Complete genome sequence of multidrug-resistant avian pathogenic Escherichia coli strain APEC-O2-MS1170

Authors: LI, T - Mississippi State University; CASTANEDA, D - Mississippi State University; ARICK, M - Mississippi State University; HSU, C - Mississippi State University; KIESS, A - Mississippi State University; ZHANG, L - Mississippi State University

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/9/2020
Publication Date: 12/2/2020
Citation: Li, T., Castaneda, D., Arick, M., Hsu, C., Kiess, A., Zhang, L. 2020. Complete genome sequence of multidrug-resistant avian pathogenic Escherichia coli strain APEC-O2-MS1170. Journal of Global Antimicrobial Resistance. 23:401-403. https://doi.org/10.1016/j.jgar.2020.11.009.
DOI: https://doi.org/10.1016/j.jgar.2020.11.009

Interpretive Summary: Escherichia coli (E. coli) is one of the leading causes of devastating diseases in the poultry industry that result in major economic losses. This study aimed to determine resistance properties in the genome sequence of a multidrug-resistant E. coli strain. This strain of E. coli was isolated from the internal yolk sac of a 14-day-old chick. Antimicrobial susceptibility testing and genome sequencing were run to obtain an accurate sequence. The genome size of this strain is 4,993,909 basepair with a Guanine-Cytosine content of 50.7% and 4,651 protein producing sequences. Various databases were used to identify the genes responsible for disease and resistance. In conclusion, this genome sequence provides valuable information on resistance mechanisms and pathogenic characteristics of E. coli, as well as information for tracing the potential spread of this multidrug-resistant strain.

Technical Abstract: Objectives Avian pathogenic Escherichia coli (APEC) causes colibacillosis, one of the leading causes of mortality and morbidity associated with significant economic losses in the poultry industry. This study aimed to determine antimicrobial resistance and to characterise the genome sequence of a multidrug-resistant (MDR) APEC strain isolated from a broiler chicken. Methods Strain APEC-O2-MS1170 was isolated from the broiler yolk sac of a 14-day-old broiler. Antimicrobial susceptibility testing was performed using a Sensititre National Antimicrobial Resistance Monitoring System (NARMS) Gram-negative panel. Whole-genome sequencing was performed using both the long-read sequencing approach with a Nanopore GridION sequencer and short-read sequencing with an Illumina HiSeq X-Ten sequencer to obtain a complete scaffold of the genome and an accurate sequence. Results The genome size of strain APEC-O2-MS1170 is 4,993,909 bp with a GC content of 50.7% and 4,651 protein-coding sequences. Public databases were used to identify the virulence-associated gene and antimicrobial resistance gene cargo. Plasmid comparison showed that pAPEC-O2-MS1170-R is a large multidrug resistance IncB/O/K/Z plasmid, while pAPEC-O2-MS1170-ColV shares homology with the APEC ColV virulence plasmid. Conclusion The genome sequence of APEC-O2-MS1170 provides valuable information on resistance mechanisms and virulence characteristics of pathogenic E. coli as well as information for tracing the potential spread of this MDR strain.