Microarray based comparison of two Escherichia coli O157:H7 lineages

Ultrasensitive and rapid count of Escherichia coli using magnetic nanoparticle probe under dark-field microscope

Background

Escherichia coli (E. coli) is one of the best-known zoonotic bacterial species, which pathogenic strain can cause infections in humans and animals. However, existing technologies or methods are deficient for quickly on-site identifying infection of E. coli before they breakout. Herein, we present an ultrasensitive and on-site method for counting E. coli using magnetic nanoparticle (MNP) probe under a dark-field in 30 min.

Results

The antibodies functionalized MNP, binding to E. coli to form a golden ring-like structure under a dark-field microscope, allowing for counting E. coli. This method via counting MNP-conjugated E. coli under dark-field microscope demonstrated the sensitivity of 6 CFU/μL for E. coli detection. Importantly, due to the advantages such as time-saving (only 30 min) and almost free of instrument (only require a portable microscope), our MNP-labeled dark-field counting strategy has the potential of being a universal tool for on-site quantifying a variety of pathogens with size ranges from a few hundreds of nanometers to a few micrometers.

Conclusion

In summary, the MNP-labeled dark-field counting strategy is a rapid, simple, sensitive as well as low-cost assay strategy, which has the potential of being a universal tool for on-site quantification of micrometer-size pathogens like E. coli.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1241-5) contains supplementary material, which is available to authorized users.

Estimating Bacterial Pathogen Levels in New Zealand Bulk Tank Milk

Zoonotic bacteria such as Campylobacter, Listeria, and Shiga toxin-producing Escherichia coli have been found in bulk tank milk in many countries, and the consumption of raw milk has been implicated in outbreaks of disease in New Zealand. Fecal contamination at milking is probably the most common source of pathogenic bacteria in bulk tank milk. Raw milk was collected from 80 New Zealand dairy farms during 2011 and 2012 and tested periodically for Campylobacter, E. coli O157, Listeria monocytogenes, and Salmonella. Milk quality data such as coliform counts, total bacterial counts, and somatic cell counts also were collected. By treating the total bacterial count as a proxy for fecal contamination of milk and utilizing farm and animal level prevalence and shedding rates of each pathogen, a predictive model for the level of pathogenic bacteria in bulk tank raw milk was developed. The model utilizes a mixture distribution to combine the low level of contamination inherent in the milking process with isolated contamination events associated with significantly higher pathogen levels. By simulating the sampling and testing process, the predictive model was validated against the observed prevalence of each pathogen in the survey. The predicted prevalence was similar to the observed prevalence for E. coli O157 and Salmonella, although the predicted prevalence was higher than that observed in samples tested for Campylobacter.

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.

Microscopy and genomic analysis of Mycoplasma parvum strain Indiana

Mycoplasma parvum [Eperythrozoon parvum] is the second hemotrophic mycoplasma (hemoplasma) described in pigs. Unlike M. suis, its closest phylogenetic relative, M. parvum, is considered a non-pathogenic bacterium in this host species. Natural infection of a domestic, 6-month-old splenectomized pig with M. parvum strain Indiana is described herein. Light and scanning electron microscopy of the bacteria were performed in addition to whole genome sequencing, analysis, and comparison to the genome of M. suis strain Illinois. Neither clinical signs nor anemia were observed during the infection. Microscopy analyses revealed coccoid to rod- shaped organisms varying from 0.2 to 0.5 μm; they were observed individually or in short chains by both light and electron microscopy, however less than 30% of the red blood cells were infected at peak bacteremia. The single circular chromosome of M. parvum was only 564 395 bp, smaller than M. genitalium, previously considered the tiniest member of the Mollicutes. Its general genomic features were similar to others in this class and species circumscription was verified by phylogenomic analysis. A gene-by-gene comparison between M. suis and M. parvum revealed all protein coding sequences (CDS) with assigned functions were shared, including metabolic functions, transporters and putative virulence factors. However, the number of CDS in paralogous gene families was remarkably different with about half as many paralogs in M. parvum. The differences in paralogous genes may be implicated in the different pathogenic potential of these two species, however variable gene expression may also play a role. Both are areas of ongoing investigation.

Identification and characterization of a peculiar vtx2-converting phage frequently present in verocytotoxin-producing Escherichia coli O157 isolated from human infections

Certain verocytotoxin-producing Escherichia coli (VTEC) O157 phage types (PTs), such as PT8 and PT2, are associated with severe human infections, while others, such as PT21, seem to be restricted to cattle. In an attempt to delve into the mechanisms underlying such a differential distribution of PTs, we performed microarray comparison of human PT8 and animal PT21 VTEC O157 isolates. The main differences observed were in the vtx2-converting phages, with the PT21 strains bearing a phage identical to that present in the reference strain EDL933, BP933W, and all the PT8 isolates displaying lack of hybridization in some regions of the phage genome. We focused on the region spanning the gam and cII genes and developed a PCR tool to investigate the presence of PT8-like phages in a panel of VTEC O157 strains belonging to different PTs and determined that a vtx2 phage reacting with the primers deployed, which we named Φ8, was more frequent in VTEC O157 strains from human disease than in bovine strains. No differences were observed in the production of the VT2 mRNA when Φ8-positive strains were compared with VTEC O157 possessing BP933W. Nevertheless, we show that the gam-cII region of phage Φ8 might carry genetic determinants downregulating the transcription of the genes encoding the components of the type III secretion system borne on the locus of enterocyte effacement pathogenicity island.

