Food Protection Trends - September/October 2023 - 388

31. Parks, D. H., M. Imelfort, C. T. Skennerton,
P. Hugenholtz, and G. W. Tyson. 2015. CheckM:
assessing the quality of microbial genomes
recovered from isolates, single cells, and metagenomes.
Genome Res. 25:1043-1055.
32. Possebon, F. S., M. V. N. Alvarez, L. S.
Ullmann, and J. P. Araújo, Jr. 2021.
Antimicrobial resistance genes and class
1 integrons in MDR Salmonella strains isolated
from swine lymph nodes. Food Control
128:108190.
33. Sanchez-Maldonado, A. F., M. Aslam,
C. Service, C. Narvaez-Bravo, B. P. Avery,
R. Johnson, and T. H. Jones. 2017. Prevalence
and antimicrobial resistance of Salmonella
isolated from two pork processing plants
in Alberta, Canada. Int. J. Food Microbiol.
241:49-59.
34. Scallan, E., R. M. Hoekstra, F. J. Angulo,
R. V. Tauxe, M. A. Widdowson, S. L. Roy,
J. L. Jones, and P. M. Griffin. 2011. Foodborne
illness acquired in the United States-
major pathogens. Emerg. Infect. Dis. 17:7-15.
35. Seemann, T. 2014. Prokka: rapid prokaryotic
genome annotation. Bioinformatics
30:2068-2069.
36. Stamatakis, A. 2014. RAxML version 8:
a tool for phylogenetic analysis and postanalysis
of large phylogenies. Bioinformatics
30:1312-1313.
37. Thomas, M. K., R. Murray, L. Flockhart,
K. Pintar, A. Fazil, A. Nesbitt, B. Marshall,
J. Tataryn, and F. Pollari. 2015. Estimates of
foodborne illness-related hospitalizations and
deaths in Canada for 30 specified pathogens
and unspecified agents. Foodborne Pathog.
Dis. 12:820-827.
38. World Health Organization. 2016.
Interventions for the control of nontyphoidal
Salmonella spp. in beef and pork:
meeting report and systematic review. World
Health Organization, Geneva.
39. Young, I., B. J. Wilhelm, S. Cahill,
R. Nakagawa, P. Desmarchelier, and
A. Rajic. 2016. A rapid systematic review
and meta-analysis of the efficacy of slaughter
and processing interventions to control nontyphoidal
Salmonella in beef and pork.
J. Food Prot. 79:2196-2210.
40. Zhang, S., H. C. den Bakker, S. Li, J. Chen,
B. A. Dinsmore, C. Lane, A. C. Lauer,
P. I. Fields, and X. Deng. 2019. SeqSero2:
rapid and improved Salmonella serotype
determination using whole-genome
sequencing data. Appl. Environ. Microbiol.
85:e01746-19.
41. Zhang, Y., A. M. O'Connor, C. Wang,
J. S. Dickson, H. S. Hurd, and B. Wang.
2019. Interventions targeting deep tissue
lymph nodes may not effectively reduce
the risk of salmonellosis from ground pork
consumption: a quantitative microbial risk
assessment. Risk Anal. 39:2237-2258.
Supplemental TABLE S1. Publicly available Salmonella genomes from pork lymph nodes
that were compared with the three Salmonella isolates from this study
Isolate ID
ADRDL-1116
S1351
CFSAN031520
CFSAN031524
ADRDL-1912
1583
P3S1022
ADRDL-1130
ADRDL-1121
CFSAN031513
CFSAN031536
CFSAN031537
CFSAN031538
CFSAN074939
UFRGS-SA007
UFRGS-SA008
UFRGS-SA009
Serotype
Anatum
Barranquilla
Blockley
Braenderup
Brandenburg
Choleraesuis
Derby
Derby
Eko
Enteritidis
Enteritidis
Enteritidis
Enteritidis
Enteritidis
Enteritidis
Enteritidis
Enteritidis
Antimicrobial resistance genes
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy, tet(A), aph(6)-Id, aph(3′′)-Ib,
aph(3′)-Ia, blaTEM-1
sul1, aac(6′)-Iaa, aadA, sul2, aph(6)-Id,
aph(3′′)-Ib, blaTEM-1
sul1, aac(6′)-Iaa, aadA, aac(3)-VIa, sul2,
tet(A), aph(6)-Id, aph(3′′)-Ib
tet(B), aac(6′)-Iaa, sul2, aph(6)-Id,
aph(3′′)-Ib, aac(3)-IV, aph(4)-Ia,
blaTEM-1
aac(6′)-Iy, sul1, tet(A), ant(3′′)-IIa
aac(6′)-Iy, tet(C)
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy
aac(6′)-Iy, aph(6)-Id, aph(3′′)-Ib,
aac(3)-IV, aph(4)-Ia
388 Food Protection Trends September/October
GenBank accession
GCA_007098425.1
GCA_005584275.1
GCA_010542145.1
GCA_010765935.1
GCA_005678815.1
GCA_018359665.1
GCA_005903325.1
GCA_007098345.1
GCA_007098465.1
GCA_007763755.1
GCA_008913785.1
GCA_008913245.1
GCA_008914205.1
GCA_006076935.1
GCA_006001745.1
GCA_006144495.1
GCA_006076895.1
BioProject
PRJNA280335
PRJNA293224
PRJNA275961
PRJNA275961
PRJNA280335
PRJNA280335
PRJNA293224
PRJNA280335
PRJNA280335
PRJNA275961
PRJNA275961
PRJNA275961
PRJNA275961
PRJNA275961
PRJNA183850
PRJNA183850
PRJNA183850
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