Extraintestinal Pathogenic E. Coli Strains Research Articles

The virulence regulator AbsR in avian pathogenic Escherichia coli has pleiotropic effects on bacterial physiology

Avian pathogenic Escherichia coli (APEC) belonging to extraintestinal pathogenic E. coli (ExPEC) can cause severe infections in extraintestinal tissues in birds and humans, such as the lungs and blood. MprA (microcin production regulation, locus A, herein renamed AbsR, a blood survival regulator), a member of the MarR (multiple antibiotic resistance regulator) transcriptional regulator family, governs the expression of capsule biosynthetic genes in human ExPEC and represents a promising druggable target for antimicrobials. However, a deep understanding of the AbsR regulatory mechanism as well as its regulon is lacking. In this study, we present a systems-level analysis of the APEC AbsR regulon using ChIP-Seq (chromatin immunoprecipitation sequencing) and RNA-Seq (RNA sequencing) methods. We found that AbsR directly regulates 99 genes and indirectly regulates 667 genes. Furthermore, we showed that: 1) AbsR contributes to antiphagocytotic effects by macrophages and virulence in a mouse model for systemic infection by directly activating the capsular gene cluster; 2) AbsR positively impacts biofilm formation via direct regulation of the T2SS (type II secretion system) but plays a marginal role in virulence; and 3) AbsR directly upregulates the acid tolerance signaling system EvgAS to withstand acid stress but is dispensable in ExPEC virulence. Finally, our data indicate that the role of AbsR in virulence gene regulation is relatively conserved in ExPEC strains. Altogether, this study provides a comprehensive analysis of the AbsR regulon and regulatory mechanism, and our data suggest that AbsR likely influences virulence primarily through the control of capsule production. Interestingly, we found that AbsR severely represses the expression of the type I-F CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) systems, which could have implications in CRISPR biology and application.

Characteristics, pathogenic mechanism, zoonotic potential, drug resistance, and prevention of avian pathogenic Escherichia coli (APEC).

Although most Escherichia coli (E. coli) strains are commensal and abundant, certain pathogenic strains cause severe diseases from gastroenteritis to extraintestinal infections. Extraintestinal pathogenic E. coli (ExPEC) contains newborn meningitis E. coli (NMEC), uropathogenic E. coli (UPEC), avian pathogenic E. coli (APEC), and septicemic E. coli (SEPEC) based on their original host and clinical symptom. APEC is a heterogeneous group derived from human ExPEC. APEC causes severe respiratory and systemic diseases in a variety of avians, threatening the poultry industries, food security, and avian welfare worldwide. APEC has many serotypes, and it is a widespread pathogenic bacterium in poultry. In addition, ExPEC strains share significant genetic similarities and similar pathogenic mechanisms, indicating that APEC potentially serves as a reservoir of virulence and resistance genes for human ExPEC, and the virulence and resistance genes can be transferred to humans through food animals. Due to economic losses, drug resistance, and zoonotic potential, APEC has attracted heightened awareness. Various virulence factors and resistance genes involved in APEC pathogenesis and drug resistance have been identified. Here, we review the characteristics, epidemiology, pathogenic mechanism zoonotic potential, and drug resistance of APEC, and summarize the current status of diagnosis, alternative control measures, and vaccine development, which may help to have a better understanding of the pathogenesis and resistance of APEC, thereby reducing economic losses and preventing the spread of multidrug-resistant APEC to humans.

Differential survival of potentially pathogenic, septicemia- and meningitis-causing E. coli across the wastewater treatment train

A growing body of evidence indicates that extraintestinal pathogenic E. coli (ExPEC) readily survive wastewater treatment, raising concerns about the public health risks associated with exposure to wastewater-contaminated environments. In this study, E. coli isolates recovered from chlorinated sewage or treated wastewater effluents in Canada were screened for ExPEC virulence markers. Eighty-six isolates were identified as presumptive ExPEC, clustering within major pandemic lineages including ST131, ST95, and ST73 according to multilocus sequence typing analyses. Across the whole, core, and accessory genome, 37 isolates were extremely similar to clinical bloodborne E. coli (BBEC) and neonatal meningitic E. coli (NMEC) strains, suggesting that these wastewater isolates may exhibit a similar phenotypically related pathogenic potential. Interestingly, ExPEC strains also shared accessory gene content with naturalized wastewater strains, suggesting a common genetic capacity for surviving water treatment. Collectively, these findings suggest that E. coli strains that may cause septicemia and meningitis are surviving wastewater treatment and may be transmissible through wastewater effluents.