Variation in stress resistance patterns among stx genotypes and genetic lineages of shiga toxin-producing Escherichia coli O157

To evaluate the relationship between bacterial genotypes and stress resistance patterns, we exposed 57 strains of Shiga toxin-producing Escherichia coli (STEC) O157 to acid, freeze-thaw, heat, osmotic, oxidative, and starvation stresses. Inactivation rates were calculated in each assay and subjected to univariate and multivariate analyses, including principal component analysis (PCA) and cluster analysis. The stx genotype was determined for each strain as was the lineage-specific polymorphism assay (LSPA6) genotype. In univariate analyses, strains of the stx(1) stx(2) genotype showed greater resistance to heat than strains of the stx(1) stx(2c) genotype; moreover, strains of the stx(1) stx(2) genotype showed greater resistance to starvation than strains of the stx(2) or stx(2c) genotypes. LSPA6 lineage I (LI) strains showed greater resistance to heat and starvation than LSPA6 lineage II (LII) strains. PCA revealed a general trend that a strain with greater resistance to one type of stress tended to have greater resistance to other types of stresses. In cluster analysis, STEC O157 strains were grouped into stress-resistant, stress-sensitive, and intermediate clusters. In stx genotypes, all strains of the stx(1) stx(2) genotype were grouped with the stress-resistant cluster, whereas 72.7% (8/11) of strains of the stx(1) stx(2c) genotype grouped with the stress-sensitive cluster. In LI strains, 77.8% (14/18) of the strains were grouped with the stress-resistant cluster, whereas 64.7% (11/17) of LII strains were grouped with the stress-sensitive cluster. These results indicate that the genotypes of STEC O157 that are frequently associated with human illness, i.e., LI or the stx(1) stx(2) genotype, have greater multiple stress resistance than do strains of other genotypes.

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion

Background

Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins.

Results

Using multiple criteria including sequence similarity, nucleotide composition, phylogenetic analysis and selection pressure on gene sequence, we present evidence that META1 originated in trypanosomatids as a result of a lateral gene transfer of a bacterial heat-inducible protein, HslJ. Furthermore, within the Leishmania genome, META1 sequence is under negative selection pressure against change/substitution. Using homology modeling of Leishmania META1 based on solved NMR structure of HslJ, we show that META1 and HslJ share a similar structural fold. The best hit for other proteins with similar fold is MxiM, a protein involved in the type III secretion system in Shigella. The striking structural similarity shared by META1, HslJ and MxiM suggests a possibility of shared functions. Upon structural superposition with MxiM, we have observed a putative hydrophobic cavity in META1. Mutagenesis of select hydrophobic residues in this cavity affects the secretion of the secreted acid phosphatase (SAP), indicating META1's involvement in secretory processes in Leishmania.

Conclusions

Overall, this work uses an evolutionary biology approach, 3D-modeling and site-directed mutagenesis to arrive at new insights into functions of Leishmania META1.

Study of polymorphisms in tir, eae and tccP2 genes in enterohaemorrhagic and enteropathogenic Escherichia coli of serogroup O26

Background

Enteropathogenic (EPEC) and enterohaemorrhagic (EHEC) Escherichia coli are responsible for food poisoning (enteritis and enterotoxaemia) in humans in developed countries. Cattle are considered to be an important reservoir of EHEC and EPEC strains for humans. Moreover, some of the strains, belonging to the O26, O111, O118 serogroups, for example, are also responsible for digestive disorders in calves. The Translocated intimin receptor (Tir), the intimin (Eae) and the Tir-cytoskeleton coupling protein (TccP) represent three virulence factors implicated in the intimate attachment of the bacteria to the eukaryotic cell. Major variants have already been described for these genes among the different serogroups but minor variations have not often been studied. In this study, we examined the polymorphisms of the tir, eae and tccP2 genes of O26 strains (EPEC and EHEC isolated from bovines and from humans) with the aim to determine whether these polymorphisms are host specific or not.

Results

Of the 70 tested strains, 10 strains (14% of the strains) presented one or several polymorphisms in the tir and eae genes, which have never previously been described. Concerning tccP2 detection, 47 of the 70 strains (67% of the strains) were found to be positive for this gene. Most of the strains were found to possess tccP2 variants described in strains of serogroup O26. Nevertheless, three strains had tccP2 genes respectively described in strains of serogroup O111, O103 and O55. Moreover, none of the polymorphisms was statistically specific to the bovine or the human isolates. Nevertheless, the two major variants of tccP2 were statistically associated with the pathotype (EPEC or EHEC).

Conclusions

In conclusion, tir and eae gene polymorphisms were found not to be numerous and not to be predominantly synonymous. Moreover, no difference was observed between human and bovine strains regarding the presence of polymorphisms. Finally, some tccP2 variants appeared to be pathotype specific. Further investigations need to be performed on a larger number of strains in order to confirm this specificity.

Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir

Cattle comprise a main reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC). The significant differences in host prevalence, transmissibility, and virulence phenotypes among strains from bovine and human sources are of major interest to the public health community and livestock industry. Genomic analysis revealed divergence into three lineages: lineage I and lineage I/II strains are commonly associated with human disease, while lineage II strains are overrepresented in the asymptomatic bovine host reservoir. Growing evidence suggests that genotypic differences between these lineages, such as polymorphisms in Shiga toxin subtypes and synergistically acting virulence factors, are correlated with phenotypic differences in virulence, host ecology, and epidemiology. To assess the genomic plasticity on a genome-wide scale, we have sequenced the whole genome of strain EC869, a bovine-associated E. coli O157:H7 isolate. Comparative phylogenomic analysis of this key isolate enabled us to place accurately bovine lineage II strains within the genetically homogenous E. coli O157:H7 clade. Identification of polymorphic loci that are anchored both in the chromosomal backbone and horizontally acquired regions allowed us to associate bovine genotypes with altered virulence phenotypes and host prevalence. This study catalogued numerous novel lineage II-specific genome signatures, some of which appear to be associated intimately with the altered pathogenic potential and niche adaptation within the bovine rumen. The presented extended list of polymorphic markers is valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies of this emerging human pathogen.

