Development of primers to O-antigen biosynthesis genes for specific detection of Escherichia coli O157 by PCR

Combating Actions of Green 2D-Materials on Gram Positive and Negative Bacteria and Enveloped Viruses

Interactions of novel bi-dimensional nanomaterials and live matter such as bacteria and viruses represent an extremely hot topic due to the unique properties of the innovative nanomaterials, capable in some cases to exhibit bactericide and antiviral actions. The interactions between bacteria and viruses and two dimensional nanosheets are here investigated. We extensively studied the interaction between a gram-negative bacterium, Escherichia coli, and a gram-positive bacterium, Staphylococcus aureus, with two different types of 2D nanoflakes such as MoS₂, belonging to the Transition Metal Dichalcogenides family, and Graphene Oxide. The same two types of nanomaterials were employed to study their antiviral action toward the Herpes simplex virus type-1, (HSV-1). The experimental results showed different bactericide impacts as well as different antiviral power between the two nanomaterials. The experimental findings were interpreted in bacteria on the base of the Derjaguin–Landau–Verwey–Overbeek theory. A simple kinetic model of bacterial growth in the presence of the interacting nanosheets is also elaborated, to explain the observed results. The experimental results in viruses are really novel and somewhat surprising, evidencing a stronger antiviral action of Graphene Oxide as compared to MoS₂. Results in viruses are complicated to quantitatively interpret due to the complexity of the system under study, constituted by virus/host cell and nanoflake, and due to the lack of a well assessed theoretical context to refer to. Thus, these results are interpreted in terms of qualitative arguments based on the chemical properties of the interactors in the given solvent medium.

Detection of E. coli O157:H7 in Meat Using Polymerase Chain Reaction Method and Culture Method

Introduction: Escherichia coli O157:H7, as a pathogenic agent, can be transmitted through the foods including meat, meat products, dairy products, vegetables and water. The World Health Organization has recommended that all countries in the world, especially developing countries, should consider the investigation of E. coli O157:H7 as a research priority. The aim of this study was to determine the frequency of E. coli O157:H7 in meat of cow, sheep, goat, and camel in Kerman province of Iran using culture and polymerase chain reaction (PCR) methods. Methods: In this study, 280 meat samples consisting of sheep (90 specimens), cow (80 specimens), goat (60 specimens) and camel (50 specimens) meats were randomly separated from carcasses from April to July 2018. After the sampling, microbial culture was performed on the samples. Then, suspected E. coli O157:H7 colonies were evaluated by PCR assay. Results: Out of the 280 samples, 73 samples (26%) were contaminated with E. coli. based on bacteriological tests, and 28 samples were identified as suspected E. coli O157:H7 serotype based on the lack of sorbitol fermentation. Subsequently, sorbitol-negative samples were tested by PCR procedure using specific primers. The results revealed that out of 28 cases, 21 cases (7.5%) were E. coli O157:H7. Conclusion: As can be deduced from the observations of this study, to detect the E. coli O157, PCR as an accurate, fast, and reliable procedure can be used along with the culture method.

A rapid method for separating and concentration of food-borne pathogens using elution from ready-to-eat vegetables

BACKGROUND AND OBJECTIVES

Traditional culture methods for detection of food-borne pathogens, a major public health problem, are simple, easily adaptable and very practical, but they can be laborious and time consuming. In this study, we eliminated culturing steps by developing a new separation method and therefore, decreased the detection time of food-borne pathogens (Salmonella enterica serovar Typhimurium, Escherichia coli O157:H7 and Listeria monocytogenes) to a few hours.

MATERIALS AND METHODS

We used alkaline water and different alkaline buffers to elute bacteria from the lettuce surface as a model for ready-to-eat vegetables. Buffers used were as follows: 1) 0.05 M glycine; 2) 0.05 M glycine -100 mM Tris base -1% (w/v) beef extract; 3) buffer peptone water; 4) buffer phosphate saline. Buffers were adjusted to pH of 9, 9.5 and 10. In order to elute the bacteria, the lettuce pieces were suspended into buffers and shacked for 30, 45 and 60 min. Moreover, a multiplex PCR method for the simultaneous detection of food-borne pathogens was performed.

RESULTS

The results showed that buffer peptone water at pH 9.5 for 45 min have high ability to elute bacteria from the lettuce surface and the bacteria can be detected using multiplex PCR.

CONCLUSION

We developed a new rapid and efficient method for simultaneous separation of food-borne pathogens. This method eliminates culturing stages and permits the detection and identification of target pathogens in a few hours.

The influence of surface chemistry on the kinetics and thermodynamics of bacterial adhesion

This work is concerned with investigating the effect of substrate hydrophobicity and zeta potential on the dynamics and kinetics of the initial stages of bacterial adhesion. For this purpose, bacterial pathogens Staphylococcus aureus and Escherichia coli O157:H7 were inoculated on the substrates coated with thin thiol layers (i.e., 1-octanethiol, 1-decanethiol, 1-octadecanethiol, 16-mercaptohexadecanoic acid, and 2-aminoethanethiol hydrochloride) with varying hydrophobicity and surface potential. The time-resolved adhesion data revealed a transformation from an exponential dependence to a square root dependence on time upon changing the substrate from hydrophobic or hydrophilic with a negative zeta potential value to hydrophilic with a negative zeta potential for both pathogens. The dewetting of extracellular polymeric substances (EPS) produced by E. coli O157:H7 was more noticeable on hydrophobic substrates, compared to that of S. aureus, which is attributed to the more amphiphilic nature of staphylococcal EPS. The interplay between the timescale of EPS dewetting and the inverse of the adhesion rate constant modulated the distribution of E. coli O157:H7 within microcolonies and the resultant microcolonial morphology on hydrophobic substrates. Observed trends in the formation of bacterial monolayers rather than multilayers and microcolonies rather than isolated and evenly spaced bacterial cells could be explained by a colloidal model considering van der Waals and electrostatic double-layer interactions only after introducing the contribution of elastic energy due to adhesion-induced deformations at intercellular and substrate-cell interfaces. The gained knowledge is significant in the context of identifying surfaces with greater risk of bacterial contamination and guiding the development of novel surfaces and coatings with superior bacterial antifouling characteristics.

Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies?

