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 multidrug-resistant Salmonella Reading linked mainly to raw turkey products and alfalfa sprouts have accounted for human illness including mortality. Therefore, we downloaded and compared genome sequences of 897 Salmonella Reading isolated from 27 resources in 11 countries at 21 year-points from the National 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. Evolutionary 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 isolates differed from poultry isolate while no difference was found among continents. 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 independently to environments within its lineages.
References
[1]
Muvhali, M., Smith, A.M., Rakgantso, A.M. and Keddy, K.H. (2017) Investigation of Salmonella Enteritidis Outbreaks in South Africa Using Multi-Locus Variable-Number Tandem-Repeats Analysis, 2013-2015. BMC Infectious Diseases, 17, Article No. 661.
https://doi.org/10.1186/s12879-017-2751-8
[2]
Torgerson, P.R., Devleesschauwer, B., Praet, N., Speybroeck, N., Willingham, A.L., Kasuga, F., et al. (2015) World Health Organization Estimates of the Global and Regional Disease Burden of 11 Foodborne Parasitic Diseases, 2010: A Data Synthesis. PLoS Medicine, 12, Article ID: e1001920.
https://doi.org/10.1371/journal.pmed.1001920
[3]
Centers for Disease Control and Prevention (2019) Outbreak of Multidrug-Resistant Salmonella Infections Linked to Raw Turkey Products: Final Update. Centers for Disease Control and Prevention, Atlanta.
https://www.cdc.gov/salmonella/reading-07-18/index.html
[4]
Gupta, A., Fontana, J., Crowe, C., Bolstorff, B., Stout, A., Van Duyne, S., Hoekstra, M.P., Whichard, J.M., Barrett, T.J., Angulo, F.J. and National Antimicrobial Resistance Monitoring System PulseNet Working Group (2003) Emergence of Multidrug-Resistant Salmonella enterica Serotype Newport Infections Resistant to Expanded-Spectrum Cephalosporins in the United States. Journal of Infectious Diseases, 188, 1707-1716. https://doi.org/10.1086/379668
[5]
Founou, L.L., Founou, R.C. and Essack, S.Y. (2016) Antibiotic Resistance in the Food Chain: A Developing Country-Perspective. Frontiers in Microbiology, 7, Article No. 1881. https://doi.org/10.3389/fmicb.2016.01881
[6]
Kudirkiene, E., Andoh, L.A., Ahmed, S., Herrero-Fresno, A., Dalsgaard, A., Obiri-Danso, K., et al. (2018) The Use of a Combined Bioinformatics Approach to Locate Antibiotic Resistance Genes on Plasmids from Whole Genome Sequences of Salmonella enterica Serovars from Humans in Ghana. Frontiers in Microbiology, 9, Article No. 1010. https://doi.org/10.3389/fmicb.2018.01010
[7]
O’Neill, J. (2016) Tackling Drug-Resistant Infections Globally: Final Report and Recommendations. Review on Antimicrobial Resistance, Government of the United Kingdom, 1-84.
[8]
Rabello, R.F., Bonelli, R.R., Penna, B.A., Albuquerque, J.P., Souza, R.M. and Cerqueira, A.M.F. (2020) Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview. Animals, 10, Article No. 552. https://doi.org/10.3390/ani10040552
[9]
Yoshida, C., Kruczkiewicz, P., Laing, C.R., Lingohr, E.J., Gannon, V.P.J., Nash, J.H.E. and Taboada, E.N. (2016) The Salmonella in Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS ONE, 11, Article ID: e0147101.