Multivariate analyses revealed distinctive features differentiating human and cattle isolates of Shiga toxin-producing Escherichia coli O157 in Japan

Genotypes of Shiga toxin-producing Escherichia coli (STEC) O157 isolated from humans and cattle were analyzed by uni- and multivariable logistic regression, and population structure methods, to gain insight into transmission and the nature of human infection. Eleven genotyping assays, including PCR typing of five virulence factors (stx(1), stx(2), stx(2c), eae, and ehxA) and a lineage-specific polymorphism assay using six markers (LSPA6), were considered in the analyses. The prevalence of the stx(1), stx(2), and stx(2c) virulence factors was significantly different between human and cattle isolates. However, multivariable regression revealed that the presence of only the stx(2) gene was significantly associated with human isolates after controlling for confounding effects. LSPA6 typing demonstrated an apparent difference in the distribution of LSPA6 lineages between human and cattle isolates and a strong association between stx genotypes and LSPA6 genotypes. Population genetics tools identified three genetically distinct clusters of STEC O157. Each cluster was characterized by stx genotypes and LSPA6 genotypes. The human isolates typically comprised LSPA6 lineage I with stx(1) stx(2) strains and LSPA6 lineage I/II with stx(2c) or stx(2) stx(2c) strains [corrected]. In contrast, the cattle isolates comprised LSPA6 lineage II strains withstx(2c) or stx(1) stx(2c) strains [corrected] in addition to the clusters identified for the human isolates. Our analyses provide new evidence that the stx(2) gene is the most distinctive feature in human isolates compared to cattle isolates in Japan, and only a subset of the genetically diverse population isolated from cattle is involved in human illnesses. Our results may contribute to international comparisons and risk assessments of STEC O157.

Transcriptomic analysis for genetic mechanisms of the factors related to biofilm formation in Escherichia coli O157:H7

Two lineages of enterohemorrhagic Escherichia coli O157:H7 (EDL933, Stx1(+) and Stx2(+)) and 86-24 (Stx2(+)) were investigated to determine the genetic basis of biofilm formation on abiotic surfaces. Strain EDL933 formed a robust biofilm while strain 86-24 formed almost no biofilm on either polystyrene plates or polyethylene tubes. Whole-transcriptome profiles of EDL933 versus 86-24 revealed that in the strong biofilm-forming strain, genes involved in curli biosynthesis and cellulose production were significantly induced, whereas genes involved in indole signaling were most repressed. Additionally, 49 phage genes were highly induced and repressed between the two strains. Curli assays using Congo red plates and scanning electron microscopy corroborated the microarray data as the EDL933 strain produced a large amount of curli, while strain 86-24 formed much less curli. Moreover, EDL933 produced 19-fold more cellulose than 86-24, and indole production in EDL933 was two times lower than that of the strain 86-24. Therefore, it appears E. coli O157:H7 EDL933 produces more biofilm because of its increased curli and cellulose production and reduced indole production.

Leishmania amazonensis META2 protein confers protection against heat shock and oxidative stress

The META cluster of Leishmania amazonensis contains both META1 and META2 genes, which are upregulated in metacyclic promastigotes and encode proteins containing the META domain. Previous studies defined META2 as a 48.0-kDa protein, which is conserved in other Leishmania species and in Trypanosoma brucei. In this work, we demonstrate that META2 protein expression is regulated during the Leishmania life cycle but constitutive in T. brucei. META2 protein is present in the cytoplasm and flagellum of L. amazonensis promastigotes. Leishmania META2-null replacement mutants are more sensitive to oxidative stress and, upon heat shock, assume rounded morphology with shortened flagella. The increased susceptibility of null parasites to heat shock is reversed by extra-chromosomal expression of the META2 gene. Defective Leishmania promastigotes exhibit decreased ability to survive in macrophages. By contrast, META2 expression is decreased by 80% in RNAi-induced T. brucei bloodstream forms with no measurable effect on survival or resistance to heat shock.

Intestinal mucosa adherence and cytotoxicity of a sorbitol-fermenting, Shiga-toxin-negative Escherichia coli O157:NM isolate with an atypical type III secretion system

Reports show that sorbitol-fermenting (SF) Escherichia coli O157 isolates are implicated in animal and human diseases and may represent new emerging pathogens. We investigated the cytotoxicity and interaction with intestinal tissues of an SF, Shiga-toxin-negative E. coli O157:NM isolate. This bovine isolate was negative for stx genes and was not cytotoxic for Vero cells. We found that this E. coli O157 isolate possesses an intimin of type beta, whereas the translocated intimin receptor Tir and type III secretion system components EspA, EspB, and EspD were of type alpha. In contrast, Shiga-toxin-positive O157:H7 isolates usually possess variants of type gamma. The isolate did not present typical O157:H7 attaching and effacing lesions in the newborn pig ileal in vitro organ culture model. However, extensive effacement and elongation of the microvilli were observed. In vitro organ culture results suggest that such an SF, Shiga-toxin-negative O157:NM isolate found in cattle may potentially cause disease, such as diarrhea without hemolytic uremic syndrome, in humans.