Escherichia coli comprises a highly diverse group of Gram-negative bacteria and is a common member of the intestinal microflora of humans and animals. Generally, such colonization is asymptomatic; however, some E. coli strains have evolved to become pathogenic and thus cause clinical disease in susceptible hosts. One pathotype, the Shiga toxigenic E. coli (STEC) comprising strains expressing a Shiga-like toxin is an important foodborne pathogen. A subset of STEC are the enterohaemorrhagic E. coli (EHEC), which can cause serious human disease, including haemolytic uraemic syndrome (HUS). The diagnosis of EHEC infections and the surveillance of STEC in the food chain and the environment require accurate, cost-effective and timely tests. In this review, we describe and evaluate tests now in routine use, as well as upcoming test technologies for pathogen detection, including loop-mediated isothermal amplification (LAMP) and whole-genome sequencing (WGS). We have considered the need for improved diagnostic tools in current strategies for the control and prevention of these pathogens in humans, the food chain and the environment. We conclude that although significant progress has been made, STEC still remains an important zoonotic issue worldwide. Substantial reductions in the public health burden due to this infection will require a multipronged approach, including ongoing surveillance with high-resolution diagnostic techniques currently being developed and integrated into the routine investigations of public health laboratories. However, additional research requirements may be needed before such high-resolution diagnostic tools can be used to enable the development of appropriate interventions, such as vaccines and decontamination strategies.

Growth kinetics of Escherichia coli O157:H7 on the epicarp of fresh vegetables and fruits

Despite the increasing reports on the incidence of fresh vegetables and fruits as a possible vehicle for human pathogens, there is currently limited knowledge on the growth potential of Escherichia coli O157:H7 on different plant substrates. This study analyzed the selective adhesion and growth of E. coli O157:H7 on chili habanero (Capsicum chinense L.), cucumber (Cucumis sativus), radish (Raphanus sativus), tomato (Lycopersicon esculentum), beet (Beta vulgaris subsp. vulgaris), and onion (Allium cepa L.) under laboratory conditions. The Gompertz parameters were used to determine the growth kinetics. Scanning electron microscopy was used to visualize the adhesion of E. coli O157:H7 on the epicarp of the samples. Predictive models were constructed to compare the growth of E. coli O157:H7 on the samples with different intrinsic factors and to demonstrate the low selectivity of the pathogen. No significant difference was observed in the lag-phase duration (LPD), generation time (GT), and exponential growth rate (EGR) of the pathogen adhered to the samples. The interaction between the microorganism and the substrate was less supportive to the growth of E. coli O157:H7 for onion, whereas for tomato and cucumber, the time for the microorganism to attain the maximum growth rate (M) was significantly longer than that recorded for other samples.

DNA diversity of the wla gene cluster among serotype HS:19 and non-HS:19 Campylobacter jejuni strains

Campylobacter jejuni infection is an important trigger of Guillain-Barré syndrome (GBS), and serotype HS:19 strains are over-represented among GBS-associated isolates. Structures in C. jejuni lipooligosaccharide (LOS) resemble human gangliosides, suggesting that molecular mimicry could be important in triggering the neural injury. We assessed the genetic diversity among 36 C. jejuni serotype HS:19 and non-HS:19 strains by analysis of PCR-based restriction fragment length polymorphism (RFLP) patterns of 12 LOS biosynthesis-related genes ( wla cluster). PCR amplification revealed that the size, order, and direction of each wla gene was identical among all strains tested. However, an additional ORF, located between wlaI and wlaK, was detected in 28 of the 36 isolates examined, and nucleotide sequence analysis revealed that the gene was identical to orfE in C. jejuni strain NCTC 11168. An inverted repeat motif was found downstream of the wlaI stop codon and upstream of the orfE stop codon, an organization allowing pairing of repeated sequences that could lead to deletion of the internal segment. Digestion of the PCR products with restriction endonuclease DdeI or AluI and cluster analysis of RFLP banding patterns showed that all HS:19 strains were closely related and distinct from non-HS:19 strains, consistent with earlier analyses, suggesting that HS:19 strains represent a highly clonal population. RFLP analysis of wla genes also may be useful for epidemiological studies.

Improving detection of Shiga toxin-producing Escherichia coli by molecular methods by reducing the interference of free Shiga toxin-encoding bacteriophages

Detection of Shiga toxin-producing Escherichia coli (STEC) by culture methods is advisable to identify the pathogen, but recovery of the strain responsible for the disease is not always possible. The use of DNA-based methods (PCR, quantitative PCR [qPCR], or genomics) targeting virulence genes offers fast and robust alternatives. However, detection of stx is not always indicative of STEC because stx can be located in the genome of temperate phages found in the samples as free particles; this could explain the numerous reports of positive stx detection without successful STEC isolation. An approach based on filtration through low-protein-binding membranes and additional washing steps was applied to reduce free Stx phages without reducing detection of STEC bacteria. River water, food, and stool samples were spiked with suspensions of phage 933W and, as a STEC surrogate, a lysogen harboring a recombinant Stx phage in which stx was replaced by gfp. Bacteria were tested either by culture or by qPCR for gfp while phages were tested using qPCR targeting stx in phage DNA. The procedure reduces phage particles by 3.3 log10 units without affecting the recovery of the STEC population (culturable or assessed by qPCR). The method is applicable regardless of phage and bacteria densities and is useful in different matrices (liquid or solid). This approach eliminates or considerably reduces the interference of Stx phages in the detection of STEC by molecular methods. The reduction of possible interference would increase the efficiency and reliability of genomics for STEC detection when the method is applied routinely in diagnosis and food analysis.

Dual labeled Ag@SiO₂ core-shell nanoparticle based optical immunosensor for sensitive detection of E. coli

An optical nanobiosensor is presented using a fluorescent dye and anti-E. coli McAb anchored Ag@Silica core shell nanoparticles, for rapid and sensitive Escherichia coli detection in environmental samples. The synthesized dual labeled core shell (DLCS) nanoparticle shows intense fluorescence at 620 nm in solution, having a narrow emission with full width at half maxima (FWHM) of 10 nm, as a prerequisite to develop a sensitive detection platform for various biosensing applications. The specific E. coli was captured using an anti-E. coli antibody functionalized quartz glass, followed by a treatment with DLCS, where the photoluminescence spectroscopy was used to detect the target pathogen. The fabrication of the quartz glass based optical-immunosensor was monitored, and the results show changes in the photoluminescent patterns, which substantiate that varied species were immobilized on the surface of the antibody modified quartz glass. Consequently, the optical immunosensor demonstrated specificity and improved sensitivity, as compared to the customary methods, and was able to detect as low as 5CFU/mL. The developed DLCS based optical immunosensor was evaluated with environmental water samples, which showed acceptable precision, reproducibility and stability, and could be readily applied to the routine monitoring of pathogenic microorganisms in the environmental samples, and most importantly, demonstrate the potential of a prototype development of a simple and inexpensive diagnostic technique.

