migratory Birds

Migratory birds are carriers of multidrug resistant pathogenic Escherichia coli. However, their roles in the dissemination of these resistant pathogens are still being neglected in Bangladesh. The present study was therefore carried out to detect multidrug resistant E. coli. In addition, these isolates were also screened for the presence of avian pathogenic E. coli (APEC)-associated virulence genes. A total of 66 fecal matter samples of migratory birds were screened. E. coli were isolated and identified by culturing and biochemical tests followed by polymerase chain reaction (PCR). APEC-associated virulence genes were detected by PCR. Disk diffusion assays were employed to investigate antibiogram profiles. Bivariate analysis was performed to assess correlations in resistance patterns between antimicrobials and to assess associations between virulence genes of E. coli. Among the 66 samples assessed by PCR, 55 (83.33%) were found positive for E. coli. Of these 55 isolates, the APEC-associated virulence gene fimC was detected in 67.27% of the isolates, which was significantly higher than in the cases of iucD (29.09%) and papC (5.45%) genes. In addition, three isolates were found positive for all three virulence genes, while 23 and 12 isolates were positive for one and two virulence genes respectively. In the bivariate analysis, significant associations were detected between fimC and iucD virulence genes. Using the antibiogram, all E. coli isolates were found to be multidrug resistant (MDR). The isolates exhibited 100% resistance against ampicillin and erythromycin in addition to varying percentages of resistance against streptomycin, tetracycline, ciprofloxacin, and chloramphenicol. Highly positive correlations between tetracycline and ciprofloxacin, chloramphenicol and ciprofloxacin, chloramphenicol and tetracycline were observed by bivariate analysis. To the best of our knowledge, this is the first study that reports APEC-associated virulence genes of MDR E. coli from migratory birds in Bangladesh. Results indicate that migratory birds are reservoirs of MDR E. coli isolates carrying APEC-associated virulence genes, which can seriously contribute to the development of human and animal diseases.

Molecular Detection of Avian Pathogenic Escherichia coli (APEC) for the First Time in Layer Farms in Bangladesh and Their Antibiotic Resistance Patterns

Avian pathogenic Escherichia coli (APEC) causes significant economic losses in poultry industries. Here, we determined for the first time in Bangladesh, the prevalence of APEC-associated virulence genes in E. coli isolated from layer farms and their antibiotic resistance patterns. A total of 99 samples comprising internal organs, feces, and air were collected from 32 layer farms. Isolation was performed by culturing samples on eosin–methylene blue agar plates, while the molecular detection of APEC was performed by PCR, and antibiograms were performed by disk diffusion. Among the samples, 36 were positive for the APEC-associated virulence genes fimC, iucD, and papC. Out of 36 isolates, 7, 18, and 11 were positive, respectively, for three virulence genes (papC, fimC, and iucD), two virulence genes, and a single virulence gene. Although the detection of virulence genes was significantly higher in the internal organs, the air and feces were also positive. The antibiograms revealed that all the isolates (100%) were resistant to ampicillin and tetracycline; 97.2%, to chloramphenicol and erythromycin; 55.5%, to enrofloxacin; 50.0%, to norfloxacin and ciprofloxacin; 19.4%, to streptomycin; 11.1%, to colistin; and 8.33%, to gentamicin. Interestingly, all the isolates were multidrug-resistant (MDR). Spearman’s rank correlation coefficient analysis revealed the strongest significant correlation between norfloxacin and ciprofloxacin resistance. This is the first study in Bangladesh describing the molecular detection of APEC in layer farms. Isolated APEC can now be used for detailed genetic characterization and assessing the impact on public health.

Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration

The quantification of pathogens is important for assessing water safety and preventing disease outbreaks. Culture-independent approaches, such as quantitative PCR (qPCR) and digital PCR (dPCR), are useful techniques for quantifying pathogens in water samples. However, since pathogens are usually present at low concentrations in water, it is necessary to concentrate microbial cells before extracting their DNA. Many existing microbial concentration methods are inefficient or take a long time to perform. In this study, we applied a coagulation and foam separation method to concentrate environmental water samples of between 1000 and 5000 mL to 100 μL of DNA (i.e., a 1-5 × 10⁴-fold concentration). The concentration process took <1 h. The DNA samples were then used to quantify various target pathogens using dPCR. One gene, the Shiga toxin gene (stx₂) of Shiga toxin-producing Escherichia coli, was detected at 32 copies/100 mL in a river water sample. The coagulation and foam concentration method followed by dPCR reported herein is a fast, sensitive, and reliable method to quantify pathogen genes in environmental water samples.

