Subpathotypes of Avian Pathogenic Escherichia coli (APEC) Exist as Defined by their Syndromes and Virulence Traits

Maturana, Víctor Gonçalves; Pace, Fernanda de; Carlos, Camila; Pires, Mathias M.; Campos, Tatiana Amabile de; Nakazato, Gerson; Stheling, Eliana Guedes; Logue, Catherine M.; Nolan, Lisa K.; Silveira, Wanderley Dias da

doi:10.2174/1874285801105010055

Cited by 34 publications

(20 citation statements)

References 25 publications

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“…The phylogenetic analysis, also demonstrated, as indicated by the MLST study, that APEC strains are not a homogeneous group. Thus, the phylogenetic tree and virulence gene profiles revealed that the strains are very diverse, corroborating previous works (Maturana et al 2011, Schouler et al 2012. For strain S17, a septicaemic Brazilian APEC, both methodologies clearly showed that it has a closer genetic similarity with strain H10407, a human ETEC strain.…”

Section: Discussionsupporting

confidence: 87%

“…However, the high diversity encountered in E. coli species difficult the use of a single set of virulence factors for diagnosis (Schouler et al 2012). For Brazilian APEC strains, a recent study of our group, showed that the analysis of several biological characteristics, such as adhesion to eukaryotic cell cultures, pathogenicity levels according to the lethal dose (50%) assay, phylogenetic groups and virulence gene profiles, indicated that APEC strains could be organized into a structured set of subgroups associated with specific infectious syndromes (Maturana et al 2011). These finds demonstrated that APEC strains are very diverse and that the detection of specific genes is not sufficient to define this group.…”

Section: Discussionmentioning

confidence: 99%

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In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

et al. 2014

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Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC) associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli) and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

et al. 2014

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“…The prevalence of VGs reported in this study are similar to a number of overseas studies, which have reported variation in VG frequency and combinations in CEC and FEC isolates (Johnson et al, 2008b;Lynne et al, 2012;Maturana et al, 2011;Olsen et al, 2012;Rodriguez-Siek et al, 2005a). …”

Section: Discussionsupporting

confidence: 89%

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, a localised or systemic infection resulting in clinical diseases such as colisepticemia, chronic respiratory disease and swollen-head syndrome. Globally, avian colibacillosis is the leading cause of morbidity and mortality in poultry, and it has been associated with massive economic losses and welfare problems.This organism is of public health significance as APEC is communicable to humans. The diagnosis of avian colibacillosis relies on clinical signs, typical pathological lesions and culture of E. coli from affected tissue(s). Antimicrobial therapy is often used both for treatment and control. Previous overseas studies have characterised APEC and identified virulence genes (VGs) that can be used as molecular markers for the identification of APEC. Little is known about APEC in broiler chickens in Australia.The aim of this thesis was to gain a better understanding of the epidemiology of APEC in Australian broiler flocks and how factors including presence of VGs and phylogenetic group can improve the identification of this pathotype in Australia. Firstly, three faecal DNA extraction methods were evaluated. Faeces were collected from healthy chickens and chickens with colibacillosis from commercial broiler farms in South East Queensland (SEQ). The extracted DNA was screened by a pentaplex-PCR for five APEC-associated VGs (iroN, iutA, iss, hlyF and ompT). DNA extracted from E. coli isolates cultured from the cloaca and organs of the birds were screened using the same PCR.Repeated bead beating plus column elution was the preferred DNA extraction method, as it yielded good PCR quality and adequate quantity DNA. However, identifying APEC by direct detection of the five VGs from the faecal material was not feasible as all of these genes were also detected in all of the birds. However, the VGs were more commonly detected in E. coli isolates cultured from birds with colibacillosis.A cross-sectional study was performed to estimate APEC farm-level prevalence in healthy broiler chickens in SEQ and to identify potential risk factors associated with the carriage of APEC. At the farm-level, all of the 40 farms sampled were positive for APEC, that is at least one bird per farm carried APEC, while the within-farm prevalence was 63% (95% Confidence Interval: 55.8, 70.2).Higher APEC within-farm bird-level prevalence was significantly associated with the usage of well water as a source of drinking water, failure to disinfect the water line after each flock, farm visitors not showering before entering the shed, distances greater than 20 metres between the car park and the poultry shed and the presence of wild birds within 50 metres of the shed. Chlorinating the drinking water combined with automatic water filtration reduced within-farm bird-level APEC prevalence. Page | 3Therefore, based on the results concluded from the multivariable model, improving biosecurity and water treatments might reduce APEC prevalence, decrease the risk of co...

