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

Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken

An Escherichia spp. isolate, ECD-227, was previously identified from the broiler chicken as a phylogenetically divergent and multidrug-resistant Escherichia coli possessing numerous virulence genes. In this study, whole genome sequencing and comparative genome analysis was used to further characterize this isolate. The presence of known and putative antibiotic resistance and virulence open reading frames were determined by comparison to pathogenic (E. coli O157:H7 TW14359, APEC O1:K1:H7, and UPEC UTI89) and nonpathogenic species (E. coli K-12 MG1655 and Escherichia fergusonii ATCC 35469). The assembled genome size of 4.87 Mb was sequenced to 18-fold depth of coverage and predicted to contain 4,376 open reading frames. Phylogenetic analysis of 537 open reading frames present across 110 enteric bacterial species identifies ECD-227 to be E. fergusonii. The genome of ECD-227 contains 5 plasmids showing similarity to known E. coli and Salmonella enterica plasmids. The presence of virulence and antibiotic resistance genes were identified and localized to the chromosome and plasmids. The mutation in gyrA (S83L) involved in fluoroquinolone resistance was identified. The Salmonella-like plasmids harbor antibiotic resistance genes on a class I integron (aadA, qacEΔ-sul1, aac3-VI, and sulI) as well as numerous virulence genes (iucABCD, sitABCD, cib, traT). In addition to the genome analysis, the virulence of ECD-227 was evaluated in a 1-d-old chick model. In the virulence assay, ECD-227 was found to induce 18 to 30% mortality in 1-d-old chicks after 24 h and 48 h of infection, respectively. This study documents an avian multidrug-resistant and virulent E. fergusonii. The existence of several resistance genes to multiple classes of antibiotics indicates that infection caused by ECD-227 would be difficult to treat using antimicrobials currently available for poultry.

Ceftiofur use in finishing swine barns and the recovery of fecal Escherichia coli or Salmonella spp. resistant to ceftriaxone

The objective of this study was to investigate the association between ceftiofur use policy in finishing swine barns and recovery of fecal Escherichia coli or Salmonella spp. resistant to ceftriaxone. The study population included 54 finishing swine barns from three companies located in North Carolina. The barns were each classified according to their reported therapeutic ceftiofur use rates of "Rare," "Moderate," and "Common." Fecal samples from the barns were cultured for the presence of E. coli and Salmonella spp. resistant to ceftriaxone using selective media designed to recover rare organisms expressing the AmpC β-lactamase phenotype. A total of 1899 swine fecal samples yielded 1193 E. coli (63%) resistant to ceftriaxone. Recovery rates by ceftiofur use classification were 45% for Rare, 73% for Moderate, and 68% Common ceftiofur use groups. Barns reporting Rare ceftiofur use had a lower odds of recovery of E. coli (OR=0.32; p<0.001) resistant to ceftriaxone compared to Common use barns. The overall Salmonella spp. prevalence was 63.8% (n=714). Of these, 65 Salmonella were resistant to ceftriaxone with the highest rate (6%) found in the Common ceftiofur use group, followed by Rare (4.1%) and Moderate (0.15%). The odds of recovery of Salmonella resistant to ceftriaxone were similar for barns with ceftiofur use classified as Rare and Common. Samples from barns with ceftiofur use classified as Moderate had a lower odds (OR=0.02; p<0.01) of recovery of Salmonella resistant to ceftriaxone than barns classified as Common. Our result is consistent with the hypothesis that the use of ceftiofur in finishing swine barns, beyond its rare application, may influence the recovery of enteric E. coli with resistance to cephalosporin drugs, although other unmeasured factors appear to be important in the recovery of cephalosporin-resistant Salmonella. The dissemination of enteric bacteria with resistance to cephalosporins has the potential to impact both veterinary and human therapeutic treatment options.

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.

Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes

Escherichia coli O157:H7 strains can be classified into different genotypes based on the presence of specific Shiga toxin-encoding bacteriophage insertion sites. Certain O157:H7 genotypes predominate among human clinical cases (clinical genotypes), while others are more frequently found in bovines (bovine-biased genotypes). To determine whether inherent differences in gene expression explain the variation in infectivity of these genotypes, we compared the expression patterns of clinical genotype 1 strains with those of bovine-biased genotype 5 strains using microarrays. Important O157:H7 virulence factors, including locus of enterocyte effacement genes, the enterohemolysin, and several pO157 genes, showed increased expression in the clinical versus bovine-biased genotypes. In contrast, genes essential for acid resistance (e.g., gadA, gadB, and gadC) and stress fitness were upregulated in bovine-biased genotype 5 strains. Increased expression of acid resistance genes was confirmed functionally using a model stomach assay, in which strains of bovine-biased genotype 5 had a 2-fold-higher survival rate than strains of clinical genotype 1. Overall, these results suggest that the increased prevalence of O157:H7 illness caused by clinical genotype 1 strains is due in part to the overexpression of key virulence genes. The bovine-biased genotype 5 strains, however, are more resistant to adverse environmental conditions, a characteristic that likely facilitates O157:H7 colonization of bovines.

Genotype comparison of sorbitol-negative Escherichia coli isolates from healthy broiler chickens from different commercial farms

Hybridization on arrays was used to assess the presence of virulence-associated genes and to determine the relatedness of 32 non-O157 sorbitol-negative Escherichia coli isolates from healthy broiler chickens. These isolates were from commercial farms that used feed supplemented with different antimicrobial agents (virginiamycin, bacitracin, salinomycin, narasin, nicarbazin, or diclazuril). For each isolate, fluorescent probes were made from genomic DNA and were hybridized on DNA arrays composed of genes associated with general functions, virulence, iron uptake systems, and DNA repair genes (e.g., mut genes). Hybridization on arrays results showed that isolates from the same farm tended to be clustered but actually represented 18 genetically distinct groups of isolates. Results revealed that some isolates showed similarity to human uropathogenic E. coli or avian pathogenic E. coli. Four avian pathogenic E. coli-like isolates were detected. Another isolate possessed the intimin gene (eaeA) and typical genes of the type 3 secretion system associated with enteropathogenic E. coli and enterohemorrhagic E. coli strains. Genes from a second system (secondary type 3 secretion system) homologous to that found in Salmonella Typhimurium were detected in many isolates. Several of the studied isolates also possessed the aerobactin, salmochelin, and yersiniabactin genes involved in iron acquisition in pathogenic bacteria. Our results clearly suggest that commensal E. coli isolates from chickens are reservoirs of virulence-associated genes and may represent colibacillosis and zoonotic risks.

Multiplexed optical pathogen detection with lab-on-a-chip devices

Infectious diseases are still a main cause of human morbidity and mortality. Advanced diagnostics is considered to be a key driver to improve the respective therapeutic outcome. The main factors influencing the impact of diagnostics include: assay speed, availability, information content, in-vitro diagnostics and cost, for which molecular assays are providing the most promising opportunities. Miniaturisation and integration of assay steps into lab-on-a-chip devices has been described as an appropriate way to speed up assay time and make assays available onsite at competitive costs. As meaningful assays for infectious diseases need to include a whole range of clinical relevant information about the pathogen, multiplexed functionality is often required for which optical transduction is particularly well suited. The aim of this review is to assess existing developments in this field and to give an outlook on future requirements and solutions.