Incidence, Pathotyping, and Antibiotic Susceptibility of Avian Pathogenic Escherichia coli among Diseased Broiler Chicks

A total of 54 broiler flocks during the first two weeks of life was used to investigate the incidence of avian pathogenic E. coli in Egypt; 28 isolates (51.85%) were revealed by colony morphology and biochemical identification which then investigated for their serogroups and only 18/28 isolates were serotyped. The most prevalent serotypes were O115, O142, O158, O55, O125, O114, O27, O20, and O15. By application of polymerase chain reaction (PCR), 83.3% (15/18) of the serotyped isolates were confirmed to be E. coli, and 93.3% (14/15), 46.6% (7/15), and 20% (3/15) of isolates harbored the iss, iutA, and fimH genes, respectively. Virulence testing of the selected 13 APEC isolates on the specific-pathogen-free (SPF) chicks revealed them to be highly virulent (15.4%), moderately virulent (23.1%), and avirulent (61.5%); however, all isolates (100%) were extremely virulent towards SPF embryonated chicken eggs. Antibiotic resistance (100% of isolates (n = 13)) was observed for ampicillin, amoxycillin-clavulanic acid, and tetracyclines, colistin (92.31%; 12/13), doxycycline and spiramycin (84.62%; 11/13), florfenicol (69.23%; 9/13), cefotaxime (61.54%; 8/13), and ciprofloxacin (53.85%; 7/13). The highest percentage of sensitivity (53.85% of isolates; 7/13) was recorded for ofloxacin and enrofloxacin followed by gentamycin (46.15%; 6/13). The results suggest that the diagnosis of APEC with PCR is rapid and more accurate than traditional methods for E. coli identification; moreover, the presence or absence of iss, iutA, and/or fimH genes is not an indicator of in vivo pathogenicity of APEC. Thus, further studies, including a wider range of virulence genes and gene sequencing, are required. In addition, serotyping has no effect on the virulence of APEC.

Contribution and Interaction of Shiga Toxin Genes to Escherichia coli O157:H7 Virulence

Escherichia coli O157:H7 is the predominant cause of diarrhea-associated hemolytic uremic syndrome (HUS) worldwide. Its cardinal virulence traits are Shiga toxins, which are encoded by stx genes, the most common of which are stx1a, stx2a, and stx2c. The toxins these genes encode differ in their in vitro and experimental phenotypes, but the human population-level impact of these differences is poorly understood. Using Shiga toxin-encoding bacteriophage insertion typing and real-time polymerase chain reaction, we genotyped isolates from 936 E. coli O157:H7 cases and verified HUS status via chart review. We compared the HUS risk between isolates with stx2a and those with stx2a and another gene and estimated additive interaction of the stx genes. Adjusted for age and symptoms, the HUS incidence of E. coli O157:H7 containing stx2a alone was 4.4% greater (95% confidence interval (CI) −0.3%, 9.1%) than when it occurred with stx1a. When stx1a and stx2a occur together, the risk of HUS was 27.1% lower (95% CI −87.8%, −2.3%) than would be expected if interaction were not present. At the population level, temporal or geographic shifts toward these genotypes should be monitored, and stx genotype may be an important consideration in clinically predicting HUS among E. coli O157:H7 cases.

Relationship between enteric pathogens and acute gastroenteritis disease severity: a prospective cohort study

OBJECTIVES

To evaluate the relationship between individual bacterial and viral pathogens and disease severity.

METHODS

Children <18 years with three or more episodes of vomiting and/or diarrhoea were enrolled in two Canadian paediatric emergency departments between December 2014 and August 2016. Specimens were analysed employing molecular panels, and outcome data were collected 14 days after enrolment. The primary outcome was severe disease over the entire illness (symptom onset until 14-day follow-up), quantified employing the Modified Vesikari Scale (MVS) score. The score was additionally analysed in two other time periods: index (symptom onset until enrolment) and follow-up (enrolment until 14-day follow-up).