ESBL Producing Escherichia coli in Faecal Sludge Treatment Plants: An Invisible Threat to Public Health in Rohingya Camps, Cox's Bazar, Bangladesh.

Introduction: Human faecal sludge contains diverse harmful microorganisms, making it hazardous to the environment and public health if it is discharged untreated. Faecal sludge is one of the major sources of E. coli that can produce extended-spectrum β-lactamases (ESBLs).Objective: This study aimed to investigate the prevalence and molecular characterization of ESBL-producing E. coli in faecal sludge samples collected from faecal sludge treatment plants (FSTPs) in Rohingya camps, Bangladesh.Methods: ESBL producing E. coli were screened by cultural as well as molecular methods and further characterized for their major ESBL genes, plasmid profiles, pathotypes, antibiotic resistance patterns, conjugation ability, and genetic similarity.Results: Of 296 isolates, 180 were phenotypically positive for ESBL. All the isolates, except one, contained at least one ESBL gene that was tested (blaCTX−M−1, blaCTX−M−2, blaCTX−M−8, blaCTX−M−9, blaCTX−M−15, blaCTX−M−25, blaTEM, and blaSHV). From plasmid profiling, it was observed that plasmids of 1–211 MDa were found in 84% (151/180) of the isolates. Besides, 13% (24/180) of the isolates possessed diarrhoeagenic virulence genes. From the remaining isolates, around 51% (79/156) harbored at least one virulence gene that is associated with the extraintestinal pathogenicity of E. coli. Moreover, 4% (3/156) of the isolates were detected to be potential extraintestinal pathogenic E. coli (ExPEC) strains. Additionally, all the diarrhoeagenic and ExPEC strains showed resistance to three or more antibiotic groups which indicate their multidrug-resistant potential. ERIC-PCR differentiated these pathogenic isolates into seven clusters. In addition to this, 16 out of 35 tested isolates transferred plasmids of 32–112 MDa to E. coli J53 recipient strain.Conclusion: The present study implies that the faecal sludge samples examined here could be a potential origin for spreading MDR pathogenic ESBL-producing E. coli. The exposure of Rohingya individuals, living in overcrowded camps, to these organisms poses a severe threat to their health.

Virulence genes of Escherichia coli vaginal isolates associated with postpartum dysgalactia syndrome in sows

Objective: Identify the occurrence of certain virulence genes of Escherichia coli vaginal isolates associated with postpartum dysgalactia syndrome (PDS) in sows. Materials and methods: Two hundred and two sows from 5 Macedonian pig farms were clinically examined for PDS 12 to 24 hours after farrowing. Vaginal swabs for bacteriological testing were taken from PDS-affected (PDSA, n = 47) and PDS-unaffected (PDSU, n = 155) sows. In total, 74 isolates of E coli were tested by multiplex polymerase chain reaction for the presence of virulence genes related to specific pathogenic strains. Results: Genes associated with extra-intestinal pathogenic E coli (ExPEC) strains were the most prevalent among all tested E coli isolates. The most dominant gene among all E coli isolates was fimC. The iss gene was more prevalent in PDSA sows compared to PDSU sows (P = .02). Multivariable logistic regression showed that lower parity sows (P ≤ .001) and presence of the iss (P = .003) and astA genes (P = .03) were correlated with the occurrence of PDS. Implications: Lower parity sows vaginally infected with E coli associated with particular ExPEC strains are at higher risk of developing PDS. Positive vaginal swabs for E coli and iss gene found early after farrowing were associated with PDS in sows. Classification of E coli into specific ExPEC pathotype was not possible by virulence genotyping only.