Implications of free Shiga toxin-converting bacteriophages occurring outside bacteria for the evolution and the detection of Shiga toxin-producing Escherichia coli

In this review we highlight recent work that has increased our understanding of the distribution of Shiga toxin-converting phages that can be detected as free phage particles, independently of Shiga toxin-producing bacteria (STEC). Stx phages are a quite diverse group of temperate phages that can be found in their prophage state inserted within the STEC chromosome, but can also be found as phages released from the cell after activation of their lytic cycle. They have been detected in extraintestinal environments such as water polluted with feces from humans or animals, food samples or even in stool samples of healthy individuals. The high persistence of phages to several inactivation conditions makes them suitable candidates for the successful mobilization of stx genes, possibly resulting in the genes reaching a new bacterial genomic background by means of transduction, where ultimately they may be expressed, leading to Stx production. Besides the obvious fact that Stx phages circulating between bacteria can be, and probably are, involved in the emergence of new STEC strains, we review here other possible ways in which free Stx phages could interfere with the detection of STEC in a given sample by current laboratory methods and how to avoid such interference.

Identification of EnterohemorrhagicEscherichia coliO157-Specific DNA Sequence Obtained from Amplified Fragment Length Polymorphism Analysis

An approximately 1.1 kbp fragment that was commonly observed only in the enterohemorrhagic Escherichia coli (EHEC) O157 strains in an analysis of amplified fragment length polymorphism was found to be a partial gene sequence encoding the locus of toxB and a useful molecular marker for the identification of EHEC O157.

Detection of Escherichia coli O157:H7 using immunomagnetic separation and mPCR in Turkish foods of animal origin

The present study was conducted to investigate the presence of Escherichia coli O157:H7 in food samples of animal origin and to detect its virulence genes by immunomagnetic separation technique and multiplex PCR (mPCR). A total of 500 samples (consisting of diced meat, minced meat, burger, raw cow's milk and raw cow's milk cheese) were analysed. Escherichia coli O157:H7 was detected in 5 (1%) of 500 analysed samples including two diced meat, one minced meat and two raw-milk cheese. None of the burger samples tested contained E. coli O157:H7. Three isolates obtained from minced and diced meat were found to carry stx1 , stx2 , hlyA and eaeA genes whereas two isolates from raw-milk cheese were found to harbour the stx1 , eaeA and hlyA genes. The results of this study suggest that raw meat and raw-milk cheese tested could pose public health problems in consumers with regard to their virulence factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Escherichia coli (E. coli) O157:H7 is an important human pathogen. Escherichia coli 0157:H7 infections have been associated with consumption of uncooked meat and meat products, as well as unpasteurized dairy products. This study demonstrated that without specific tests for E. coli virulence factors raw meat and raw-milk cheese could pose public health problems to Turkish consumers.

Development of a novel multiplex lateral flow assay using an antimicrobial peptide for the detection of Shiga toxin-producing Escherichia coli

The binding capacity of peptides with broad antimicrobial activity, or antimicrobial peptides (AMPs), to microbes has recently been applied to the specific detection of bacteria and viruses. We established a novel lateral flow assay (LFA) that combines AMPs labeled with colloidal gold and a target-specific antibody immobilized on a nitrocellulose membrane. α-Helical AMPs, especially cecropin P1 (CP1), magainin 2 (MG2), and ceratotoxin A (CtxA), were shown to have optimal properties as probes in LFA. We also established a multiplex LFA for the simultaneous detection and identification of three serogroups of Shiga toxin-producing Escherichia coli (STEC) using the CP1 probe with polyclonal antibodies anti-O157, anti-O26, and anti-O111. Each serogroup of E. coli could easily and rapidly be detected by multiplex LFA using CP1 and each was clearly visualized in a different position on the LFA strip. The multiplex LFA could detect all tested E. coli strains from serogroups O157 (22/22), O26 (17/17), and O111 (7/7), and the detection limit was 10(4)CFU/mL. No other serogroups of E. coli, including STEC O45, O91, O103, O121, and O145, or non-E. coli strains, reacted. The multiplex LFA could detect E. coli O157, O26, and O111 in food samples at very low levels (6.3, 2.9, and 5.6 CFU per 25 g of ground beef, respectively) after 18-h enrichment, and these results were in accordance with the results of the culture method, immunochromatography (IC) strip, and PCR. Given the broad binding capacity, AMP probes in combination with specific antibodies in the novel multiplex LFA may have the potential to detect various microbes simultaneously with identification on a single strip.

Identification of the anti-terminator qO111:H)- gene in Norwegian sorbitol-fermenting Escherichia coli O157:NM

Sorbitol-fermenting Escherichia coli O157:NM (SF O157) is an emerging pathogen suggested to be more virulent than nonsorbitol-fermenting Escherichia coli O157:H7 (NSF O157). Important virulence factors are the Shiga toxins (stx), encoded by stx1 and/or stx2 located within prophages integrated in the bacterial genome. The stx genes are expressed from p(R) (') as a late protein, and anti-terminator activity from the Q protein is necessary for read through of the late terminator t(R) (') and activation of p(R) (') . We investigated the regulation of stx2(EDL933) expression at the genomic level in 17 Norwegian SF O157. Sequencing of three selected SF O157 strains revealed that the anti-terminator q gene and genes upstream of stx2(EDL933) were identical or similar to the ones observed in the E. coli O111:H- strain AP010960, but different from the ones observed in the NSF O157 strain EDL933 (AE005174). This suggested divergent stx2(EDL933) -encoding bacteriophages between NSF O157 and the SF O157 strains (FR874039-41). Furthermore, different DNA structures were detected in the SF O157 strains, suggesting diversity among bacteriophages also within the SF O157 group. Further investigations are needed to elucidate whether the q(O111:H) (-) gene observed in all our SF O157 contributes to the increased virulence seen in SF O157 compared to NSF O157. An assay for detecting q(O111:H) (-) was developed.