RESULTS

Median participant age was 20.7 (IQR: 11.3, 44.2) months; 47.4% (518/1093) and 73.4% (802/1093) of participants had index and total MVS scores ≥11, respectively. The most commonly identified pathogens were rotavirus (289/1093; 26.4%) and norovirus (258/1093; 23.6%). In multivariable analysis, severe disease over the entire illness was associated with rotavirus (OR = 9.60; 95%CI: 5.69, 16.19), Salmonella (OR = 6.61; 95%CI: 1.50, 29.17), adenovirus (OR = 2.53; 95%CI: 1.62, 3.97), and norovirus (OR = 1.43; 95%CI: 1.01, 2.01). Pathogens associated with severe disease at the index visit were: rotavirus only (OR = 6.13; 95%CI: 4.29, 8.75), Salmonella (OR = 4.59; 95%CI: 1.71, 12.29), adenovirus only (OR = 2.06; 95%CI: 1.41, 3.00), rotavirus plus adenovirus (OR = 3.15; 95%CI: 1.35, 7.37), and norovirus (OR = 0.68; 95%CI: 0.49, 0.94). During the follow-up period, rotavirus (OR = 2.21; 95%CI: 1.50, 3.25) and adenovirus (OR = 2.10; 95%CI: 1.39, 3.18) were associated with severe disease.

CONCLUSIONS

In children presenting for emergency department care with acute gastroenteritis, pathogens identified were predominantly viruses, and several of which were associated with severe disease. Salmonella was the sole bacterium independently associated with severe disease.

Zoonotic Agents in Feral Pigeons (Columba livia) from Costa Rica: Possible Improvements to Diminish Contagion Risks

Most studies on zoonotic agents in pigeons have been conducted in the Palearctic region, but the scarcity of data is notorious in the Neotropical region, where these birds can breed all year around and are in close contact with humans. In this study, we used a combination of culture-dependent and culture-independent methods to identify infectious agents in 141 fecal samples from pigeons collected at four urban parks from Costa Rica. Of these we identified 34 positive samples for Salmonella enterica subsp. enterica serovar Braenderup (24.1%), 13 for Chlamydophila psittaci (9.2%), 9 for enteropathogenic Escherichia coli (6.4% eaeA, 0% stx-1 and 0% stx-2), and 2 for Campylobacter jejuni (1.4%). These populations of pigeons pose low risk for healthy adult humans, however, they may pose a health risk to immunocompromised patients or children. This study provides scientific data, which can be incorporated into educational programs aiming to reverse the public attitude toward pigeon feeding and to rationally justify population control efforts.

Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants

Escherichia coli has been proposed to have two habitats—the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains of E. coli have evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the surviving E. coli strains were found to contain a genetic insertion element (IS30) located within the uspC-flhDC intergenic region. The positional location of the IS30 element was not observed across a library of 845 E. coli isolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animal E. coli isolates (n = 1,177). Phylogenetics clustered the IS30 element-containing wastewater E. coli isolates into a distinct clade, and biomarker analysis revealed that these wastewater isolates contained a single nucleotide polymorphism (SNP) biomarker pattern that was specific for wastewater. These isolates belonged to phylogroup A, possessed generalized stress response (RpoS) activity, and carried the locus of heat resistance, features likely relevant to nonhost environmental survival. Isolates were screened for 28 virulence genes but carried only the fimH marker. Our data suggest that wastewater contains a naturalized resident population of E. coli. We developed an endpoint PCR targeting the IS30 element within the uspC-flhDC intergenic region, and all raw sewage samples (n = 21) were positive for this marker. Conversely, the prevalence of this marker in E. coli-positive surface and groundwater samples was low (≤5%). This simple PCR assay may represent a convenient microbial source-tracking tool for identification of water samples affected by municipal wastewater.

IMPORTANCE The results of this study demonstrate that some strains of E. coli appear to have evolved to become naturalized populations in the wastewater environment and possess a number of stress-related genetic elements likely important for survival in this nonhost environment. The presence of non-host-adapted strains in wastewater challenges our understanding of using E. coli as a microbial indicator of wastewater treatment performance, suggesting that the E. coli strains present in human and animal feces may be very different from those found in treated wastewater.

