Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States

Authors: FENG, A - University Of Missouri; AKTER, S - University Of Missouri; Leigh, Spencer; WANG, H - Mississippi State University; PHARR, G - Mississippi State University; Evans, Jeffrey - Jeff; BRANTON, S - Retired ARS Employee; LANDINEZ, M - Mississippi State University; PACE, L - Mississippi State University; WAN, XIU-FENG - Mississippi State University

Submitted to: BMC Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2022
Publication Date: 1/16/2023
Citation: Feng, A., Akter, S., Leigh, S.A., Wang, H., Pharr, G.T., Evans, J.D., Branton, S.L., Landinez, M.P., Pace, L., Wan, X. 2023. Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States. BMC Microbiology. 23:15. https://doi.org/10.1186/s12866-022-02721-9.
DOI: https://doi.org/10.1186/s12866-022-02721-9

Interpretive Summary: Avian pathogenic E. coli (APEC) can be part of the normal bacteria of the chicken intestine but may also cause extra-intestinal disease in chickens. Further, APEC may harbor antimicrobial resistant genes which can complicate treatment of disease and be a reservoir for antimicrobial resistance in other bacteria. Genomic sequencing of a diverse set of isolates has identified a larger number of antibiotic resistance genes present in these strains as well as a range of virulence factors that may contribute to disease. These genome sequences will help provide a means of identifying virulence genes that are responsible for the ability of APEC to cause disease in chickens and the provide information on what antimicrobial resistance genes are present and provide DNA signatures to help track these genes as they move though bacterial populations.

Technical Abstract: Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic APEC isolates in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. The objective of this study was to explore the genomic and pathogenic diversity among E. coli isolates in Mississippian poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from George, by considering epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both the Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closes to each other than those in the public database. However, whole genome analyses showed that these 10 isolates were APEC with diverse sets of virulence and AMR factors, belong to at least nine O:H serotypes, and are genetically clustered with at least three different groups of APEC isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among APEC E. coli isolates in Mississippian poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.