Differential gene expression and adherence of Escherichia coli O157:H7 in vitro and in ligated pig intestines

BACKGROUND

Escherichia coli O157:H7 strain 86-24 grown in MacConkey broth (MB) shows almost no adherence to cultured epithelial cells but adheres well in pig ligated intestines. This study investigated the mechanisms associated with the difference between in-vitro and in-vivo adherence of the MB culture.

METHODOLOGY/PRINCIPAL FINDINGS

It was found that decreased adherence in vitro by bacteria grown in MB was mainly due to lactose, possibly implicating the involvement of carbon catabolite repression (CCR). Expression of selected virulence-related genes associated with adherence and CCR was then examined by quantitative PCR. When bacteria were grown in MB and Brain Heart Infusion with NaHCO(3) (BHIN) plus lactose, pH was reduced to 5.5-5.9 and there was a significant decrease in expression of the locus of enterocyte effacement (LEE) genes eae, tir, espD, grlA/R and ler, and an increase in cya (cAMP), and two negative regulators of the LEE, gadE and hfq. Putative virulence genes stcE, hlyA, ent and nleA were also decreased in vitro. Reversal of these changes was noted for bacteria recovered from the intestine, where transcripts for qseF and fis and putative virulence factors AidA(15), TerC and Ent/EspL2 were significantly increased, and transcripts for AIDA(48), Iha, UreC, Efa1A, Efa1B, ToxB, EhxA, StcE, NleA and NleB were expressed at high levels.

CONCLUSIONS/SIGNIFICANCE

Presence of lactose resulted in decreased expression of LEE genes and the failure of EHEC O157:H7 to adhere to epithelial cells in vitro but this repression was overcome in vivo. CCR and/or acidic pH may have played a role in repression of the LEE genes. Bacterial pathogens need to integrate their nutritional metabolism with expression of virulence genes but little is known of how this is done in E. coli O157:H7. This study indicates one aspect of the subject that should be investigated further.

Pepper mild mottle virus as an indicator of fecal pollution

Accurate indicators of fecal pollution are needed in order to minimize public health risks associated with wastewater contamination in recreational waters. However, the bacterial indicators currently used for monitoring water quality do not correlate with the presence of pathogens. Here we demonstrate that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution. Quantitative PCR was used to determine the abundance of PMMoV in raw sewage, treated wastewater, seawater exposed to wastewater, and fecal samples and/or intestinal homogenates from a wide variety of animals. PMMoV was present in all wastewater samples at concentrations greater than 1 million copies per milliliter of raw sewage. Despite the ubiquity of PMMoV in human feces, this virus was not detected in the majority of animal fecal samples tested, with the exception of chicken and seagull samples. PMMoV was detected in four out of six seawater samples collected near point sources of secondary treated wastewater off southeastern Florida, where it co-occurred with several other pathogens and indicators of fecal pollution. Since PMMoV was not found in nonpolluted seawater samples and could be detected in surface seawater for approximately 1 week after its initial introduction, the presence of PMMoV in the marine environment reflects a recent contamination event. Together, these data demonstrate that PMMoV is a promising new indicator of fecal pollution in coastal environments.

A rapid screen of broth enrichments for Salmonella enterica serovars enteritidis, Hadar, Heidelberg, and Typhimurium by Using an allelotyping multiplex PCR that targets O- and H-antigen alleles

Salmonella continues to cause significant foodborne outbreaks, best illustrated with recent outbreaks associated with peanut butter, raw tomatoes, and serrano peppers. To ascertain the likely source of the outbreak, bacterial typing is essential to this process. While PCR has become an important detection tool for pathogens in foods, PCR can also identify strain differences by targeting gene(s) or sequences exhibiting polymorphisms or variability in its distribution within the bacterial population. Over 2,500 Salmonella enterica serovars identified based on antigenic differences in lipopolysaccharide and flagellin have been identified to date. We developed an allelotyping PCR scheme that identifies the O and H alleles associated with S. enterica serovars Enteritidis, Hadar, Heidelberg, Typhimurium, and others, with the same antigen alleles but in different O- and H-allele combinations (e.g., S. enterica Kentucky), and validated it as a screen to identify samples contaminated with these Salmonella serovars. We correctly identified poultry samples containing S. enterica serovars Enteritidis, Kentucky, and Typhimurium from our multiplex screen of primary enrichments of environmental drag swabs. PCR agreed well (kappa values = 0.81 to 1.0) with conventional serotyping methods used to type salmonellae isolated from primary enrichment. Coupled with Salmonella-specific PCR, such as invA, this allelotyping PCR could prove useful in the identification of Salmonella and specific S. enterica serovars present in foods or the environment and could decrease the time and cost associated with conventional serotyping methods.

Pepper mild mottle virus as an indicator of fecal pollution

Accurate indicators of fecal pollution are needed in order to minimize public health risks associated with wastewater contamination in recreational waters. However, the bacterial indicators currently used for monitoring water quality do not correlate with the presence of pathogens. Here we demonstrate that the plant pathogen Pepper mild mottle virus (PMMoV) is widespread and abundant in wastewater from the United States, suggesting the utility of this virus as an indicator of human fecal pollution. Quantitative PCR was used to determine the abundance of PMMoV in raw sewage, treated wastewater, seawater exposed to wastewater, and fecal samples and/or intestinal homogenates from a wide variety of animals. PMMoV was present in all wastewater samples at concentrations greater than 1 million copies per milliliter of raw sewage. Despite the ubiquity of PMMoV in human feces, this virus was not detected in the majority of animal fecal samples tested, with the exception of chicken and seagull samples. PMMoV was detected in four out of six seawater samples collected near point sources of secondary treated wastewater off southeastern Florida, where it co-occurred with several other pathogens and indicators of fecal pollution. Since PMMoV was not found in nonpolluted seawater samples and could be detected in surface seawater for approximately 1 week after its initial introduction, the presence of PMMoV in the marine environment reflects a recent contamination event. Together, these data demonstrate that PMMoV is a promising new indicator of fecal pollution in coastal environments.