Study of a classification algorithm for AIEC identification in geographically distinct E. coli strains

Adherent-invasive Escherichia coli (AIEC) have been extensively implicated in Crohn’s disease pathogenesis. Currently, AIEC is identified phenotypically, since no molecular marker specific for AIEC exists. An algorithm based on single nucleotide polymorphisms was previously presented as a potential molecular tool to classify AIEC/non-AIEC, with 84% accuracy on a collection of 50 strains isolated in Girona (Spain). Herein, our aim was to determine the accuracy of the tool using AIEC/non-AIEC isolates from different geographical origins and extraintestinal pathogenic E. coli (ExPEC) strains. The accuracy of the tool was significantly reduced (61%) when external AIEC/non-AIEC strains from France, Chile, Mallorca (Spain) and Australia (82 AIEC, 57 non-AIEC and 45 ExPEC strains in total) were included. However, the inclusion of only the ExPEC strains showed that the tool was fairly accurate at differentiating these two close pathotypes (84.6% sensitivity; 79% accuracy). Moreover, the accuracy was still high (81%) for those AIEC/non-AIEC strains isolated from Girona and Mallorca (N = 63); two collections obtained from independent studies but geographically close. Our findings indicate that the presented tool is not universal since it would be only applicable for strains from similar geographic origin and demonstrates the need to include strains from different origins to validate such tools.

Characterization of Pathogenic Escherichia coli in River Water by Simultaneous Detection and Sequencing of 14 Virulence Genes

The occurrence of pathogenic Escherichia coli in environmental waters increases the risk of waterborne disease. In this study, 14 virulence genes in 669 E. coli isolates (549 isolates from the Yamato River in Japan, and 30 isolates from each of the following hosts: humans, cows, pigs, and chickens) were simultaneously quantified by multiplex PCR and dual index sequencing to determine the prevalence of potentially pathogenic E. coli. Among the 549 environmental isolates, 64 (12%) were classified as extraintestinal pathogenic E. coli (ExPEC) while eight (1.5%) were classified as intestinal pathogenic E. coli (InPEC). Only ExPEC-associated genes were detected in human isolates and pig isolates, and 11 (37%) and five (17%) isolates were classified as ExPEC, respectively. A high proportion (63%) of cow isolates possessed Shiga-toxin genes (stx1 or stx2) and they were classified as Shiga toxin-producing E. coli (STEC) or enterohemorrhagic E. coli (EHEC). Among the chicken isolates, 14 (47%) possessed iutA, which is an ExPEC-associated gene. This method can determine the sequences as well as the presence/absence of virulence genes. By comparing the sequences of virulence genes, we determined that sequences of iutA were different among sources and may be useful for discriminating isolates, although further studies including larger numbers of isolates are needed. Results indicate that humans are a likely source of ExPEC strains in the river.

Urinary tract infections attributed to diverse ExPEC strains in food animals: evidence and data gaps.

Between 70 and 95% of urinary tract infections (UTI) are caused by strains of Escherichia coli. These strains, often termed Extraintestinal Pathogenic E. coli (ExPEC), possess specific virulence traits allowing them to colonize more inhospitable environments, such as the urogenital tract. Some ExPEC isolates from humans have similar virulence factor profiles to ExPEC isolates from animals, and because of the potential for these strains to cause UTI in people, these infections have been referred to as foodborne UTI, or FUTI. Finding similarities in ExPEC in animals and humans is not necessarily proof of transmission, particularly a unidirectional pathway from animals to humans; similarities in virulence factor profiles should be expected given the specific bacterial requirements for colonizing physiological compartments with similar characteristics in all animals. Many of the most important strains of human ExPEC globally, such as ST131, are highly virulent and clonal implying routes of transmission other than food. Documenting routes of transmission is particularly difficult due to the wide range of potential ExPEC sources, including the human intestinal tract, and non-human reservoirs such as food animals and retail meat products, sewage and other environmental sources, and companion animals. The significant environmental reservoir of ExPEC, including strains such as ST131, could potentially explain much more completely the global dissemination of virulent ExPEC clones and the rapid dissemination of new strains within the community. Taken in its totality, the link between ExPEC in animals and UTI in humans might exist, but studies conducted to date do not enable an estimation of the relative importance of this route of transmission. To reduce the burden of illness associated with ExPEC, the scientific community needs to push forward with ecologically-based, scientifically-sound study designs that can address the plethora of ways in which E. coli can spread.

Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation.

