PMID- 27875980 OWN - NLM STAT- MEDLINE DCOM- 20170825 LR - 20201209 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 17 IP - 1 DP - 2016 Nov 22 TI - Comparative genomics of European avian pathogenic E. Coli (APEC). PG - 960 LID - 960 AB - BACKGROUND: Avian 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). RESULTS: The 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. CONCLUSIONS: The 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 to define APEC with clarity, reaffirming the need for whole genome analysis approaches which we describe here. This study highlights the presence of previously unreported serotypes and MLSTs for APEC in Europe. Moreover, it is a first step on a cautious reconsideration of the merits of classical identification criteria such as R typing, phylogrouping and serotyping. FAU - Cordoni, Guido AU - Cordoni G AD - Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, UK. guidocordoni@yahoo.it. FAU - Woodward, Martin J AU - Woodward MJ AD - Department of Food and Nutritional Sciences, University of Reading, Reading, UK. FAU - Wu, Huihai AU - Wu H AD - Bioinformatics Core Facility, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK. FAU - Alanazi, Mishaal AU - Alanazi M AD - Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, UK. FAU - Wallis, Tim AU - Wallis T AD - Ridgeway Biologicals Ltd, Units 1-3 Old Station Business Park, Compton, Berkshire, RG20 6NE, UK. FAU - La Ragione, Roberto M AU - La Ragione RM AD - Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, UK. LA - eng SI - figshare/10.6084/m9.figshare.4055469.v1 PT - Journal Article DEP - 20161122 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (Virulence Factors) SB - IM MH - Animals MH - Cluster Analysis MH - Computational Biology/methods MH - Data Mining MH - Drug Resistance, Bacterial MH - Escherichia coli/classification/drug effects/*genetics MH - Escherichia coli Infections/*veterinary MH - *Genome, Bacterial MH - *Genomics/methods MH - High-Throughput Nucleotide Sequencing MH - Machine Learning MH - Multilocus Sequence Typing MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Poultry Diseases/*microbiology MH - Serotyping MH - Virulence Factors/genetics PMC - PMC5120500 OTO - NOTNLM OT - Avian Pathogenic E. coli OT - Comparative genomics OT - Multiplex PCR OT - Virulence factors analysis EDAT- 2016/11/24 06:00 MHDA- 2017/08/26 06:00 PMCR- 2016/11/22 CRDT- 2016/11/24 06:00 PHST- 2016/03/22 00:00 [received] PHST- 2016/11/14 00:00 [accepted] PHST- 2016/11/24 06:00 [entrez] PHST- 2016/11/24 06:00 [pubmed] PHST- 2017/08/26 06:00 [medline] PHST- 2016/11/22 00:00 [pmc-release] AID - 10.1186/s12864-016-3289-7 [pii] AID - 3289 [pii] AID - 10.1186/s12864-016-3289-7 [doi] PST - epublish SO - BMC Genomics. 2016 Nov 22;17(1):960. doi: 10.1186/s12864-016-3289-7.