Gene and antigen markers of shiga-toxin producing E. coli from Michigan and Indiana river water: occurrence and relation to recreational water quality criteria

The relation of bacterial pathogen occurrence to fecal indicator bacteria (FIB) concentrations used for recreational water quality criteria (RWQC) is poorly understood. This study determined the occurrence of Shiga-toxin producing Escherichia coli (STEC) markers and their relation to FIB concentrations in Michigan and Indiana river water. Using 67 fecal coliform (FC) bacteria cultures from 41 river sites in multiple watersheds, we evaluated the occurrence of five STEC markers: the Escherichia coli (EC) O157 antigen and gene, and the STEC virulence genes eaeA, stx1, and stx2. Simple isolations from selected FC cultures yielded viable EC O157. By both antigen and gene assays, EC O157 was detected in a greater proportion of samples exceeding rather than meeting FC RWQC (P < 0.05), but was unrelated to EC and enterococci RWQC. The occurrence of all other STEC markers was unrelated to any FIB RWQC. The eaeA, stx2, and stx1 genes were found in 93.3, 13.3, and in 46.7% of samples meeting FC RWQC and in 91.7, 0.0, and 37.5% of samples meeting the EC RWQC. Although not statistically significant, the percentage of samples positive for each STEC marker except stx1 was lower in samples that met, as opposed to exceeded, FIB RWQC. Viable STEC were common members of the FC communities in river water throughout southern Michigan and northern Indiana, regardless of FIB RWQC. Our study indicates that further information on the occurrence of pathogens in recreational waters, and research on alternative indicators of their occurrence, may help inform water-resource management and public health decision-making.

Escherichia coli O157 prevalence in different cattle farm types and identification of potential risk factors

Although the prevalence of Escherichia coli O157 on cattle farms has been examined extensively, the relationship between this pathogen and farm type has been established only rarely. A large-scale study was designed to determine the prevalence of E. coli O157 in the Flemish region of Belgium on farms of dairy cattle, beef cattle, mixed dairy and beef cattle, and veal calves. The effect of various factors on the occurrence at the pen level also was evaluated. In 2007, 180 farms were randomly selected based on region, farm size, and number of animals purchased and were examined using the overshoe sampling method. When possible, overshoes used in areas containing animals in three different age categories (< 8 months, 8 to 30 months, and > 30 months) were sampled on each farm. In total, 820 different pens were sampled and analyzed for the presence of E. coli O157 by enrichment, immunomagnetic separation, and plating on selective agar. Presumptive E. coli O157 colonies were identified using a multiplex PCR assay for the presence of the rfb(O157) and fliC(H7) genes. The statistical analysis was carried out with Stata SE/10.0 using a generalized linear regression model with a logit link function and a binomial error distribution. The overall farm prevalence of E. coli O157 was 37.8% (68 of 180 farms). The highest prevalence was found on dairy cattle farms (61.2%, 30 of 49 farms). The prevalences on beef, mixed dairy and beef, and veal calf farms were 22.7% (17 of 75 farms), 44.4% (20 of 45 farms), and 9.1% (1 of 11 farms), respectively. A significant positive correlation between age category and E. coli O157 prevalence was found only on mixed dairy and beef farms and dairy farms. No influence of farm size or introduction of new animals was demonstrated.

Occurrence of non-sorbitol fermenting, verocytotoxin-lacking Escherichia coli O157 on cattle farms

Escherichia coli O157 is often associated with hemorrhagic colitis and the hemolytic uremic syndrome (HUS). The verocytotoxins are considered to be the major virulence determinants. However, vt-negative E. coli O157 were recently isolated from patients with HUS. Several transmission routes to humans are described, but cattle feces are the primary source from which both the food supply and the environment become contaminated with E. coli O157. In a prevalence study performed on dairy, beef, mixed dairy/beef and veal farms in the summer of 2007, vt-negative isolates were detected on 11.8% (8/68) of the positive farms. From these eight farms, a total of 43 sorbitol-negative E. coli O157:H7 were collected. On five farms, only strains negative for the vt genes were present whereas both vt-negative and vt-positive strains could be detected on three other farms. Further characterization revealed that all isolates carried the eaeA and hlyA genes. Pulsed-field gel electrophoresis (PFGE) of all isolates resulted in nine different PFGE types and within the vt-negative strains, four different genotypes were identified, indicating that certain genetic clones are widespread over the cattle population.

A Preliminary Investigation of Fecal Indicator Bacteria, Human Pathogens, and Source Tracking Markers in Beach Water and Sand

Data suggesting that fecal indicating bacteria may persist and/or regrow in sand has raised concerns that fecal indicators may become uncoupled from sources of human fecal pollution. To investigate this possibility, wet and dry beach sand, beach water, riverine water, canal water, and raw sewage samples were screened by PCR for certain pathogenic microbes and molecular markers of human fecal pollution. The targets included in this study were human specific Bacteroides (HF8 marker), human-specific enterococci (esp gene), Staphylococcus aureus, Escherichia coli 0157:H7, Campylobacter jejuni, and adenovirus. Sewage samples were also tested for Salmonella species. The results were compared to concentrations of enterococci, Escherichia coli, and Bacteroides species, as determined by membrane filtration methods. Molecular analysis yielded positive results for human specific Bacteroides, and S. aureus, in samples of raw sewage. Two of the environmental samples were positive for human specific Bacteroides and one was positive for S. aureus. The PCR screen was negative for other samples and targets, despite exceedance of EPA single sample guidelines for recreational waters on several of the sample dates (5/11 dates). However, estimates of the number of cells delivered to the PCR reaction suggested that few of the samples met the detection limit of the PCR reaction due to a variety of factors. The analysis indicated a need to improve nucleic acid processing in order to enable better delivery of DNA to downstream molecular methods.

Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators

The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with <50 EC 100 mL(-1), human pharmaceuticals or chemical indicators of wastewater treatment plant effluent occurred in six, veterinary antibiotics were detected in three, and stx1 or stx2 genes (indicating varying animal sources of STEC) were detected in eight. Only the EC eaeA gene was positively correlated with FIB concentrations. Human-source fecal pollution was indicated by the esp gene and the human pharmaceutical carbamazepine in one of the nine samples that met all FIB recreational water quality standards. Escherichia coli rfbO157 and stx2c genes, which are typically associated with cattle sources and are of potential human health significance, were detected in one sample in the absence of tested chemicals. Chemical and gene-based indicators of fecal contamination may be present even when FIB standards are met, and some may, unlike FIB, indicate potential sources. Application of multiple water quality indicators with variable environmental persistence and fate may yield greater confidence in fecal pollution assessment and may inform remediation decisions.

