Table 1. Metadata of the draft genomes of 98 Salmonella Infantis strains isolated from food (n = 31), environmental (n = 26), human (n = 28), animal (n = 9), and animal feed (n = 4) sources analyzed in this study.
| Country± | Strain | Year | Isolation source | Isolation material | GenBank accession | Pathogen Detection SNP Cluster |
|---|---|---|---|---|---|---|
| Brazil (PR) | SI 1348/13 | 2013 | Human | Human feces | GCA_015005295.1 | PDS000029248.42 |
| Brazil (PR) | SI 2385/13*,# | 2013 | Food | Soy | GCA_015004955.1 | PDS000106150.2 |
| Brazil (AL) | SI 2950/13 | 2013 | Human | Human feces | GCA_015005655.1 | PDS000074308.3 |
| Brazil (AL) | SI 2951/13 | 2013 | Human | Human feces | GCA_015005535.1 | PDS000074308.3 |
| Brazil (SC) | SI 3156/13 | 2013 | Environment | Disposable shoe cover | GCA_015004835.1 | PDS000018462.80 |
| Brazil (SC) | SI 5025/13* | 2013 | Human | Human feces | GCA_015004775.1 | – |
| Brazil (RS) | SI 124/14 | 2014 | Animal | Swine feces | GCA_015000505.1 | PDS000074309.3 |
| Brazil (SC) | SI 210/14 | 2014 | Environment | Dragging swab | GCA_015000845.1 | PDS000018462.80 |
| Brazil (SC) | SI 212/14 | 2014 | Environment | Dragging swab | GCA_015000465.1 | PDS000018462.80 |
| Brazil (SP) | SI 388/14*# | 2014 | Animal feed | Soybean animal meal | GCA_015000865.1 | – |
| Brazil (SC) | SI 583/14 | 2014 | Food | Chicken carcass | GCA_015000785.1 | PDS000018462.80 |
| Brazil (SC) | SI 584/14 | 2014 | Food | Pasta containing ham | GCA_015001025.1 | PDS000018462.80 |
| Brazil (SC) | SI 677/14* | 2014 | Food | Carcass cleaning wipe | GCA_015004135.1 | – |
| Brazil (SC) | SI 723/14 | 2014 | Environment | Dragging swab | GCA_015003895.1 | PDS000018462.80 |
| Brazil (RS) | SI 982/14 | 2014 | Animal | Chicken feces | GCA_015005755.1 | PDS000074309.3 |
| Brazil (RS) | SI 1143/14* | 2014 | Animal | Chicken feces | GCA_015005715.1 | PDS000074309.3 |
| Brazil (SC) | SI 1284/14 | 2014 | Environment | Dragging swab | GCA_015006215.1 | PDS000018462.80 |
| Brazil (RS) | SI 1380/14 | 2014 | Animal | Chicken feces | GCA_015005255.1 | PDS000074309.3 |
| Brazil (RS) | SI 1408/14 | 2014 | Human | Human feces | GCA_015005915.1 | PDS000029248.42 |
| Brazil (RS) | SI 1409/14 | 2014 | Human | Human feces | GCA_015005275.1 | PDS000029248.42 |
| Brazil (RS) | SI 1441/14* | 2014 | Food | Mayonnaise | GCA_015005515.1 | PDS000029248.42 |
| Brazil (RS) | SI 1711/14 | 2014 | Animal | Chicken feces | GCA_016437325.1 | PDS000074309.3 |
| Brazil (SC) | SI 2378/14 | 2014 | Environment | Truck swab | GCA_015005635.1 | PDS000018462.80 |
| Brazil (SC) | SI 2430/14 | 2014 | Food | Mixed meat sausage | GCA_015005595.1 | PDS000018462.80 |
| Brazil (SC) | SI 2461/14 | 2014 | Food | Chicken carcass | GCA_015004875.1 | PDS000018462.80 |
| Brazil (SC) | SI 2463/14 | 2014 | Food | Chicken carcass | GCA_016437365.1 | PDS000018462.80 |
| Brazil (RS) | SI 2548/14 | 2014 | Animal | Chicken feces | GCA_015000545.1 | PDS000029248.42 |
| Brazil (RS) | SI 3836/14* | 2014 | Environment | Dragging swab | GCA_015243075.1 | PDS000075101.1 |
| Brazil (MG) | SI 4882/14* | 2014 | Food | Chicken carcass | GCA_015244115.1 | PDS000074994.3 |
| Brazil (MG) | SI 4892/14 | 2014 | Food | Chicken wings | GCA_015223455.1 | PDS000074994.3 |
| Brazil (MG) | SI 4895/14 | 2014 | Food | Chicken carcass | GCA_015221915.1 | PDS000074994.3 |
| Brazil (MG) | SI 4901/14 | 2014 | Food | Pig snout | GCA_015223515.1 | PDS000074994.3 |