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“…An interesting hypothesis generated out of the Nolan laboratory suggests that, although there are many disease presentations possibly arising through the expression of many combinations of virulence determinants, perhaps there exists a minimal set of genes that define APEC [18]. Maturana et al (2011) used PCR to detect APEC virulence genes including yjaA, tspE4.C2, iucA, irp-2, fepC, crl, csgA, tsh, lpfAO141, lpfAO154, iha, sitA, fyuA, fimA, papA of which crl, csgA, lpfAO141, lpfAO154, fimA, papA and concluded that not all APEC strains have all determinants and different combinations of determinants in a strain will contribute to pathogenic potential [19]. …”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of European avian pathogenic E. Coli (APEC)

Cordoni

Woodward

et al. 2016

BMC Genomics

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BackgroundAvian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS).ResultsThe most prevalent phylogroups were B2 (47%) and A1 (22%), although there were national differences with Germany presenting group B2 (35.3%), Italy presenting group A1 (53.3%) and UK presenting group B2 (56.1%) as the most prevalent. R-type R1 was the most frequent type (55%) among APEC, but multiple R-types were also frequent (26.8%). Following compilation of all the PCR data which covered a total of 15 virulence genes, it was possible to build a similarity tree using each PCR result unweighted to produce 9 distinct groups. The average number of virulence genes was 6–8 per isolate, but no positive association was found between phylogroup and number or type of virulence genes. A total of 95 isolates representing each of these 9 groupings were genome sequenced and analysed for in silico serotype, Multilocus Sequence Typing (MLST), and antimicrobial resistance (AMR). The UK isolates showed the greatest variability in terms of serotype and MLST compared with German and Italian isolates, whereas the lowest prevalence of AMR was found for German isolates. Similarity trees were compiled using sequencing data and notably single nucleotide polymorphism data generated ten distinct geno-groups. The frequency of geno-groups across Europe comprised 26.3% belonging to Group 8 representing serogroups O2, O4, O18 and MLST types ST95, ST140, ST141, ST428, ST1618 and others, 18.9% belonging to Group 1 (serogroups O78 and MLST types ST23, ST2230), 15.8% belonging to Group 10 (serogroups O8, O45, O91, O125ab and variable MLST types), 14.7% belonging to Group 7 (serogroups O4, O24, O35, O53, O161 and MLST type ST117) and 13.7% belonging to Group 9 (serogroups O1, O16, O181 and others and MLST types ST10, ST48 and others). The other groups (2, 3, 4, 5 and 6) each contained relatively few strains.However, for some of the genogroups (e.g. groups 6 and 7) partial overlap with SNPs grouping and PCR grouping (matching PCR groups 8 (13 isolates on 22) and 1 (14 isolates on 16) were observable). However, it was not possible to obtain a clear correlation between genogroups and unweighted PCR groupings. This may be due to the genome plasticity of E. coli that enables strains to carry the same virulence factors even if the overall genotype is substantially different.ConclusionsThe conclusion to be drawn from the lack of correlations is that firstly, APEC are very diverse and secondly, it is not possible to rely on any one or more basic molecular or phenotypic tests t...

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Subpathotypes of Avian Pathogenic Escherichia coli (APEC) Exist as Defined by their Syndromes and Virulence Traits

Cited by 34 publications

References 25 publications

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Comparative genomics of European avian pathogenic E. Coli (APEC)

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