https://doi.org/10.1371/journal.pone.0147101
[10]
Kumar, S., Nei, M., Dudley, J. and Tamura, K. (2008) MEGA: A Biologist-Centric Software for Evolutionary Analysis of DNA and Protein Sequences. Briefings in Bioinformatics, 9, 299-306. https://doi.org/10.1093/bib/bbn017
[11]
Bortolaia, V., Kaas, R.F., Ruppe, E., Roberts, M.C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R.L., Rebelo, A.R., Florensa, A.R., Fagelhauer, L., Chakraborty, T., Neumann, B., Werner, G., Bender, J.K., Stingl, K., Nguyen, M., Coppens, J., Xavier, B.B., Malhotra-Kumar, S., Westh, H., Pinholt, M., Anjum, M.F., Duggett, N.A., Kempf, I., Nykäsenoja, S., Olkkola, S., Wieczorek, K., Amaro, A., Clemente, L., Mossong, J., Losch, S., Ragimbeau, C., Lund, O. and Aarestrup, F.M. (2020) ResFinder 4.0 for Predictions of Phenotypes from Genotypes. Journal of Antimicrobial Chemotherapy, 75, 3491-3500. https://doi.org/10.1093/jac/dkaa345
[12]
NCBI (National Centre for Biotechnology Information) (1988) Basic Local Alignment Search Tools. National Centre for Biotechnology Information, Rockville.
[13]
Majowicz, S.E., Musto, J., Scallan, E., Angulo, F.J., Kirk, M., O’Brien, S.J., et al. (2010) The Global Burden of Nontyphoidal Salmonella Gastroenteritis. Clinical Infectious Diseases, 50, 882-889. https://doi.org/10.1086/650733
[14]
Mellor, K.C., Petrovska, L., Thomson, N.R., Harris, K., Reid, S.W.J. and Mather, A.E. (2019) Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals. Frontiers in Microbiology, 10, Article No. 708. https://doi.org/10.3389/fmicb.2019.00708
[15]
Davis, M.A., Hancock, D.D. and Besser, T.E. (2002) Multiresistant Clones of Salmonella enterica: The Importance of Dissemination. Journal of Laboratory and Clinical Medicine, 140, 135-141. https://doi.org/10.1067/mlc.2002.126411
[16]
Borie, C., Robeson, J. and Galarce, N. (2014) Lytic Bacteriophages in Veterinary Medicine: A Therapeutic Option against Bacterial Pathogens. Archivos de Medicina Veterinaria, 46, 167-179. https://doi.org/10.4067/S0301-732X2014000200002
[17]
Nobrega, F.L., Costa, A.R., Kluskens, L.D. and Azeredo, J. (2015) Revisiting Phage Therapy: New Applications for Old Resources. Trends in Microbiology, 23, 185-191.
https://doi.org/10.1016/j.tim.2015.01.006
[18]
Pulido, R.P., Burgos, M.J.G., Gálvez, A. and López, R.L. (2016) Application of Bacteriophages in Post-Harvest Control of Human Pathogenic and Food Spoiling Bacteria. Critical Reviews in Biotechnology, 36, 851-861.
https://doi.org/10.3109/07388551.2015.1049935
[19]
Switt, A.I.M., den Bakker, H.C., Vongkamjan, K., Hoelzer, K., Warnick. L.D., Cummings, K.J. and Wiedmann, M. (2013) Salmonella Bacteriophage Diversity Reflects Host Diversity on Dairy Farms. Food Microbiology, 36, 275-285.
https://doi.org/10.1016/j.fm.2013.06.014
[20]
Wongsuntornpoj, S., Switt, A.I.M., Bergholz, P., Wiedmann, M. and Chaturongakul, S. (2014) Salmonella Phages Isolated from Dairy Farms in Thailand Show Wider Host Range than a Comparable Set of Phages Isolated from U.S. Dairy Farms. Veterinary Microbiology, 172, 345-352.
https://doi.org/10.1016/j.vetmic.2014.05.023
[21]
Que, F., Wu, S. and Huang, R. (2013) Salmonella Pathogenicity Island 1(SPI-1) at Work. Current Microbiology, 66, 582-587.
https://doi.org/10.1007/s00284-013-0307-8