| Brazil (MG) | SI 5247/14 | 2014 | Food | Chicken upper leg and thigh | GCA_015221895.1 | PDS000074994.3 |
| Brazil (SC) | SI 342/15 | 2015 | Food | Swine heart | GCA_015527045.1 | PDS000018462.80 |
| Brazil (SC) | SI 444/15 | 2015 | Food | Pork filet | GCA_015526385.1 | PDS000018462.80 |
| Brazil (SC) | SI 447/15 | 2015 | Food | Smoked and salted pork meat | GCA_015525665.1 | PDS000018462.80 |
| Brazil (SC) | SI 1809/15*,# | 2015 | Animal feed | Meat animal meal | GCA_015526085.1 | PDS000018462.80 |
| Brazil (SC) | SI 1816/15 | 2015 | Animal feed | Poultry viscera animal meal | GCA_015527645.1 | PDS000018462.80 |
| Brazil (SC) | SI 2280/15 | 2015 | Food | Chicken carcass | GCA_015527445.1 | PDS000018462.80 |
| Brazil (SC) | SI 2302/15 | 2015 | Environment | Cleaning wipe | GCA_015527305.1 | PDS000029248.42 |
| Brazil (SC) | SI 2370/15 | 2015 | Food | Carcass cleaning wipe | GCA_015527525.1 | PDS000029248.42 |
| Brazil (MG) | SI 2869/15 | 2015 | Food | Chicken upper leg | GCA_015527575.1 | PDS000074994.3 |
| Brazil (MG) | SI 3056/15 | 2015 | Food | Chicken carcass | GCA_015527355.1 | PDS000074994.3 |
| Brazil (SC) | SI 4764/15 | 2015 | Environment | Cleaning wipe | GCA_015527945.1 | PDS000018462.80 |
| Brazil (SC) | SI 5391/15 | 2015 | Environment | Disposable shoe cover | GCA_015527425.1 | PDS000020042.7 |
| Brazil (SC) | SI 5837/15*,# | 2015 | Environment | Disposable shoe cover | GCA_015526805.1 | PDS000026846.6 |
| Brazil (SC) | SI 5853/15*,# | 2015 | Environment | Disposable shoe cover | GCA_015598965.2 | PDS000020042.7 |
| Brazil (SC) | SI 5859/15 | 2015 | Environment | Disposable shoe cover | GCA_015528025.1 | PDS000020042.7 |
| Brazil (SC) | SI 5911/15 | 2015 | Environment | Cleaning wipe | GCA_015527665.1 | PDS000018462.80 |
| Brazil (SC) | SI 5912/15 | 2015 | Environment | Cleaning wipe | GCA_016436965.1 | PDS000018462.80 |
| Brazil (SC) | SI 5915/15 | 2015 | Environment | Cleaning wipe | GCA_016437765.1 | PDS000018462.80 |
| Brazil (SC) | SI 5923/15 | 2015 | Environment | Cleaning wipe | GCA_016437485.1 | PDS000018462.80 |
| Brazil (SC) | SI 220/16 | 2016 | Environment | Cleaning wipe | GCA_016437465.1 | PDS000018462.80 |
| Brazil (SC) | SI 3687/16 | 2016 | Food | Chicken carcass | GCA_016437445.1 | PDS000018462.80 |
| Brazil (SC) | SI 4447/16 | 2016 | Food | Pork sausage | GCA_016437565.1 | PDS000018462.80 |
| Brazil (SC) | SI 5946/16 | 2016 | Food | Pork rib | GCA_016211625.1 | PDS000018462.80 |
| Brazil (MA) | SI 6987/16*,# | 2016 | Human | Human feces | GCA_016230965.1 | PDS000140572.1 |
| Brazil (RS) | SI 7876/16 | 2016 | Human | Human feces | GCA_016220265.1 | PDS000018462.80 |
| Brazil (PR) | SI 11/17*,# | 2017 | Environment | Dragging swab | GCA_016224725.1 | PDS000028532.4 |
| Brazil (PR) | SI 23/17 | 2017 | Environment | Dragging swab | GCA_016222525.1 | PDS000028532.4 |
| Brazil (PR) | SI 238/17 | 2017 | Environment | Dragging swab | GCA_016222645.1 | PDS000029248.42 |
| Brazil (MG) | SI 872/17 | 2017 | Food | Chicken carcass | GCA_016220425.1 | PDS000078491.1 |
| Brazil (SP) | SI 1171/17* | 2017 | Environment | Soil | GCA_016217285.1 | – |
| Brazil (SP) | SI 1256/17*,# | 2017 | Environment | Soil | GCA_016222625.1 | – |
| Brazil (SC) | SI 2580/17* | 2017 | Human | Human feces | GCA_016438385.1 | PDS000016779.5 |
| Brazil (GO) | SI 2953/17 | 2017 | Human | Human fecal swab | GCA_016437405.1 | PDS000078459.1 |
| Brazil (GO) | SI 2954/17 | 2017 | Human | Human fecal swab | GCA_016437305.1 | PDS000078459.1 |