Pooled Nucleic Acid Amplification Test for Screening of Stool Specimens for Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC)-associated enteric illness is attributed to O157 and non-O157 serotypes; however, traditional culture-based methods underdetect non-O157 STEC. Labor and cost of consumables are major barriers to implementation of the CDC recommendation to test all stools for both O157 and non-O157 serotypes. We evaluated the feasibility of a pooled nucleic acid amplification test (NAAT) as an approach for screening stool specimens for STEC. For retrospective evaluation, 300 stool specimens were used to create pools of 10 samples each. The sensitivity was 83% for the preenrichment pooling strategy and 100% for the postenrichment pooling strategy compared with those for individual NAAT results. The difference in cycle threshold (C_T) between individual and pooled NAAT results for specimens was significantly lower and more consistent for postenrichment pooling (stx₁ mean = 3.90, stx₂ mean = 4.28) than those for preenrichment pooling (excluding undetected specimens; stx₁ mean = 9.34, stx₂ mean = 8.96) (P ≤ 0.0013). Cost of consumables and labor time savings of 48 to 81% and 6 to 66%, respectively, were estimated for the testing of 90 specimens by the postenrichment pooled NAAT strategy on the basis of an expected 1 to 2% positivity rate. A 30-day prospective head-to-head clinical trial involving 512 specimens confirmed the sensitivity and labor savings associated with the postenrichment pooled NAAT strategy. The postenrichment pooled NAAT strategy described here is suitable for efficient large-scale surveillance of all STEC serotypes. Comprehensive detection of STEC will result in accurate estimation of STEC burden and, consequently, appropriate public health interventions.

The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks

A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.

Detection, Characterization, and Typing of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) are responsible for gastrointestinal diseases reported in numerous outbreaks around the world. Given the public health importance of STEC, effective detection, characterization and typing is critical to any medical laboratory system. While non-O157 serotypes account for the majority of STEC infections, frontline microbiology laboratories may only screen for STEC using O157-specific agar-based methods. As a result, non-O157 STEC infections are significantly under-reported. This review discusses recent advances on the detection, characterization and typing of STEC with emphasis on work performed at the Alberta Provincial Laboratory for Public Health (ProvLab). Candidates for the detection of all STEC serotypes include chromogenic agars, enzyme immunoassays (EIA) and quantitative real time polymerase chain reaction (qPCR). Culture methods allow further characterization of isolates, whereas qPCR provides the greatest sensitivity and specificity, followed by EIA. The virulence gene profiles using PCR arrays and stx gene subtypes can subsequently be determined. Different non-O157 serotypes exhibit markedly different virulence gene profiles and a greater prevalence of stx1 than stx2 subtypes compared to O157:H7 isolates. Finally, recent innovations in whole genome sequencing (WGS) have allowed it to emerge as a candidate for the characterization and typing of STEC in diagnostic surveillance isolates. Methods of whole genome analysis such as single nucleotide polymorphisms and k-mer analysis are concordant with epidemiological data and standard typing methods, such as pulsed-field gel electrophoresis and multiple-locus variable number tandem repeat analysis while offering additional strain differentiation. Together these findings highlight improved strategies for STEC detection using currently available systems and the development of novel approaches for future surveillance.

Assessment of commercial chromogenic solid media for the detection of non-O157 Shiga toxin-producing Escherichia coli (STEC)

Detection of Shiga toxin-producing Escherichia coli (STEC) has evolved significantly since the introduction of sorbitol-MacConkey agar. This study compares four chromogenic media (CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157, and Colorex® O157) in their identification of non-O157 STEC. When 161 non-O157 STEC were directly inoculated onto each medium, detection rates on CHROMagar™ STEC, Rainbow® O157 agar, CHROMagar™ O157 and Colorex® O157 were 90%, 70%, 3.7% and 6.8%, respectively. Tellurite minimal inhibitory concentrations (MICs) correlated with growth on CHROMagar™ STEC as 20 of 22 isolates with poor or no growth had MICs ≤1μg/mL. Stool spiking experiments revealed that CHROMagar™ STEC had the highest recovery of the six most common non-O157 STEC, ranging from 30% (in mucoid stool) to 98% (in watery stool). When using clinical stool samples, CHROMagar™ STEC had a sensitivity, specificity, positive predictive value, and negative predictive value of 84.6%, 87%, 13.9%, and 99.6%, respectively.