Lineage and host source are both correlated with levels of Shiga toxin 2 production by Escherichia coli O157:H7 strains

Escherichia coli O157:H7 strains fall into three major genetic lineages that differ in their distribution among humans and cattle. Several recent studies have reported differences in the expression of virulence factors between E. coli O157:H7 strains from these two host species. In this study, we wished to determine if important virulence-associated "mobile genetic elements" such as Shiga toxin 2 (Stx2)-encoding prophage are lineage restricted or are host source related and acquired independently of the pathogen genotype. DNA sequencing of the stx(2) flanking region from a lineage II (LII) strain, EC970520, revealed that the transcriptional activator gene Q in LI strain EDL933 (upstream of stx(2)) is replaced by a pphA (serine/threonine phosphatase) homologue and an altered Q gene in this and all other LII strains tested. In addition, nearly all LI strains carried stx(2), whereas all LII strains carried variant stx(2c) and 4 of 14 LI/II strains had copies of both stx(2) and variant stx(2c). Real-time PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) demonstrated that LI and LI/II strains produce significantly more stx(2) mRNA and Stx2 than LII strains. However, among LI strains significantly more Stx2 is also produced by strains from humans than from cattle. Therefore, lineage-associated differences among E. coli O157:H7 strains such as prophage content, toxin type, and toxin expression may contribute to host isolation bias. However, the level of Stx2 production alone may also play an important role in the within-lineage association of E. coli O157:H7 strains with human clinical disease.

Role of RpoS in virulence of pathogens

Understanding mechanisms of bacterial pathogenesis is critical for infectious disease control and treatment. Infection is a sophisticated process that requires the participation of global regulators to coordinate expression of not only genes coding for virulence factors but also those involved in other physiological processes, such as stress response and metabolic flux, to adapt to host environments. RpoS is a key response regulator to stress conditions in Escherichia coli and many other proteobacteria. In contrast to its conserved well-understood role in stress response, effects of RpoS on pathogenesis are highly variable and dependent on species. RpoS contributes to virulence through either enhancing survival against host defense systems or directly regulating expression of virulence factors in some pathogens, while RpoS is dispensable, or even inhibitory, to virulence in others. In this review, we focus on the distinct and niche-dependent role of RpoS in virulence by surveying recent findings in many pathogens.

Controlled vocabularies for microbial virulence factors

Knowledge about pathogenesis is increasing dramatically, and most of this information is stored in the scientific literature or in sequence databases. This information can be made more accessible by the use of ontologies or controlled vocabularies. Recently, several ontologies, controlled vocabularies and databases have been developed or adapted for virulence factors and their roles in pathogenesis. Here, we discuss these systems, how they are being used in research and the challenges that remain for developing and applying ontologies for virulence factors.

In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

Background

Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains.

Results

In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains.

Conclusion

The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

Escherichia coli O157:H7 strain origin, lineage, and Shiga toxin 2 expression affect colonization of cattle

Enterohemorrhagic Escherichia coli O157:H7 has evolved into an important human pathogen with cattle as the main reservoir. The recent discovery of E. coli O157:H7-induced pathologies in challenged cattle has suggested that previously discounted bacterial virulence factors may contribute to the colonization of cattle. The objective of the present study was to examine the impact of lineage type, cytotoxin activity, and cytotoxin expression on the amount of E. coli O157:H7 colonization of cattle tissue and cells in vitro. Using selected bovine- and human-origin strains, we determined that lineage type predicted the amount of E. coli O157:H7 strain colonization: lineage I > intermediate lineages > lineage II. All E. coli O157:H7 strain colonization was dose dependent, with threshold colonization at 10(3) to 10(5) CFU and maximum colonization at 10(7) CFU. We also determined that an as-yet-unknown factor of strain origin was the most dominant predictor of the amount of strain colonization in vitro. The amount of E. coli O157:H7 colonization was also influenced by strain cytotoxin activity and the inclusion of cytotoxins from lineage I or intermediate lineage strains increased colonization of a lineage II strain. There was a higher level of expression of the Shiga toxin 1 gene (stx(1)) in human-origin strains than in bovine-origin strains. In addition, lineage I strains expressed higher levels of the Shiga toxin 2 gene (stx(2)). The present study supports a role for strain origin, lineage type, cytotoxin activity, and stx(2) expression in modulating the amount of E. coli O157:H7 colonization of cattle.

Genomic regions conserved in lineage II Escherichia coli O157:H7 strains

Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determined, much less is known about the genomes of lineage II strains. In this study, suppression subtractive hybridization (SSH) was used to identify genomic features that define lineage II populations. Three SSH experiments were performed, yielding 1,085 genomic fragments consisting of 811 contigs. Bacteriophage sequences were identified in 11.3% of the contigs, 9% showed insertions and 2.3% deletions with respect to E. coli O157:H7 Sakai, and 23.2% did not have significant identity to annotated sequences in GenBank. In order to test for the presence of these novel loci in lineage I and II strains, 27 PCR primer sets were designed based on sequences from these contigs. All but two of these PCR targets were found in the majority (51.9% to 100%) of 27 lineage II strains but in no more than one (<6%) of the 17 lineage I strains. Several of these lineage II-related fragments contain insertions/deletions that may play an important role in virulence. These lineage II-related loci were also shown to be useful markers for genotyping of E. coli O157:H7 strains isolated from human and animal sources.