BackgroundThe mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic E. coli (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the mutS gene and the o454-nlpD genomic region among 510 E. coli strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of E. coli, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the o454-nlpD region.MethodsSize variation in the o454-nlpD region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between mutS gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between o454-nlpD patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of o454-nlpD patterns was investigated by means of Random Forest algorithm.ResultsFour main structures (patterns I-IV) of the o454-nlpD region among ExPEC and commensal E. coli strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (csgA, malX, chuA, sit, and vat) to be suitable to predict pattern III strains.ConclusionThe significant association between pattern III and group B2 strains suggested the o454-nlpD region to be of great value in identifying highly virulent strains among the mixed population of E. coli promising to be the basis of a future typing tool for ExPEC and their gut reservoir. Furthermore, top-ranked VAGs for classification and prediction of pattern III were identified. These data are most valuable for defining ExPEC pathotype in future in vivo assays.

Heteropathogenic virulence and phylogeny reveal phased pathogenic metamorphosis in Escherichia coli O2:H6

Extraintestinal pathogenic and intestinal pathogenic (diarrheagenic) Escherichia coli differ phylogenetically and by virulence profiles. Classic theory teaches simple linear descent in this species, where non-pathogens acquire virulence traits and emerge as pathogens. However, diarrheagenic Shiga toxin-producing E. coli (STEC) O2:H6 not only possess and express virulence factors associated with diarrheagenic and uropathogenic E. coli but also cause diarrhea and urinary tract infections. These organisms are phylogenetically positioned between members of an intestinal pathogenic group (STEC) and extraintestinal pathogenic E. coli. STEC O2:H6 is, therefore, a ‘heteropathogen,’ and the first such hybrid virulent E. coli identified. The phylogeny of these E. coli and the repertoire of virulence traits they possess compel consideration of an alternate view of pathogen emergence, whereby one pathogroup of E. coli undergoes phased metamorphosis into another. By understanding the evolutionary mechanisms of bacterial pathogens, rational strategies for counteracting their detrimental effects on humans can be developed.Subject Categories Microbiology, Virology & Host Pathogen Interaction

Food-Borne Origins of Escherichia coli Causing Extraintestinal Infections

Most human extraintestinal Escherichia coli infections, including those involving antimicrobial resistant strains, are caused by the members of a limited number of distinctive E. coli lineages, termed extraintestinal pathogenic E. coli (ExPEC), that have a special ability to cause disease at extraintestinal sites when they exit their usual reservoir in the host's intestinal tract. Multiple lines of evidence suggest that many of the ExPEC strains encountered in humans with urinary tract infection, sepsis, and other extraintestinal infections, especially the most extensively antimicrobial-resistant strains, may have a food animal source, and may be transmitted to humans via the food supply. This review summarizes the evidence that food-borne organisms are a significant cause of extraintestinal E. coli infections in humans.

Intracellular Macrophage Infections with E. coli under Nitrosative Stress.

Escherichia coli (E. coli) produces disseminated infections of the urinary tract, blood, and central nervous system where it encounters professional phagocytes such as macrophages, which utilize reactive nitrogen intermediates (RNI) to arrest bacteria. In vitro, extraintestinal pathogenic E. coli (ExPEC) can survive within bone marrow-derived macrophages for greater than 24 h post-infection within a LAMP1+ vesicular compartment, and ExPEC strains, in particular, are better adapted to intracellular macrophage survival than commensal strains (Bokil et al., 2011). This protocol details an intracellular murine macrophage-like cell infection, including modulation of the host nitrosative stress response, to model this host-pathogen interaction in vitro. To accomplish this, RAW 264.7 murine macrophage-like cells are pre-incubated with either L-arginine, an NO precursor, or IFNγ to yield a high nitric oxide (NO) physiological state, or L-NAME, an inducible NO synthase (iNOS)-specific inhibitor, to yield a low NO physiological state. This protocol has been successfully utilized to assess the contribution of a novel ExPEC regulator to intracellular survival and the nitrosative stress response during macrophage infections (Bateman and Seed, 2012), but can be adapted for use with a variety of E. coli strains or isogenic deletions.