Rapid screening of Salmonella enterica serovars Enteritidis, Hadar, Heidelberg and Typhimurium using a serologically-correlative allelotyping PCR targeting the O and H antigen alleles

BACKGROUND

Classical Salmonella serotyping is an expensive and time consuming process that requires implementing a battery of O and H antisera to detect 2,541 different Salmonella enterica serovars. For these reasons, we developed a rapid multiplex polymerase chain reaction (PCR)-based typing scheme to screen for the prevalent S. enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium.

RESULTS

By analyzing the nucleotide sequences of the genes for O-antigen biosynthesis including wba operon and the central variable regions of the H1 and H2 flagellin genes in Salmonella, designated PCR primers for four multiplex PCR reactions were used to detect and differentiate Salmonella serogroups A/D1, B, C1, C2, or E1; H1 antigen types i, g, m, r or z10; and H2 antigen complexes, I: 1,2; 1,5; 1,6; 1,7 or II: e,n,x; e,n,z15. Through the detection of these antigen gene allele combinations, we were able to distinguish among S. enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium. The assays were useful in identifying Salmonella with O and H antigen gene alleles representing 43 distinct serovars. While the H2 multiplex could discriminate between unrelated H2 antigens, the PCR could not discern differences within the antigen complexes, 1,2; 1,5; 1,6; 1,7 or e,n,x; e,n,z15, requiring a final confirmatory PCR test in the final serovar reporting of S. enterica.

CONCLUSION

Multiplex PCR assays for detecting specific O and H antigen gene alleles can be a rapid and cost-effective alternative approach to classical serotyping for presumptive identification of S. enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium.

Molecular detection of Leptospira interrogans in human tissues and environmental samples in a lethal case of leptospirosis

A forensic case of suspected Leptospirosis with fatal course was resolved by the molecular detection of Leptospira interrogans in postmortem human tissues and in environmental samples. Polymerase chain reaction analysis and DNA sequencing confirmed the clinical diagnosis of Weil syndrome, and the death was considered to be an occupational accident with all the legal implications.

Electrochemical detection of harmful algae and other microbial contaminants in coastal waters using hand-held biosensors

Standard methods to identify microbial contaminants in the environment are slow, laborious, and can require specialized expertise. This study investigated electrochemical detection of microbial contaminants using commercially available, hand-held instruments. Electrochemical assays were developed for a red tide dinoflagellate (Karenia brevis), fecal-indicating bacteria (Enterococcus spp.), markers indicative of human sources of fecal pollution (human cluster Bacteroides and the esp gene of Enterococcus faecium), bacterial pathogens (Escherichia coli 0157:H7, Salmonella spp., Campylobacter jejuni, Staphylococcus aureus), and a viral pathogen (adenovirus). For K. brevis, two assay formats (Rapid PCR-Detect and Hybrid PCR-Detect) were tested and both provided detection limits of 10 genome equivalents for DNA isolated from K. brevis culture and amplified by PCR. Sensitivity with coastal water samples was sufficient to detect K. brevis that was "present" ( Collapse

Key Words

• electrochemical biosensor
• karenia brevis
• pathogen detection
• recreational water quality
• source tracking

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MESH Headings

• Animals
• Dinoflagellida/genetics
• Dinoflagellida/isolation & purification
• Electrochemistry
• Environmental Monitoring/instrumentation
• Environmental Monitoring/methods
• Eukaryota/genetics
• Eukaryota/isolation & purification
• Reproducibility of Results
• Seawater/analysis
• Seawater/microbiology
• Water Microbiology
• Water Pollutants/analysis

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Grants

• P50 ES12736 NIEHS NIH HHS
• ES 05705 NIEHS NIH HHS
• P50 ES012736 NIEHS NIH HHS
• P30 ES005705 NIEHS NIH HHS
• F32 ES005705 NIEHS NIH HHS

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Affiliation(s)

Michael J LaGier Cooperative Institute of Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA.
Jack W Fell
Kelly D Goodwin

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Collaborators Collapse

Real-time PCR and enzyme-linked fluorescent assay methods for detecting Shiga-toxin-producingEscherichia coliin mincemeat samples

This work aimed to compare real-time polymerase chain reaction (PCR) with the commercially available enzyme-linked fluorescent assay (ELFA) VIDAS ECOLI O157™ for detecting Escherichia coli O157 in mincemeat. In addition, a PCR-based survey on Shiga-toxin-producing E. coli (STEC) in mincemeat collected in Italy is presented. Real-time PCR assays targeting the stx genes and a specific STEC O157 sequence (SILO157, a small inserted locus of STEC O157) were tested for their sensitivity on spiked mincemeat samples. After overnight enrichment, the presence of STEC cells could be clearly determined in the 25 g samples containing 10 bacterial cells, while the addition of five bacteria provided equivocal PCR results with Ct values very close to or above the threshold of 40. The PCR tests proved to be more sensitive than the ELFA-VIDAS ECOLI O157™, whose detection level started from 50 bacterial cells/25 g of mincemeat. The occurrence of STEC in 106 mincemeat (bovine, veal) samples collected from September to November 2004 at five different points of sale in Italy (one point of sale in Arezzo, Tuscany, central Italy, two in Mantova, Lombardy, Northern Italy, and two in Bologna, Emilia-Romagna, upper-central Italy) was less than 1%. Contamination by the main STEC O-serogroups representing a major public health concern, including O26, O91, O111, O145, and O157, was not detected. This survey indicates that STEC present in these samples are probably not associated with pathogenesis in humans.

Evaluation of enrichment-free PCR-based detection on the rfbE gene of Escherichia coli O157--application to municipal wastewater

Escherichia coli O157 strains have emerged as important human enteric pathogens. Strains that express the O-antigen 157 are commonly associated with severe clinical manifestations, including bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. E. coli O157 strains may be transmitted in a variety of ways, including food, water and person-to-person or animal-to-person contact. Fecal contamination is one source of environmental contamination and is responsible for the presence of these pathogens in the environment. We used a specific and sensitive PCR assay based on the rfbE gene to detect low levels of these pathogens in wastewater. The set of primers used was designed to amplify an intragenic segment of the rfbE gene. The amplification assay detected 200 CFU of E. coli O157 in pure water. The prevalence of E. coli O157 in the effluents of 44 wastewater treatment plants was determined (7%).