Enterohemorrhagic Escherichia coli O157:H7 gene expression profiling in response to growth in the presence of host epithelia

Background

The pathogenesis of enterohemorrhagic Escherichia coli (EHEC) O157∶H7 infection is attributed to virulence factors encoded on multiple pathogenicity islands. Previous studies have shown that EHEC O157∶H7 modulates host cell signal transduction cascades, independent of toxins and rearrangement of the cytoskeleton. However, the virulence factors and mechanisms responsible for EHEC-mediated subversion of signal transduction remain to be determined. Therefore, the purpose of this study was to first identify differentially regulated genes in response to EHEC O157∶H7 grown in the presence of epithelial cells, compared to growth in the absence of epithelial cells (that is, growth in minimal essential tissue culture medium alone, minimal essential tissue culture medium in the presence of 5% CO₂, and Penassay broth alone) and, second, to identify EHEC virulence factors responsible for pathogen modulation of host cell signal transduction.

Methodology/Principal Findings

Overnight cultures of EHEC O157∶H7 were incubated for 6 hr at 37°C in the presence or absence of confluent epithelial (HEp-2) cells. Total RNA was then extracted and used for microarray analyses (Affymetrix E. coli Genome 2.0 gene chips). Relative to bacteria grown in each of the other conditions, EHEC O157∶H7 cultured in the presence of cultured epithelial cells displayed a distinct gene-expression profile. A 2.0-fold increase in the expression of 71 genes and a 2.0-fold decrease in expression of 60 other genes were identified in EHEC O157∶H7 grown in the presence of epithelial cells, compared to bacteria grown in media alone.

Conclusion/Significance

Microarray analyses and gene deletion identified a protease on O-island 50, gene Z1787, as a potential virulence factor responsible for mediating EHEC inhibition of the interferon (IFN)-γ-Jak1,2-STAT-1 signal transduction cascade. Up-regulated genes provide novel targets for use in developing strategies to interrupt the infectious process.

Escherichia coli O157:H7 lineages in healthy beef and dairy cattle and clinical human cases in Alberta, Canada

The aim of this study was to examine the prevalence and distribution of Escherichia coli O157:H7 lineage-specific polymorphism assay (LSPA) 6 genotypes from cattle (n = 313) and clinical human (n = 203) isolates from northern and southern Alberta, Canada, to understand possible associations of genotypes with host and geographic location. The majority of cattle isolates (feedlot and dairy) typed as LSPA-6 111111 (72.2%), with proportionately higher LSPA-6 222222 (19.4%) than other LSPA-6 genotypes (10.7%). Clinical human isolates also typed primarily as LSPA-6 111111 (90.1%), but a higher percentage of genotypes (6.8%) other than LSPA-6 222222 (3.1%) was observed. A significantly higher frequency of LSPA-6 111111 in southern Alberta cattle (P < 0.0001) and a significant difference in LSPA-6 genotypes between human versus feedlot cattle from northern Alberta (P < 0.0001) were detected. LSPA-6 211111 genotype was third and second most common in cattle and humans, respectively, and several new LSPA-6 genotypes (n = 19) were also discovered. Despite avoiding over-representation of isolates from specific farms or outbreaks, higher strain diversity among cattle by pulsed-field gel electrophoresis (PFGE; 50 genotypes) in contrast to human (9 PFGE genotypes) isolates was observed. The majority of cattle (74.4%) and human (90.6%) isolates were susceptible to the antimicrobials tested. Within resistant cattle isolates, sulfisoxazole-tetracycline resistance was common (62.5%) and was accounted for by the presence of sul1 and sul2, and tet(A) and tet(B) determinants. An association between LSPA-6 and PFGE genotypes but not between geographic location and PFGE genotype for both hosts was evident.

Detection of virulence-associated genes in Escherichia coli O157 and non-O157 isolates from beef cattle, humans, and chickens

Food-producing animals can be reservoirs of pathogenic Escherichia coli strains that can induce diseases in animals or humans. Contamination of food by E. coli O157:H7 raises immediate concerns about public health, although it is not clear whether all E. coli O157 isolates of animal origin are equally harmful to humans. Inversely, the pathogenic potential of atypical E. coli O157 isolates and several non-O157 serotypes often is ignored. We used a DNA microarray capable of detecting a subset of 346 genes to compare the virulence-associated genes present in eight E. coli O157 isolates from human cases, 14 antibiotic-resistant and/or hypermutable E. coli O157 isolates from beef cattle, and four antibiotic-resistant, sorbitol-negative, non-O157 E. coli isolates from healthy broiler chickens. Hybridization on arrays (HOA) revealed that O157 isolates from beef cattle and humans were genetically distinct, although they possessed most of the same subset of virulence genes. HOA allowed discrimination between hypermutable and antibiotic-resistant O157 isolates from beef cattle based on hybridization results for the stx2 and ycgG genes (hypermutable) or ymfL, stx1, stx2, and hlyE(avian) genes (resistant). However, the absence of hybridization to gene yfdR characterized human isolates. HOA also revealed that an atypical sorbitol-fermenting bovine O157 isolate lacked some genes of the type 3 secretion system, plasmid pO157, and the stx1 and stx2 genes. This isolate had a particular pathotype (eaeA(beta) tir(alpha) espA(alpha) espB(alpha) espD(alpha)) not found in typical E. coli O157:H7. HOA revealed that some non-O157 E. coli isolates from healthy chickens carried genes responsible for salmochelin- and yersiniabactin-mediated iron uptake generally associated with pathogenic strains.