Detection of Shiga Toxin-Producing Escherichia coli from Nonhuman Sources and Strain Typing

Shiga toxin-producing Escherichia coli (STEC) strains are commonly found in the intestine of ruminant species of wild and domestic animals. Excretion of STEC with animal feces results in a broad contamination of food and the environment. Humans get infected with STEC through ingestion of contaminated food, by contact with the environment, and from STEC-excreting animals and humans. STEC strains can behave as human pathogens, and some of them, called enterohemorrhagic E. coli (EHEC), may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Because of the diversity of STEC types, detection strategies for STEC and EHEC are based on the identification of Shiga toxins or the underlying genes. Cultural enrichment of STEC from test samples is needed for identification, and different protocols were developed for this purpose. Multiplex real-time PCR protocols (ISO/CEN TS13136 and USDA/FSIS MLG5B.01) have been developed to specifically identify EHEC by targeting the LEE (locus of enterocyte effacement)-encoded eae gene and genes for EHEC-associated O groups. The employment of more genetic markers (nle and CRISPR) is a future challenge for better identification of EHEC from any kinds of samples. The isolation of STEC or EHEC from a sample is required for confirmation, and different cultivation protocols and media for this purpose have been developed. Most STEC strains present in food, animals, and the environment are eae negative, but some of these strains can cause HC and HUS in humans as well. Phenotypic assays and molecular tools for typing EHEC and STEC strains are used to detect and characterize human pathogenic strains among members of the STEC group.

Virulence genes, antibiotic resistance and integrons in Escherichia coli strains isolated from synanthropic birds from Spain

The aim of this study was to determine the presence of virulence genes and antibiotic resistance profiles in 164 Escherichia coli strains isolated from birds (feral pigeons, hybrid ducks, house sparrows and spotless starlings) inhabiting urban and rural environments. A total of eight atypical enteropathogenic E. coli strains were identified: one in a house sparrow, four in feral pigeons and three in spotless starlings. Antibiotic resistance was present in 32.9% (54) of E. coli strains. The dominant type of resistance was to tetracycline (21.3%), ampicillin (19.5%) and sulfamethoxazole (18.9%). Five isolates had class 1 integrons containing gene cassettes encoding for dihydrofolate reductase A (dfrA) and aminoglycoside adenyltransferase A (aadA), one in a feral pigeon and four in spotless starlings. To our knowledge, the present study constitutes the first detection of virulence genes from E. coli in spotless starlings and house sparrows, and is also the first identification worldwide of integrons containing antibiotic resistance gene cassettes in E. coli strains from spotless starlings and pigeons.

Development and validation of a 3-Plex RT-qPCR assay for the simultaneous detection and quantitation of the three PML-RARa fusion transcripts in acute promyelocytic leukemia

Rapid diagnosis of acute promyelocytic leukemia (APL) with promyelocytic leukemia-retinoic acid receptor alpha (PML-RARa) contributes to a highly effective therapy with all-trans retinoic acid (ATRA). Real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) is a valuable tool to diagnose APL with PML-RARa. However, a single RT-qPCR analysis, which is laborious and costly, has to be performed in three reactions to determine whether one of the three PML-RARa transcripts is present and to quantify the involved transcript. This paper describes a novel TaqMan MGB probe-based 3-plex RT-qPCR assay in a single reaction to detect simultaneously the three PML-RARa transcripts. Specific primers and probe were designed, and the results were further normalized to the Abelson gene. The detection results for the serially diluted plasmid indicate that the analytical sensitivity was 10 copies per reaction for PML-RARa bcr1, bcr2, and bcr3. A relatively high sensitivity of 10^-4 was achieved with this assay when analyzing the bcr1 transcripts obtained from the NB4 cell line. The reproducibility was satisfactory because the coefficients of variation of cycle threshold values were less than 3% for both inter- and intra-assays. After testing 319 newly diagnosed patients with leukemia (including 61 APL cases), the results of the 3-plex RT-qPCR assay completely agreed with the traditional methods used for the detection of PML-RARa. The quantitative results of the 3-plex RT-qPCR were highly correlated with the single RT-qPCR and showed similar assay sensitivity for 60 PML-RARa positive APL samples at diagnosis and 199 samples from 57 patients during follow-up. Interestingly, one PML-RARa bcr2 case at diagnosis with breakpoint at 1579, which was not detected by the single RT-q-PCR, was detected by the 3-plex RT-qPCR assay. The 3-plex RT-qPCR assay is a specific, sensitive, stable, and cost-effective method that can be used for the rapid diagnosis and treatment monitoring of APL with PML-RARa.