Development of PCR primers based on a fragment from randomly amplified polymorphic DNA for the detection of Escherichia coli O157:H7/NM

Serotype O157:H7 of EHEC is by far the most prevalent serotype associated with haemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS). Although PCR methods aimed on the detection of genes associated with the pathogenicity of Escherichia coli O157:H7 have been reported, tests allowing the direct identification of this serotype are rare. In this study, we used RAPD-PCR tests to analyze strains of E. coli O157:H7 serotype, strains of non-pathogenic E. coli, and strains of other pathotypes, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), and enteroaggregation E. coli (EAggEC). One RAPD fragment co-shared by serotype O157:H7 strains was observed when 10-mer primer termed as OPQ3 was used. After sequencing this fragment, three primers were designed and combined to form two PCR primer pairs. These two primer pairs were highly specific to the strains belonging to E. coli O157:H7/NM (non-motile).

Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan

Cladophora glomerata, a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attached Cladophora, obtained from the Lake Michigan and Burns Ditch (Little Calumet River, Indiana) sides of a breakwater during the summers of 2004 and 2005, harbored the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC), Salmonella, Shigella, and Campylobacter. The presence of potential pathogens and numbers of organisms were determined by using cultural methods and by using conventional PCR, most-probable-number PCR (MPN-PCR), and quantitative PCR (QPCR) performed with genus- and toxin-specific primers and probes. While Shigella and STEC were detected in 100% and 25%, respectively, of the algal samples obtained near Burns Ditch in 2004, the same pathogens were not detected in samples collected in 2005. MPN-PCR and QPCR allowed enumeration of Salmonella in 40 to 80% of the ditch- and lakeside samples, respectively, and the densities were up to 1.6 x 10(3) cells per g Cladophora. Similarly, these PCR methods allowed enumeration of up to 5.4 x 10(2) Campylobacter cells/g Cladophora in 60 to 100% of lake- and ditchside samples. The Campylobacter densities were significantly higher (P < 0.05) in the lakeside Cladophora samples than in the ditchside Cladophora samples. DNA fingerprint analyses indicated that genotypically identical Salmonella isolates were associated with geographically and temporally distinct Cladophora samples. However, Campylobacter isolates were genetically diverse. Since animal hosts are thought to be the primary habitat for Campylobacter and Salmonella species, our results suggest that Cladophora is a likely secondary habitat for pathogenic bacteria in Lake Michigan and that the association of these bacteria with Cladophora warrants additional studies to assess the potential health impact on beach users.

Evaluation of a PCR detection method for Escherichia coli O157:H7/H- bovine faecal samples

AIMS

Combinations of PCR primer sets were evaluated to establish a multiplex PCR method to specifically detect Escherichia coli O157:H7 genes in bovine faecal samples.

METHODS AND RESULTS

A multiplex PCR method combining three primer sets for the E. coli O157:H7 genes rfbE, uidA and E. coli H7 fliC was developed and tested for sensitivity and specificity with pure cultures of 27 E. coli serotype O157 strains, 88 non-O157 E. coli strains, predominantly bovine in origin and five bacterial strains other than E. coli. The PCR method was very specific in the detection of E. coli O157:H7 and O157:H- strains, and the detection limit in seeded bovine faecal samples was <10 CFU g(-1) faeces, following an 18-h enrichment at 37 degrees C, and could be performed using crude DNA extracts as template.

CONCLUSIONS

A new multiplex PCR method was developed to detect E. coli O157:H7 and O157:H-, and was shown to be highly specific and sensitive for these strains both in pure culture and in crude DNA extracts prepared from inoculated bovine faecal samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This new multiplex PCR method is suitable for the rapid detection of E. coli O157:H7 and O157:H- genes in ruminant faecal samples.

Detection of Escherichia coli O157 using equal-length double-stranded fluorescence probe in a real-time polymerase chain reaction assay

BACKGROUND

Enterohemorrhagic Escherichia coli (E. coli) O157 is a dangerous pathogen, which causes bloody diarrhea and severe hemolytic uremic syndrome (HUS). Although several assay systems based on real-time polymerase chain reaction (PCR) have been integrated to detect this pathogen, most of them are not specific. We report a real-time quantitative PCR method targeting rfbE, a gene specifically expressed in E. coli O157. This method can therefore be used to diagnose enterohemorrhagic Escherichia coli (E. coli) O157.

METHODS

A nucleic acid based diagnostic assay system, combining equal-length double-stranded fluorescence probe technique and real-time PCR, was developed to detect E. coli O157. This assay system take advantage of the highly conserved rfbE O-antigen synthesis gene, and a pair of fluorescence-quenching probes complementary to rfbE gene were used in a real-time PCR to quantify the presence of the pathogen.

RESULTS

The specificity of the diagnostic method was assessed by comparing test results on 14 different related pathogens including common E. coli, enteroinvasive Escherichia coli (EIEC), Salmonella, Shigella and E. coli O157. The detection limit of the method was determined using 10-fold serial dilutions of an E. coli O157 standard sample, and as few as 1.49 x 10(3) CFU/ml could be detected. All E. coli with serotype O157, which expresses rfbE gene, were positive in this assay, while all other species without rfbE gene expression were negative.

CONCLUSIONS

By combining equal-length double-stranded fluorescence probe technique and real-time PCR, we have developed a simple, rapid, specific and sensitive method to detect E. coli O157.

Isolation and characterization of verocytotoxin-producing Escherichia coli O157 from Turkish cattle

The objective of this study was to collect rectal swabs from the cattle in a slaughterhouse located in Hatay (Turkey) immediately after slaughter for the isolation and characterization of verotoxin-producing Escherichia coli O157 in each month during a 1-year period. The rectal swab samples were analyzed for the isolation of E. coli O157 through pre-enrichment, immunomagnetic separation and selective plating on CT-SMAC agar. E. coli O157 was isolated from 77 (13.6%) of the samples. The presence of E. coli O157 changed during a 1-year period, in that the occurrence of E. coli O157 was the highest in July and November and lowest in February. A total of 66 isolates out of 77 were serotype O157:H7 and 11 were serotype O157:NM. PCR analysis of E. coli O157 virulence genes revealed that all O157:H7/NM were positive for rbf(O157), 74 positive for EhlyA, 72 positive for eaeA, 62 positive for vtx2, and 3 positive for both vtx1 and vtx2. It was presented by cytotoxicity tests that many of E. coli O157 isolates showed high cytotoxicity on Vero cells. All of the isolates containing EhlyA showed enterohaemolysin production.