Comparison of Shiga-like toxin II expression between two genetically diverse lineages of Escherichia coli O157:H7

The existence of two separate lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that one of these lineages (lineage I) might be more pathogenic toward human hosts. We postulated that the lineage more pathogenic expresses higher levels of Shiga toxin 2 (Stx2) than do the nonpathogenic lineage II. A comprehensive set of methodologies were used to investigate the difference in Stx2 protein and mRNA expression between the two lineages. An initial Stx2-specific enzyme-linked immunosorbent assay was conducted, and lineage I overall demonstrated significantly more toxin proteins expressed (P < 0.01). Gene expression analyses all showed significantly higher stx2 gene expression in lineage I (P = 0.02). PCR mapping revealed a possible explanation for decreased amounts of stx2 transcripts in the potentially nonpathogenic lineage II isolates, suggesting that genomic changes have modified the toxin-encoding region of the phage. This study provides additional data to support the existence of two diverse lineages of E. coli O157:H7, one of which may have lower pathogenic potential in relation to human hosts. The PCR described also provides a possible screening tool for E. coli O157 populations to differentiate these lineages. This study provides useful information on the ecology of E. coli O157, with broad implications within the clinical, scientific, and livestock industries.

In situ gene expression in cheese matrices: application to a set of enterococcal genes

Transcriptional approaches are increasingly used to compare the behaviour of pathogenic and non-pathogenic bacteria in different culture conditions. The purpose of this study was to apply these methods in cheese to better characterize food and clinical Enterococcus faecalis isolates during cheese processing. Because of the complex biochemical composition of the cheese matrix, e.g. the presence of casein and fat, we developed an efficient method to recover total RNA from bacteria in a semi-hard cheese model. To validate the RNA extraction method, we analysed expression of 7 genes from two E. faecalis strains (one clinical and one food isolate) in both cheese and culture medium by semi-quantitative RT-PCR. We then used PCR-based DNA macro-arrays to compare expression of 154 genes from two E. faecalis strains in both cheese and culture medium. The food strain isolated from cheese is transcriptionally active in cheese, as reflected by the higher transcript levels of various genes. Conversely, overall transcript levels of the V583 clinical isolate were lower in cheese, suggesting that the food strain may be more adapted to a dairy environment than the clinical strain. The method described here constitutes a very promising tool for future transcriptomic studies in cheese matrices. Global profiling in foods may prove to be a valid criterion for differentiating food from clinical isolates.

SMAP29 congeners demonstrate activity against oral bacteria and reduced toxicity against oral keratinocytes

INTRODUCTION

Cathelicidins are antimicrobial peptides found in epithelial and mucosal tissues as well as the secondary granules of neutrophils. SMAP29, a sheep cathelicidin, has differential antimicrobial properties against various pathogens, including periodontal organisms. The purpose of this study was to evaluate the antimicrobial properties and cytotoxicity of SMAP29, SMAP28, and three congeners (SMAP18A, SMAP18D, and SMAP14A).

METHODS

The peptides at concentrations ranging from 0.25 to 250 microg/ml were tested for their activity against multiple strains of Streptococcus mutans, Streptococcus sanguis, Actinomyces israelii, Actinomyces naeslundii, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Peptostreptococcus micros, and Porphyromonas gingivalis using a radial diffusion assay. Cytotoxicity of keratinocytes was evaluated by measuring lactate dehydrogenase release after incubation with the individual peptides.

RESULTS

SMAP28, thought to be the biologically active peptide, was the most potent antimicrobial (range of minimum inhibitory concentrations 0.06-7.03 microg/ml, P < 0.05); however, the activity of SMAP28 and SMAP29 was strongly associated (r = 0.933). The congeners also demonstrated antimicrobial activity against the bacteria tested (range of minimum inhibitory concnetrations 0.21-79 microg/ml). Overall, F. nucleatum was the most susceptible organism, while P. gingivalis was the least susceptible. Keratinocyte cytotoxicity was dependent on peptide length and dose. SMAP28 was the most cytotoxic, while SMAP14A was the least cytotoxic.

CONCLUSION

The antimicrobial activities against oral microorganisms and the minimal toxicity seen in this study suggest that the congeners of SMAP29 may serve as an alternative to traditional antibiotics in the prevention and treatment of periodontal and other oral diseases.

Anaerobic conditions promote expression of Sfp fimbriae and adherence of sorbitol-fermenting enterohemorrhagic Escherichia coli O157:NM to human intestinal epithelial cells

The sfp gene cluster, unique to sorbitol-fermenting (SF) enterohemorrhagic Escherichia coli (EHEC) O157:NM strains, encodes fimbriae that mediate mannose-resistant hemagglutination in laboratory E. coli strains but are not expressed in wild-type SF EHEC O157:NM strains under standard laboratory conditions. We investigated whether Sfp fimbriae are expressed under conditions that mimic the intestinal environment and whether they contribute to the adherence of SF EHEC O157:NM strains to human intestinal epithelial cells. The transcription of sfpA (encoding the major fimbrial subunit) was upregulated in all strains investigated, and all expressed SfpA and possessed fimbriae that reacted with an anti-SfpA antibody when the strains were grown on solid media under anaerobic conditions. Sfp expression was absent under aerobic conditions and in liquid media. Sfp upregulation under anaerobic conditions was significantly higher on blood agar and a medium simulating the colonic environment than on a medium simulating the ileal environment (P < 0.05). The induction of Sfp fimbriae in SF E. coli O157:NM strains correlates with increased adherence to Caco-2 and HCT-8 cells. Our data indicate that the expression of Sfp fimbriae in SF E. coli O157:NM strains is induced under conditions resembling those of the natural site of infection and that Sfp fimbriae may contribute to the adherence of the organisms to human intestinal epithelium.

