Computational Molecular Bioscience, 2021, 11, 57-68 https://www.scirp.org/journal/cmb ISSN Online: 2165-3453 ISSN Print: 2165-3445 DOI: 10.4236/cmb.2021.113004 Sep. 30, 2021 57 Computational Molecular Bioscience Global Genomic Variations of Pathogenic Bacteria Salmonella Reading Woo Hyung Lee 1 , Yein Jeon 2 , Jonathan S. Chung 3,4 , Woo Jun Shim 4,5 , Min Jae Shin 4,6 , Seok Gyu Han 4,6 , Seunghan Baek 6 , James Kim 7,8 , Jaewoo Kim 4,8 , Paul S. Chung 2,8 1 Biotechnology, School of Sciences, Hong Kong University of Science of Technology, Hong Kong, China 2 Fuzbien Technology Institute, Rockville, USA 3 Ernest Mario School of Pharmacy, Rutgers University, New Brunswick, USA 4 College of Letters & Sciences, University of California, Los Angeles, USA 5 Biology, Bachelor of Science, California Institute of Technology, Pasadena, USA 6 School of Arts & Sciences, Johns Hopkins University, Baltimore, USA 7 School of Arts & Sciences, University of Michigan, Ann Arbor, USA 8 Youth with Talents, Fairfax, USA Abstract US Centers for Disease Control and Prevention (CDC) estimates food-borne pathogenic Salmonella bacteria cause about 1.35 million infections, 26,500 hospitalizations, and 420 deaths in the U.S. every year. Outbreaks of multi- drug-resistant Salmonella Reading linked mainly to raw turkey products and alfalfa sprouts have accounted for human illness including mortality. There- fore, we downloaded and compared genome sequences of 897 Salmonella Read- ing isolated from 27 resources in 11 countries at 21 year-points from the Na- tional Center for Biotechnology Information database. Isolates were clustered into 10 clades which consisted of 3 major and 7 minor or single node clades. Although 3 major clades included both Europe and American isolates, one clade consisted of 605 North American isolates out of 614 isolates. Evolutio- nary distance is more related to the continent than the source of isolation. The host source, continent (North America and Europe) and phylogenetic clade were related to the prevalence of isolates encoding Antimicrobial Resistance Genes (ARGs). Prevalence of prophages was greater in bovine and swine isolates than poultry and human isolates and the least prevalence was found in human isolates. Between continents, the prevalence of phage was greater in North Ame- rican isolates than European. The diversity of virulence factors in swine iso- lates differed from poultry isolate while no difference was found among con- tinents. In conclusion, evolutionary distance is related to isolation host source rather than the continent, and genome features were distinguished by host and cluster. Our genomic analysis implies that Salmonella Reading evolved inde- How to cite this paper: Lee, W.H., Jeon, Y., Chung, J.S., Shim, W.J., Shin, M.J., Han, S.G., Baek, S., Kim, J., Kim, J. and Chung, P.S. (2021) Global Genomic Variations of Pa- thogenic Bacteria Salmonella Reading. Com- putational Molecular Bioscience, 11, 57-68. https://doi.org/10.4236/cmb.2021.113004 Received: September 1, 2021 Accepted: September 27, 2021 Published: September 30, 2021 Copyright © 2021 by author(s) and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY 4.0). http://creativecommons.org/licenses/by/4.0/ Open Access