Shiga Toxin Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) is among the common causes of foodborne gastroenteritis. STEC is defined by the production of specific toxins, but within this pathotype there is a diverse group of organisms. This diversity has important consequences for understanding the pathogenesis of the organism, as well as for selecting the optimum strategy for diagnostic testing in the clinical laboratory. This review includes discussions of the mechanisms of pathogenesis, the range of manifestations of infection, and the several different methods of laboratory detection of Shiga toxin-producing E coli.

Evaluation of enzyme immunoassays and real-time PCR for detecting Shiga toxin-producing Escherichia coli in Southern Alberta, Canada

Two immunoassays (Shiga Toxin Chek and Shiga Toxin Quik Chek) and real-time PCR were used to detect Shiga toxin-producing Escherichia coli. For enriched culture, the sensitivity and specificity of the three methods ranged from 80.0% to 98.2% and 98.0% to 100.0%, respectively. STEC isolates were identified in 2.6% of the 784 samples.

Probiotic Escherichia coli Nissle 1917 reduces growth, Shiga toxin expression, release and thus cytotoxicity of enterohemorrhagic Escherichia coli

Due to increased release or production of Shiga toxin by Enterohemorrhagic Escherichia coli (EHEC) after exposure to antimicrobial agents, the role of antimicrobial agents in EHEC mediated infections remains controversial. Probiotics are therefore rapidly gaining interest as an alternate therapeutic option. The well-known probiotic strain Escherichia coli Nissle 1917 (EcN) was tested in vitro to determine its probiotic effects on growth, Shiga toxin (Stx) gene expression, Stx amount and associated cytotoxicity on the most important EHEC strains of serotype O104:H4 and O157:H7. Following co-culture of EcN:EHEC in broth for 4 and 24 h, the probiotic effects on EHEC growth, toxin gene expression, Stx amount and cytotoxicity were determined using quantitative real time-PCR, Stx-ELISA and Vero cytotoxicity assays. Probiotic EcN strongly reduced EHEC numbers (cfu) of O104:H4 up to (68%) and O157:H7 to (72.2%) (p<0.05) in LB broth medium whereas the non-probiotic E. coli strain MG1655 had no effect on EHEC growth. The level of stx expression was significantly down-regulated, particularly for the stx2a gene. The stx down-regulation in EcN co-culture was not due to reduced numbers of EHEC. A significant inhibition in Stx amounts and cytotoxicity were also observed in sterile supernatants of EcN:EHEC co-cultures. These findings indicate that probiotic EcN displays strong inhibitory effects on growth, Shiga toxin gene expression, amount and cytotoxicity of EHEC strains. Thus, EcN may be considered as a putative therapeutic candidate, in particular against EHEC O104:H4 and O157:H7.

A sensitive multiplex, real-time PCR assay for prospective detection of Shiga toxin-producing Escherichia coli from stool samples reveals similar incidences but variable severities of non-O157 and O157 infections in northern California

Rapid and accurate detection of Shiga toxin-producing Escherichia coli (STEC) of all serotypes from patients with diarrhea is critical for medical management and for the prevention of ongoing transmission. In this prospective study, we assessed the performance of a multiplex, real-time PCR assay targeting stx1 and stx2 for the detection of O157 and non-O157 STEC in diarrheal stool samples enriched in Gram-negative broth. We show that the assay is 100% sensitive (95% confidence interval [CI], 89.1% to 100%) and 98.5% specific (95% CI, 90.6% to 99.9%) based on a panel of 40 known STEC-positive specimens and 65 known negative specimens. During a 2-year postvalidation period, the assay detected more positive samples from patients in northern California than did culture and PCR testing performed at a public health reference laboratory, with a positive predictive value of 95.6% (95% CI, 87.6% to 99.1%). Serotyping data showed an incidence rate of 51.2% for non-O157 STEC strains, with 5.8% of patients (1/17) with non-O157 strains and 42.9% (6/14) with O157 strains (P = 0.03) developing hemolytic-uremic syndrome. The findings from this study underscore the recommendations of the CDC for laboratories to test all diarrheal stool samples from patients with acute community-acquired diarrhea for non-O157 STEC in addition to the O157 serotype by using a sensitive assay. Additionally, a survey of 17 clinical laboratories in northern California demonstrated that nearly 50% did not screen all stool specimens for the presence of Shiga toxins, indicating that many clinical microbiology laboratories still do not routinely screen all stool specimens for the presence of Shiga toxins as recommended in the 2009 CDC guidelines.