FourU: a novel type of RNA thermometer in Salmonella

The translation of many heat shock and virulence genes is controlled by RNA thermometers. Usually, they are located in the 5'-untranslated region (5'-UTR) and block the Shine-Dalgarno (SD) sequence by base pairing. Destabilization of the structure at elevated temperature permits ribosome binding and translation initiation. We have identified a new type of RNA thermometer in the 5'-UTR of the Salmonella agsA gene, which codes for a small heat shock protein. Transcription of the agsA gene is controlled by the alternative sigma factor sigma(32). Additional translational control depends on a stretch of four uridines that pair with the SD sequence. Mutations in this region affect translation in vivo. Structure probing experiments demonstrate a temperature-controlled opening of the SD region in vitro. Toeprinting (primer extension inhibition) shows that ribosome binding is dependent on high temperatures. Together with a postulated RNA thermometer upstream of the Yersinia pestis virulence gene lcrF (virF), the 5'-UTR of Salmonella agsA might be the founding member of a new class of RNA thermometers that we propose to name 'fourU' thermometers.

Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall, and stress response

Listeria monocytogenes is a food-borne, opportunistic, bacterial pathogen causing a wide spectrum of diseases, including meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13 L. monocytogenes serovars described, human listeriosis is mostly associated with strains of serovars 4b, 1/2b, and 1/2a. Within the species L. monocytogenes, three phylogenetic lineages are described. Serovar 1/2a belongs to phylogenetic lineage I, while serovars 4b and 1/2b group in phylogenetic lineage II. To explore the role of gene expression in the adaptation of L. monocytogenes strains of these two major lineages to different environments, as well as in virulence, we performed whole-genome expression profiling of six L. monocytogenes isolates of serovars 4b, 1/2b, and 1/2a of distinct origins, using a newly constructed Listeria multigenome DNA array. Comparison of the global gene expression profiles revealed differences among strains. The expression profiles of two strains having distinct 50% lethal doses, as assessed in the mouse model, were further analyzed. Gene ontology term enrichment analysis of the differentially expressed genes identified differences in protein-, nucleic acid-, carbon metabolism-, and virulence-related gene expression. Comparison of the expression profiles of the core genomes of all strains revealed differences between the two lineages with respect to cell wall synthesis, the stress-related sigma B regulon and virulence-related genes. These findings suggest different patterns of interaction with host cells and the environment, key factors for host colonization and survival in the environment.

Escherichia coliO157:H7 gene expression in the presence of catecholamine norepinephrine

Various forms of host stresses (e.g. physiological, psychological) are thought to influence susceptibility to pathogenic microorganisms. Catecholamines such as norepinephrine are released into the GI environment during acute stress and may influence the infective process of bacterial pathogens associated with the GI tract. To examine the effects of norepinephrine on expression of virulence factors in Escherichia coli O157:H7, the clinical-type isolate EDL933 (ATCC 43895) was grown in serum-Standard American Petroleum Institute media in the presence or absence of norepinephrine. After 5 h of exposure to norepinephrine, treatment and control cultures (not exposed to norepinephrine) were harvested, their RNA isolated, and gene expression evaluated. There was a dramatic increase in the expression of virulence factor transcripts including stx1, stx2, and eae. Also induced were transcripts involved in iron metabolism. Conversely, there was comparative repression of iron acquisition and phage shock protein-related transcripts in the presence of norepinephrine. Novel observations from these data suggested that exposure to norepinephrine induced glutamate decarboxylase acid resistance as well as an SOS response in E. coli O157:H7. The results corroborate many of the previous findings detailed in the literature and provide new observations that could expand the scope of microbial endocrinology.

Genome evolution in major Escherichia coli O157:H7 lineages

Background

Genetic analysis of Escherichia coli O157:H7 strains has shown divergence into two distinct lineages, lineages I and II, that appear to have distinct ecological characteristics, with lineage I strains more commonly associated with human disease. In this study, microarray-based comparative genomic hybridization (CGH) was used to identify genomic differences among 31 E. coli O157:H7 strains that belong to various phage types (PTs) and different lineage-specific polymorphism assay (LSPA) types.

Results

A total of 4,084 out of 6,057 ORFs were detected in all E. coli O157:H7 strains and 1,751 were variably present or absent. Based on this data, E. coli O157:H7 strains were divided into three distinct clusters, which consisted of 15 lineage I (LSPA type 111111), four lineage I/II (designated in this study) (LSPA type 211111) and 12 lineage II strains (LSPA 222222, 222211, 222212, and 222221), respectively. Eleven different genomic regions that were dominant in lineage I strains (present in ≥80% of lineage I and absent from ≥ 92% of lineage II strains) spanned segments containing as few as two and up to 25 ORFs each. These regions were identified within E. coli Sakai S-loops # 14, 16, 69, 72, 78, 83, 85, 153 and 286, Sakai phage 10 (S-loops # 91, 92 and 93) and a genomic backbone region. All four lineage I/II strains were of PT 2 and possessed eight of these 11 lineage I-dominant loci. Several differences in virulence-associated loci were noted between lineage I and lineage II strains, including divergence within S-loop 69, which encodes Shiga toxin 2, and absence of the non-LEE encoded effector genes nleF and nleH1-2 and the perC homologue gene pchD in lineage II strains.

Conclusion

CGH data suggest the existence of two dominant lineages as well as LSPA type and PT-related subgroups within E. coli O157:H7. The genomic composition of these subgroups supports the phylogeny that has been inferred from other methods and further suggests that genomic divergence from an ancestral form and lateral gene transfer have contributed to their evolution. The genomic features identified in this study may contribute to apparent differences in the epidemiology and ecology of strains of different E. coli O157:H7 lineages.