Detection of water-borne E. coli O157 using the integrating waveguide biosensor

Escherichia coli O157:H7, the most common serotype of enterohemorrhagic E. coli (EHEC), is responsible for numerous food-borne and water-borne infections worldwide. An integrating waveguide biosensor is described for the detection of water-borne E. coli O157, based on a fluorescent sandwich immunoassay performed inside a glass capillary waveguide. The genomic DNA of captured E. coli O157 cells was extracted and quantitative real-time PCR subsequently performed to assess biosensor-capture efficiency. In vitro microbial growth in capillary waveguide is also documented. The biosensor allows for quantitative detection of as few as 10 cells per capillary (0.075 ml volume) and can be used in conjunction with cell amplification, PCR and microarray technologies to positively identify a pathogen.

Identification of putative adhesin genes in shigatoxigenic Escherichia coli isolated from different sources

Shiga toxin-producing Escherichia coli (STEC) is an important pathogen responsible for severe human intestinal and systemic infections. The bacterial factors required for colonization of the hosts are still not well defined. In this study, the prevalence of seven putative adhesive genes that are not encoded in the locus of enterocyte effacement (LEE) in 74 STEC strains isolated from humans (n=39), food (n=6), cattle (n=11), and pigs (n=18) was investigated by PCR. In addition, Shiga toxin (stx) and intimin (eaeA including alpha, beta, gamma, delta, epsilon, zeta variants) genes were tested. The most prevalent adhesin was that encoded by toxB gene (52 of 74 isolates; 70.3%). This marker was found in all 12 strains of O157:H7 serotype and in 23 of 32 (71.9%) isolates of the O157:NM serogroup. Moreover, this gene was also present in other 17 STEC of the non-O157 serogroup. The second most prevalent adhesin was that encoded by the lpfAO157/OI-154 gene (43 isolates; 58.1%). This marker was detected in LEE-positive strains of the O157 serogroup but also in 9 LEE-negative isolates of porcine origin. Several STEC isolates tested (42 strains; 56.7%) had the efa1 gene of the Efa1 putative adhesive marker. This adhesin was almost exclusively found among eaeA-positive strains recovered from humans, food and cattle. On the other hand, iha marker was detected either in LEE-positive (29 isolates) or LEE-negative (12 strains) STEC. Only two eaeA-negative strains had the saa putative adhesive gene. These results show that STEC strains may be able to express several putative adhesins. However, further studies are needed to evaluate the role of the genes identified in the present study in the pathogenesis of human infections.

Detection of Escherichia coli serogroup O103 by real-time polymerase chain reaction

AIMS

The aims of the study were to identify the specific genes of O-antigen gene cluster from Shiga toxin-producing Escherichia coli (STEC) O103 and to provide the basis for a specific real-time PCR test for rapid detection of E. coli O103.

METHODS AND RESULTS

The published primers complementary to JUMPstart and gnd gene, the conserved flanking sequences of O-antigen genes clusters in E. coli and related species, were used to amplify the 12-kbp O103 O-antigen biosynthesis locus of STEC O103. A DNA library representative of this cluster allowed two O103-specific probes to be identified in the flippase (wzx) and UDP-galactose-4-epimerase (galE) genes. Two specific O103 serotyping real-time PCR tests based on these two genes were successfully developed.

CONCLUSIONS

These results confirm that the O-antigen gene cluster sequences of E. coli allow rapidly a specific O-antigen real-time PCR assay to be designed.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings increase the number of real-time PCR-assays available to replace the classical O-serotyping among E. coli O-antigen.

Detection by 5'-nuclease PCR of Shiga-toxin producing Escherichia coli O26, O55, O91, O103, O111, O113, O145 and O157:H7, associated with the world's most frequent clinical cases

This paper describes 5'-nuclease PCR assays for detecting eight O-serogroups, H7 flagellar antigen and stx genes from the Shiga toxin-producing Escherichia coli (STEC) associated with the world's most frequent clinical cases. A single set of primers was used to detect the genes stx1 and stx2 in the same reaction by 5'-nuclease PCR. Serotyping by 5'-nuclease PCR of STEC was based on the selection of primers and probes targeting the O-antigen gene clusters of E. coli O26, O55, O91, O111, O113, O157, the eae gene of E. coli O103, the O-island 29 of E. coli O145, and the flagellar H7 antigen gene. Results obtained on a collection of 190 strains indicate that the 5'-nuclease PCR assays used here could serve as a basis for rapid specific stx, O and H7 typing of these major pathogenic serogroups of E. coli. This work provides sensitive and specific tests for the rapid, reliable detection of the main pathogenic E. coli O-serogroups of major public health concern.

Inhibition of PCR amplification by phytic acid, and treatment of bovine fecal specimens with phytase to reduce inhibition

Development of effective polymerase chain reaction (PCR)-based diagnostic tests using ruminant fecal specimens has been thwarted by excessive inhibition. A PCR system based on amplification of 1000 copies of bacteriophage lambda-DNA was used as a model to evaluate inhibition levels in bovine feces. Dilution experiments using a bovine fecal specimen suggested that as little as 40 microg of feces (in a 100-microl PCR) affected the efficiency of amplification. It was discovered that phytic acid (the hexaphosphoric ester of inositol) is a powerful inhibitor of PCR. Above 0.3 mM phytate, the PCR is completely inhibited. In a very narrow range around 0.2 mM target-specific amplification proceeds efficiently. At concentrations between 10 and 100 microM, phytate nonspecific amplification (e.g., primer-dimer formation) is dominant. Below 10 microM, phytate target-specific amplification proceeds efficiently. A simple processing procedure using 50 units/ml of Aspergillus niger 3-phytase [E.C. 3.1.3.8] was developed that reduced PCR inhibition levels in bovine fecal specimens by approximately 500-fold.