Mallard ducks – a waterfowl species with high risk of distributing Escherichia coli pathogenic for humans

Mallard ducks may pose a so far underestimated risk to human and animal health by transmitting pathogenic Escherichia coli via their faecal deposits to various environmental sources. We processed Mallard duck faecal samples for E. coli and unique clones, as defined by pulsed-field gel electrophoresis (PFGE), were subsequently investigated for their virulence genotype and phylogenetic background. Multilocus sequence typing and in vivo experiments were performed for selected clones. Of 60 clones identified among 142 E. coli isolated from 175 samples, 15 (25%) were recovered from multiple individuals (up to 23 per clone). None of the clones harboured stx1 and stx2 genes and other intestinal pathogenic E. coli virulence-associated genes were only occasionally identified in the collection. In contrast, the clones possessed considerable numbers of VAGs (up to 30) linked with extraintestinal pathogenic E. coli (ExPEC). Their pathogenic potential was confirmed in chicken infection experiments. Moreover, selected clones were assigned to sequence types (STs) being most prominent for human ExPEC strains, including ST95 and ST73. One clone exhibited a multi-resistant phenotype against several antibiotics including beta-lactams, tetracyclines and sulfonamides. Mallard ducks have therefore to be considered as an important reservoir for zoonotic E. coli strains, thus serving as a substantial non-point source especially of strains capable of causing extraintestinal diseases.

Phylogenetic Background and Virulence Genotype of Ciprofloxacin‐Susceptible and Ciprofloxacin‐ResistantEscherichia coliStrains of Human and Avian Origin

Previous studies have suggested that fluoroquinolone-resistant strains of Escherichia coli that infect humans probably emerged as a consequence of using fluoroquinolones in poultry. This study aims to provide further insight into the possible avian origin of fluoroquinolone-resistant extraintestinal pathogenic E. coli (ExPEC) strains that infect humans. We compared the phylogenetic backgrounds, virulence gene profiles, and genetic relatedness of 125 ExPEC strains recovered from humans (61 were ciprofloxacin susceptible and 64 were ciprofloxacin resistant) and 113 E. coli strains recovered from poultry (47 were ciprofloxacin susceptible and 66 were ciprofloxacin resistant). Ciprofloxacin-resistant strains of both human and avian origin harbored fewer virulence genes than did ciprofloxacin-susceptible strains, but ciprofloxacin-resistant strains from humans were found to be clearly distinct from ciprofloxacin-resistant avian strains, based on their phylogenetic backgrounds and virulence gene profiles. The phylogenetic background of ciprofloxacin-susceptible and ciprofloxacin-resistant strains of human origin was not different, and no shift from the phylogenetic group B2 toward other groups was detected in association with ciprofloxacin resistance. No genetic relatedness was observed among human and avian strains that belonged to the major virulence profile (traT-iucD-iutA). Our results did not support the hypothesis of an avian origin for the ciprofloxacin-resistant human ExPEC strains analyzed. Nevertheless, prudent use of fluoroquinolones in both human and veterinary medicine is recommended.

A killed, genetically engineered derivative of a wild-type extraintestinal pathogenic E. coli strain is a vaccine candidate

Infections due to extraintestinal pathogenic E. coli (ExPEC) result in significant morbidity, mortality and increased healthcare costs. An efficacious vaccine against ExPEC would be desirable. In this report, we explore the use of killed-whole E. coli as a vaccine immunogen. Given the diversity of capsule and O-antigens in ExPEC, we have hypothesized that alternative targets are viable vaccine candidates. We have also hypothesized that immunization with a genetically engineered strain that is deficient in the capsule and O-antigen will generate a greater immune response against antigens other than the capsular and O-antigen epitopes than a wild-type strain. Lastly, we hypothesize that mucosal immunization with killed E. coli has the potential to generate a significant immune response. In this study, we demonstrated that nasal immunization with a formalin-killed ExPEC derivative deficient in capsule and O-antigen results in a significantly greater overall humoral response compared to its wild-type derivative (which demonstrates that capsule and/or the O-antigen impede the development of an optimal humoral immune response) and a significantly greater immune response against non-capsular and O-antigen epitopes. These antibodies also bound to a subset of heterologous ExPEC strains and enhanced neutrophil-mediated bactericidal activity against the homologous and a heterologous strain. Taken together, these studies support the concept that formalin-killed genetically engineered ExPEC derivatives are whole cell vaccine candidates to prevent infections due to ExPEC.