Comparison between ImmunoCard STAT!(®) and real-time PCR as screening tools for both O157:H7 and non-O157 Shiga toxin-producing Escherichia coli in Southern Alberta, Canada

An increasing number of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections and outbreaks have been reported. In this study, we evaluated the performance of ImmunoCard STAT!(®) (Meridian Bioscience, Inc., Cincinnati, OH, USA) as a method to screen stool specimens for STEC (O157 and non-O157). An in-house real-time PCR method was used as the "gold standard". We also evaluated the prevalence and clinical characteristics of STEC infections in the Alberta South West Zone. From July to November 2011, 819 stool specimens submitted for routine stool culture were tested. With our in-house real-time PCR, 7 O157:H7 and 10 non-O157 STEC isolates were identified for a total of 17 STECs. In comparison, ImmunoCard STAT!(®) identified a total of 6, resulting in a sensitivity and specificity of 35% and 99%, respectively (P < 0.05). Because of the low sensitivity, ImmunoCard STAT!(®) cannot be recommended as a routine screening test for STEC from enriched stool specimens. The rate of STEC positivity as detected by PCR was 2.08%, of which 0.86% was O157:H7 and 1.22% non-O157 STEC. Five of the 7 cases of STEC O157 infection experienced bloody diarrhea, and 1 developed hemolytic uremic syndrome.

Real-time PCR as a diagnostic tool for bacterial diseases

In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.

Comparison of three different methods for detection of Shiga toxin-producing Escherichia coli in a tertiary pediatric care center

Shiga toxin-producing Escherichia coli (STEC) is a well-known cause of sporadic and epidemic food-borne gastroenteritis. A low infectious dose, approximately 10 microorganisms, is sufficient to cause disease that may lead to hemolytic-uremic syndrome. The objective of this study was to compare the performances of an in-house real-time PCR, a commercial enzyme immunoassay (EIA) (Premier EHEC; Meridian Bioscience), and culture on sorbitol MacConkey agar for the detection of STEC in a tertiary care pediatric hospital. Of 632 stool samples tested, 21 were positive for STEC. All were detected by PCR, 6 were detected by EIA, and only 5 O157 STEC isolates were identified by culture. Among the 15 specimens falsely negative by EIA, there were 9 Stx1, 2 Stx2, and 4 Stx1 and Stx2 STEC isolates. The latter group included 2 O157 STEC isolates that would have been missed if only EIA had been performed. To our knowledge, this is the first prospective study performed in a pediatric hospital which demonstrates the superiority of PCR over EIA for the detection of STEC. We conclude that PCR is specific and more sensitive than EIA. PCR should be considered for routine use in clinical settings where molecular detection facilities are available. Its lower limit of detection, equivalent to the infectious dose, is an obvious advantage for patient care and public health surveillance.

Escherichia coli O104:H4 infections and international travel

We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. Despite extensive genomic similarity between these strains, key differences included the distribution of toxin and antimicrobial drug–resistance determinants.

Prevalence of shiga toxin-producing Escherichia coli as detected by enzyme-linked immunoassays and real-time PCR during the summer months in northern Alberta, Canada

Shiga toxin-producing Escherichia coli (STEC) in northern Alberta was detected using two enzyme immunoassays and an in-house real-time PCR. Of 2,328 stool samples, 8 were positive for O157:H7 STEC and 13 were positive for non-O157 STEC. No significant gender (P = 0.17) or age (P = 0.81) differences between groups were seen. Most positive diarrheal stool samples were nonbloody.

Bacteriophages carrying Shiga toxin genes: genomic variations, detection and potential treatment of pathogenic bacteria

Although most Escherichia coli strains occur in the mammalian intestine as commensals, some of them, including enterohemorrhagic E. coli (EHEC), are capable of causing disease in humans. The most notorious virulence factors of EHEC are Shiga toxins, encoded by genes located on genomes of lambdoid prophages. Production and release of these toxins is strongly stimulated after the induction of these prophages. Many antibiotics used to treat bacterial infections stimulate induction of Shiga toxin-converting prophages, enhancing severity of the disease symptoms. Hence, treatment with antibiotics is not recommended if infection with EHEC is confirmed or even suspected. In this light, rapid detection of EHEC is crucial, and understanding the mechanisms of prophage induction and phage development in the human intestine is important to facilitate development of procedures preventing or alleviating Shiga toxin-caused diseases.

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.