Research On The Genomic Epidemiology Of The Avian Pathogenic Escherichia Coli

Extraintestinal pathogenic Escherichia coli(ExPEC)bacteria are involved in infections of human and farm animals.They are often classified base on the host resource or pathogenicity as avian pathogenic E.coli(APEC),uropathogenic E.coli(UPEC)and neonatal meningitis E.coli(NMEC).ExPEC have many virulence-associated genes,including adhesins,toxins,iron acquisition factors,lipopolysaccharides,polysaccharide capsules,and invasins,which are usually encoded on pathogenicity islands,plasmids,and other mobile genetic elements.UPEC and NMEC is human-derived ExPEC strains,which are associated with the infectious diseases such as urinary tract infections,neonatal meningitis or sepsis.APEC cause localized or systemic infection in poultry herd,called colibacillosis.It manifests in diverse ways,including acute fatal septicemia,subacute pericarditis,airsacculitis,salpingitis,peritonitis,and cellulitis.It is one of the most commonly occurring and economically devastating bacterial diseases of worldwide poultry industry.Besides,APEC strains can be carried from birds to human by food chain or direct contact with birds and their feces,which could be a potential zoonotic pathogen,with unknown mechanisms underlie cross-host transmission.Thus,we analyzed the typing,virulence factors and resistance genes among prevalent isolates,and preliminarily explored the host adaptation genes for ExPEC strains,hoping to have implications for poultry industry,food safety and public health.1 Genetic characteristics and epidemiological analysis of APEC isolatesIn this study,we sequenced 128 APEC isolates from chickens and ducks with obvious clinical symptoms in the poultry farms in China.And 37 ExPEC complete genomes sequences downloaded from NCBI served as reference strains.Then we analyzed the phylogenetic characteristics,virulence genes and antibiotic resistance gene for APEC isolates.The composition of APEC isolates is very diverse.We identified 29 O antigen types and 26 MLST types.All 8 phylo-groups of E.coli can be found among APEC isolates.The three most common phylo-groups are C(28.13%),F(26.56%)and B1(21.88%).Analysis of antibiotic resistance genes revealed that all isolates contained beta-lactam resistance genes,and Extended-Spectrum β-Lactamases(ESBL)gene blaTEM could be detected in 59.38%of the isolates.The proportion of aminoglycoside resistance genes and tetracycline resistance genes among the isolates was also as high as 96.09%and 92.19%,indicating that excessive use of antibiotics could cause multidrug resistance problems.The detection of virulence genes proved that the group B2 APEC isolates have the largest number of ExPEC virulence-associated genes.Group B2 is also the most common phylo-group of human-derived ExPEC strains,which indicates that the group B2 APEC strains would present the higher risk of zoonotic infection.We provide the commonly distributed genes in the APEC isolates,which might be used as molecular markers to identify ExPEC strains.2 Study on the pangenomic characteristics and host-adaptation of ExPEC strainsA bacterial species can be described by its pangenome,which is composed of a "core genome" containing genes present in all strains,mainly related to their basic biological functions,and a "dispensable genome" containing genes present in two or more strains or genes unique to single strains,which mostly reflect the diversity of bacterial genome.This study including the complete genome of 37 ExPEC strains and 3 commensal E.coli strains.The results of the analysis of pangenome for ExPEC genome showed that the relative proportion of its core genome to the average genome size was 51.5%,indicating that the gene composition of ExPEC genome has high genetic diversity.The pathogen-associated core genome is obtained by calculating the difference between the core genome of non-pathogenic commensal E.coli and pathogenic ExPEC genome.The unique part of the pathogen-associated core genome of UPEC and NMEC was screened by 128 APEC isolates for genes that exist in less than 20%of the isolates.These host-associated core genes might be related to the ability for ExPEC strains to infect humans.And these genes located in the isolates mostly belong to group B2,which indicates the high risk of causing zoonotic diseases.This study may provide an understanding for further clarification to the mechanism of cross-host transmission for ExPEC.3 Pathogenicity study of B2 group of ExPEC strain in different hostsThe similarity of virulence genes among APEC,UPEC and NMEC indicates that avian-derived ExPEC strain might have the potential for zoonotic infection.The largest number of ExPEC-associated virulence genes and host-associated core genes,which is unique in human-derived strains,distributed in group B2 APEC strains increasing risk of infecting people through the food chain or direct contact.This study compared the pathogenicity differences between the eight group B2 ExPEC strains in the mouse model and chicken model.The results showed that the group B2 avian-derived ExPEC strains has both pathogenicity in mouse and chicken models,while 2 of human-derived ExPEC strains showed host specificity,which confirmed the risk of zoonotic infection causing by group B2 APEC strains.