| Brazil (GO) | SI 3380/17* | 2017 | Human | Human fecal swab | GCA_016438725.1 | PDS000078459.1 |
| Brazil (MG) | SI 3877/17 | 2017 | Food | Chicken wings | GCA_016437385.1 | PDS000078491.1 |
| Brazil (SP) | SI 3906/17 | 2017 | Environment | Sieve residue | GCA_016437045.1 | PDS000018462.80 |
| Brazil (PR) | SI 4065/17 | 2017 | Human | Human feces | GCA_016436945.1 | PDS000018462.80 |
| Brazil (PR) | SI 4067/17 | 2017 | Human | Human feces | GCA_016437525.1 | PDS000018462.80 |
| Brazil (PR) | SI 4069/17 | 2017 | Human | Human blood | GCA_016437225.1 | PDS000074309.3 |
| Brazil (MG) | SI 52/18 | 2018 | Food | Chicken carcass | GCA_016437345.1 | PDS000078491.1 |
| Brazil (GO) | SI 331/18* | 2018 | Human | Human fecal swab | GCA_016436865.1 | – |
| Brazil (SC) | SI 623/18 | 2018 | Human | Human feces | GCA_016437505.1 | PDS000029248.42 |
| Brazil (MS) | SI 661/18*,# | 2018 | Human | Human feces | GCA_016438625.1 | PDS000078471.1 |
| Brazil (RS) | SI 942/18 | 2018 | Human | Human fecal swab | GCA_016437265.1 | PDS000018462.80 |
| Brazil (SC) | SI 1634/18 | 2018 | Food | Yellowtail amberjack fish meat | GCA_016436825.1 | PDS000029248.42 |
| Brazil (GO) | SI 2676/18*,# | 2018 | Animal | Avian reproductive matrix | GCA_016437245.1 | PDS000078491.1 |
| Australia | AUSMDU00032459*,# | 2019 | Human | Clinical | GCA_032723255.1 | PDS000027076.745 |
| Bolivia | SBO17 | 2015 | Environmental | Hospital | GCA_012223145.1 | PDS000029248.42 |
| Germany | 15-SA02526*,# | 2015 | Food | Food | GCA_010615385.1 | PDS000032463.111 |
| Germany | 17-SA00182*,# | 2016 | Animal | Animal | GCA_010614605.1 | PDS000003948.23 |
| Hungary | SIB16*,# | 2012 | Animal | Broiler feces | GCA_016944915.1 | PDS000077501.33 |
| Israel | 119944*,# | 2008 | Human | Stool | GCA_000506925.1 | PDS000032399.9 |
| Mexico | MPSPSA2193-1*,# | 2022 | Environmental | Dam | GCA_032351395.1 | PDS000108885.76 |
| Paraguay | ERS13618234 | 2020 | Human | Blood | GCA_026305245.1 | PDS000018462.80 |
| Peru | 3.591-2010*,# | 2010 | Food | Meat | GCA_005970285.1 | PDS000089910.508 |
| Russia | VGNKI000011*,# | 2017 | Animal feed | Chicken feed | GCA_008361015.1 | – |
| South Africa | 741581*,# | 2013 | Human | Stool | GCA_024369075.1 | PDS000032399.9 |
| Turkey | MET-S1-498*,# | 2012 | Food | Chicken meat | GCA_010937355.1 | PDS000091376.17 |
| United Kingdom | 528502 | 2018 | Food | Food | GCA_007269555.1 | PDS000026846.6 |
| United Kingdom | 279940 | 2016 | Human | Human | GCA_009520195.1 | PDS000016779.5 |
| United Kingdom | hPHE_193 | 2013 | Human | Human | GCA_018844535.1 | PDS000074308.3 |
| United States | PNUSAS339754 | 2023 | Human | Human | GCA_029442055.1 | PDS000140572.1 |
| United States | PNUSAS208452 | 2021 | Human | Human | GCA_019046105.1 | PDS000028532.4 |
| United States | PNUSAS082678 | 2019 | Human | Human | GCA_007620775.1 | PDS000075101.1 |
Notes.
±
The codes between parenthesis in the strains from Brazil represent the following states of the country: RS, Rio Grande do Sul; PR, Paraná; SC, Santa Catarina; SP, São Paulo; MG, Minas Gerais; MS, Mato Grosso do Sul; GO, Goiás; BA, Bahia; AL, Alagoas; PE, Pernambuco; MA, Maranhão.
*
Strains selected for the analysis of genome plasticity using Blast Ring Image Generator and gene synteny using Mauve.
#
Strains selected for the search of orthologous protein clusters using OrthoVenn2.
Data regarding the 80 Brazilian genomes are available in Vilela et al. (2021).