Current and future uses of real-time polymerase chain reaction and microarrays in the study of intestinal microbiota, and probiotic use and effectiveness

Probiotics are defined as live microorganisms that confer a health benefit to the host when administered in adequate amounts. In addition to human health benefits, probiotics can improve various aspects of growth and performance in livestock and poultry, as well as control undesirable microorganisms in food animals. Studies indicate that probiotics can prevent or treat certain conditions, including atopic disease in infants, food allergy, infection after surgery, acute diarrhea, and symptoms associated with irritable bowel syndrome. Understanding the complete mechanism, effectiveness, and potential use of probiotics is limited by the availability and sensitivity of current methods (i.e., culturing techniques). In recent years, real-time polymerase chain reaction (PCR) and microarrays have become prominent and promising methods to examine quantitative changes of specific members of the microbial community and the influence of probiotics on the structure and function of human and animal intestinal ecosystems. Culture-independent studies have established that only a fraction of organisms present in feces are cultivable, therefore, results obtained by cultivation are limited. Conversely, in-depth knowledge of microbial genomes has enabled real-time PCR and microarrays to be more sensitive and has resulted in precise methods for comprehensive analysis of the complex gut microbiota. Additionally, these technologies can assess the influence of intestinal microorganisms on host metabolism, nutrient status, and disease. This paper reviews method technologies and applications of real-time PCR and microarray assays as they relate to the effect and use of probiotics on the intestinal microbiota and gastrointestinal disease.

Differential Expression of Virulence-Related Genes in A Salmonella enterica Serotype Typhimurium luxS Mutant in Response to Autoinducer AI-2 And Poultry Meat–Derived AI-2 Inhibitor

Bacterial cells communicate with each other and respond to external stimuli using signal molecules called autoinducers (AIs). Poultry meat contains inhibitors that apparently interfere with AI-2 signaling. Our objective was to understand the expression of Salmonella Typhimurium genes (using spotted microarrays) in response to AI-2 in the presence, and absence, of poultry meat (PM) derived AI-2 inhibitors. Expression of 1136 virulence-related genes in Salmonella Typhimurium wildtype and its isogenic luxS mutant strain (unable to produce AI-2) was monitored when the cells were exposed for 3 hours to different treatments containing in vitro synthesized AI-2 and a PM inhibitor (AI-2, AI-2 + PM, or PM alone). The responses of the genes were unique in the presence of in vitro synthesized AI-2. Of 1136 genes on the array, 23 genes were differentially expressed (either upregulated or downregulated) at least 1.5-fold (P < 0.05) in the presence of AI-2. Exposure to the PM inhibitor resulted in 36 genes being differentially expressed, while the combined AI-2 + PM treatment resulted in 22 genes being differentially expressed, of which only 7 genes showed overlap with the PM treatment, suggesting a unique response when AI-2 interacts with the inhibitor molecules. The results suggest that Salmonella gene expression can vary depending on the presence or absence of the poultry meat matrix and/or AI-2 molecules. Understanding the interaction of AI-2 and inhibitors of AI-2 activity found in poultry meat can help explain Salmonella survival and virulence on poultry products.

Shiga toxin-producing Escherichia coli: an overview

The objective of this review is to highlight the importance of cattle in human disease due to Shiga toxin-producing Escherichia coli (STEC) and to discuss features of STEC that are important in human disease. Healthy dairy and beef cattle are a major reservoir of a diverse group of STEC that infects humans through contamination of food and water, as well as through direct contact. Infection of humans by STEC may result in combinations of watery diarrhea, bloody diarrhea, and hemolytic uremic syndrome. Systems of serotyping, subtyping, and virulence typing of STEC are used to aid in epidemiology, diagnosis, and pathogenesis studies. Severe disease and outbreaks of disease are most commonly due to serotype O157:H7, which, like most other highly pathogenic STEC, colonize the large intestine by means of a characteristic attaching and effacing lesion. This lesion is induced by a bacterial type III secretion system that injects effector proteins into the intestinal epithelial cell, resulting in profound changes in the architecture and metabolism of the host cell and intimate adherence of the bacteria. Severe disease in the form of bloody diarrhea and the hemolytic uremic syndrome is attributable to Shiga toxin (Stx), which exists as 2 major types, Stx1 and Stx2. The stx genes are encoded on temperate bacteriophages in the chromosome of the bacteria, and production and release of the toxin are highly dependent on induction of the phages. Regulation of the genes involved in induction of the attaching and effacing lesion, and production of Stx is complex. In addition to these genes that are clearly implicated in virulence, there are several putative virulence factors. A major public health goal is to prevent STEC-induced disease in humans. Studies aimed at understanding factors that affect carriage and shedding of STEC by cattle and factors that contribute to development of disease in humans are considered to be important in achieving this objective.

Expression of putative virulence factors of Escherichia coli O157:H7 differs in bovine and human infections

Escherichia coli O157:H7 is a commensal organism in cattle, but it is a pathogen in humans. This differential expression of virulence suggests that specific virulence factors are regulated differently in human and bovine hosts. To test this hypothesis, relative real-time reverse transcription-PCR was used to relate the expression of several putative virulence genes (eae, espA, stx(2), rfbE, ehxA, and iha) to that of the "housekeeping" gene gnd during natural human and experimental bovine infection with E. coli O157:H7. We examined these genes in fecal samples from eight humans and four calves. iha and espA were significantly more expressed in bovine infections. rfbE and ehxA appeared to be more highly expressed in human infections, though these differences did not achieve statistical significance. Our results support the hypothesis that some virulence-associated genes of O157:H7 are differentially expressed in a host-specific manner.