PCR for specific detection of H7 flagellar variant of fliC among extraintestinal pathogenic Escherichia coli

Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis. To date, molecular epidemiological studies have yielded numerous important insights into putative virulence factors, host-pathogen relationships, phylogenetic background, reservoirs, antimicrobial-resistant strains, clinical diagnostics, and transmission pathways of ExPEC, and have delineated areas in which further study is needed. The rapid pace of discovery of new putative virulence factors and the increasing awareness of the importance of virulence factor regulation, expression, and molecular variation should stimulate many future molecular epidemiological investigations. The growing sophistication and availability of molecular typing methodologies, and of the new computational and statistical approaches that are being developed to address the huge amounts of data that whole genome sequencing generates, provide improved tools for such studies and allow new questions to be addressed.

Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCEEscherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.

Molecular Epidemiology of Extraintestinal Pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC), the specialized E. coli strains that possess the ability to overcome or subvert host defenses and cause extraintestinal disease, are important pathogens in humans and certain animals. Molecular epidemiological analysis has led to an appreciation of ExPEC as being distinct from other E. coli (including intestinal pathogenic and commensal variants) and has offered insights into the ecology, evolution, reservoirs, transmission pathways, host-pathogen interactions, and pathogenetic mechanisms of ExPEC. Molecular epidemiological analysis also provides an essential complement to experimental assessment of virulence mechanisms. This chapter first reviews the basic conceptual and methodological underpinnings of the molecular epidemiological approach and then summarizes the main aspects of ExPEC that have been investigated using this approach.

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.

Microbial source tracking in a small southern California urban watershed indicates wild animals and growth as the source of fecal bacteria

Three independent microbial source tracking (MST) methods were applied to a small urban subwatershed in Orange County, California. Fifty-seven water samples collected over summer 2002 were analyzed for human adenovirus and enterovirus. Enterococci and E. coli were isolated for antibiotic resistance analysis (ARA) and for PCR identification of human- and animal-specific toxin genes, respectively. All water samples were PCR negative for human enteroviruses and E. coli human-specific toxin gene. E. coli toxin markers revealed the presence of toxin genes specific to bird, rabbit, and cow. Enterococci ARA results supported this conclusion and indicated that fecal bacteria from bird and wild animal feces as well as soil were the predominant source found in the watershed. An E. coli, isolated from the watershed and inoculated back into the heat-sterilized storm drain water, increased 4 log units within 6 days. Collectively, these results suggest that bird and wild animal feces, soil amendments, and/or fecal coliform growth in the storm drain are the major contributors to the fecal bacterial pollution in downstream areas. However, human adenoviruses were detected on two occasions. Fecal bacterial concentrations were not elevated on these two occasions, suggesting that the elevated levels of fecal indicator bacteria in this small watershed could be unrelated to the source of human adenovirus.

Aspects of genome plasticity in pathogenic Escherichia coli

The species Escherichia coli comprises not only non-pathogenic or commensal variants that belong to the normal intestinal flora of most mammals, but also various pathogenic strains causing diverse intestinal and extraintestinal infections in man and animals. Virulence factors and mechanisms involved in pathogenesis have been successfully analyzed for many years resulting in a wealth of knowledge about many E. coli pathotypes. However, our knowledge on the genome content, diversity and variability between pathogenic and also non-pathogenic subtypes is only slowly accumulating. Pathotypes have been largely defined by the presence or absence of particular DNA segments that in most cases appear to have been acquired via horizontal gene transfer events. As these regions are frequently subjected to excisions, rearrangements, and transfers they contribute to the previously unexpected and underestimated rapid evolution of E. coli variants resulting in the development of novel strains and even pathotypes. In these studies various novel aspects of genome diversity and plasticity in extraintestinal and intestinal pathogenic E. coli pathotypes have been addressed and the results have been directly applied for the improvement of diagnostic methods.

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 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.

Genetical and functional investigation of fliC genes encoding flagellar serotype H4 in wildtype strains of Escherichia coli and in a laboratory E. coli K-12 strain expressing flagellar antigen type H48

BACKGROUND

Serotyping of O-(lipopolysaccharide) and H-(flagellar) antigens is a wideley used method for identification of pathogenic strains and clones of Escherichia coli. At present, 176 O- and 53 H-antigens are described for E. coli which occur in different combinations in the strains. The flagellar antigen H4 is widely present in E. coli strains of different O-serotypes and pathotypes and we have investigated the genetic relationship between H4 encoding fliC genes by PCR, nucleotide sequencing and expression studies.

RESULTS

The complete nucleotide sequence of fliC genes present in E. coli reference strains U9-41 (O2:K1:H4) and P12b (O15:H17) was determined and both were found 99.3% (1043 of 1050 nucleotides) identical in their coding sequence. A PCR/RFLP protocol was developed for typing of fliC-H4 strains and 88 E. coli strains reacting with H4 antiserum were investigated. Nucleotide sequencing of complete fliC genes of six E. coli strains which were selected based on serum agglutination titers, fliC-PCR genotyping and reference data revealed 96.6 to 100% identity on the amino acid level. The functional expression of flagellin encoded by fliC-H4 from strain U9-41 and from our strain P12b which is an H4 expressing variant type was investigated in the E. coli K-12 strain JM109 which encodes flagellar type H48. The fliC recombinant plasmid carrying JM109 strains reacted with both H4 and H48 specific antisera whereas JM109 reacted only with the H48 antiserum. By immunoelectron microscopy, we could show that the flagella made by the fliC-H4 recombinant plasmid carrying strain are constituted of H48 and H4 flagellins which are co-assembled into functional flagella.

CONCLUSION

The flagellar serotype H4 is encoded by closely related fliC genes present in serologically different types of E. coli strains which were isolated at different time periods and geographical locations. Our expression studies show for the first time, that flagellins of different molecular weigh are functionally expressed and coassembled in the same flagellar filament in E. coli.

Evaluation of molecular typing methods for Escherichia coli O157:H7 isolates from cattle, food, and humans

Escherichia coli O157:H7, a Shiga toxin-producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for beta-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.

Serology and genetics of the flagellar antigen of Escherichia coli O157:H7a,7c

Among Escherichia coli strains of the O55:H7 serovar, which is considered the ancestor of Shiga toxin-producing E. coli (STEC) O157:H7, two subtypes, H7a,7b and H7a,7c (briefly, H7a,b and H7a,c, respectively), of the H7 flagellar antigen have been described previously [J. Wright and R. Villanueva, J. Hyg. (Camb.) 51:39-48, 1953; Y. A. Ratiner and V. A. Sinelnikova, Zh. Microbiol. Epidemiol. Immunobiol. 3:111-116, 1969). We have now studied 13 STEC O157:H7 strains and 1 O55:H7 strain that were epidemiologically unrelated, that originated from six countries on two continents, and that had different profiles when analyzed by multilocus enzyme electrophoresis, pulsed-field gel electrophoresis, and PCR for stx and eae. They were all found to possess the H7a,c flagellar antigen. Serum cross-absorption assays confirmed that their H antigens were indistinguishable from each other and from that of E. coli O55:H7a,c but differed from the standard H7a,b antigen of E. coli H test strain U5/41. It was shown by phage-mediated transduction that the flagellin genes for these two H-antigen subserotypes were alleles of the E. coli fliC locus. On the basis of the serological data obtained in this study and the molecular characteristics of E. coli fliC(H7) alleles recently published, it is inferred that H7a,c and H7a,b are the main serological subtypes of the group of E. coli H7 flagellins.