Background
Results
cgMLST
Phylogenetic tree (ggTree) and orthologous protein clusters analysis
Groups | Biological processes (protein orthologous clusters) |
---|---|
LT2—STm07, STm12, STm16, STm19, STm20, STm21, STm22, STm24, STm25, STm26 and STm27 (Comparison 1) | Transposition (DNA-mediated), transposition, viral procapsid maturation, virion attachment to host cell, viral genome integration into host DNA, trehalose transport, DNA replication, viral capsid assembly, DNA binding, histidine catabolic process to glutamate and formate |
LT2—STm01 and STm08 (Comparison 2) | Transposition (DNA-mediated), transposition, viral genome integration into host DNA, virion attachment to host cell, DNA replication, trehalose transport, DNA replication initiation, viral procapsid maturation, formate oxidation, DNA binding |
LT2—STm04, STm09, STm10, STm11, STm13 and STm14 (Comparison 3) | Transposition (DNA-mediated), transposition, viral genome integration into host DNA, trehalose transport, histidine catabolic process to glutamate and formate |
LT2—STm02, STm03 and STm05 (Comparison 4) | Transposition (DNA-mediated), transposition, viral procapsid maturation, viral genome integration into host DNA, trehalose transport, DNA replication, response to mercury ion, mercury ion transmembrane transporter activity, formate oxidation, DNA restriction-modification system |
14028S—13,609/06, 6346/10, 9109/10, 9479/10, 948/12, 1103/12 and 1104/12 (Comparison 5) | Transposition (DNA-mediated), transposition, formate oxidation, trehalose transport, cell adhesion, DNA binding |
D23580—STm29, STm30, STm34, STm35, STm37, STm39, STm40, STm44 and STm47 (Comparison 6) | Transposition (DNA-mediated), transposition, formate oxidation, trehalose transport, lyase activity, viral tail assembly, cell adhesion |
D23580—STm29, STm30, STm34, STm35, STm36, STm37, STm39, STm40, STm44, STm47 and 3057/10 (Comparison 7) | Transposition (DNA-mediated), formate oxidation, trehalose transport, lyase activity, cell adhesion, metal ion binding |
snpTree
MLST
Prophages detection
Prophages | Humans (n = 43) (%) | Foods (n = 48) (%) | Swine (n = 26) (%) |
---|---|---|---|
Aeromo_phiO18P | Not detected | 01/48 (2.1) | 01/26 (3.8) |
Burkho_BcepMu | Not detected | 01/48 (2.1) | Not detected |
Edward_GF_2 | 02/43 (4.6) | 06/48 (12.5) | Not detected |
Entero_186 | 01/43 (2.3) | 01/48 (2.1) | 01/26 (3.8) |
Entero_BP_4795 | 01/43 (2.3) | Not detected | Not detected |
Entero_fiAA91_ss | Not detected | Not detected | 06/26 (23.1) |
Entero_mEp235 | Not detected | Not detected | 01/26 (3.8) |
Entero_N15 | 03/43 (7) | Not detected | Not detected |
Entero_P22 | 03/43 (7) | Not detected | Not detected |
Entero_Tyrion | 01/43 (2.3) | Not detected | Not detected |
Entero_UAB_Phi20 | 05/43 (11.6) | Not detected | Not detected |
Escher_RCS47 | Not detected | Not detected | 02/26 (7.7) |
Gifsy_1 | 10/43 (23) | 34/48 (71) | 19/26 (73) |
Gifsy_2 | 37/43 (86) | 33/48 (68.7) | 09/26 (34.6) |
Haemop_HP1 | 18/43 (41.9) | Not detected | 03/26 (11.5) |
Salmon_118970_sal3 | 25/43 (58.1) | 15/48 (31.2) | 06/26 (23.1) |
Salmon_118970_sal4 | 01/43 (2.3) | Not detected | Not detected |
Salmon_epsilon34 | Not detected | Not detected | 01/26 (3.8) |
Salmon_Fels_1 | Not detected | 01/48 (2.1) | Not detected |
Salmon_Fels_2 | 04/43 (9.3) | 01/48 (2.1) | 04/26 (15.4) |
Salmon_RE_2010 | 07/43 (16.3) | 02/48 (4.2) | 01/26 (3.8) |
Salmon_SEN34 | Not detected | Not detected | 01/26 (3.8) |
Salmon_SP_004 | 01/43 (2.3) | 04/48 (8.3) | 01/26 (3.8) |
Salmon_SPN1S | 17/43 (39.5) | Not detected | Not detected |
Salmon_SPN3UB | Not detected | Not detected | 02/26 (7.7) |
Salmon_SPN9CC | Not detected | 03/48 (6.2) | Not detected |
Salmon_SSU5 | Not detected | 02/48 (4.2) | 01/26 (3.8) |
Salmon_ST64T | 01/43 (2.3) | 02/48 (4.2) | Not detected |
Shigel_Sfll | Not detected | 01/48 (2.1) | 01/26 (3.8) |
Efflux pumps
Genes | Humans (n = 43) (query cover %) (identity %) | Food (n = 48) (query cover %) (identity %) | Swine (n = 26) (query cover %) (identity %) |
---|---|---|---|
acrA
| 43/43 (100) (91.69) | 48/48 (100) (91.69) | 26/26 (100) (91.69) |
acrB
| 43/43 (100) (94.66) | 48/48 (100) (94.66) | 26/26 (100) (94.66) |
macA
| 43/43 (100) (88.65–88.84) | 48/48 (100) (88.65–88.84) | 26/26 (100) (88.39–88.84) |
macB
| 43/43 (100) (88.60–88.70) | 48/48 (100) (88.70) | 26/26 (100) (88.29–88.70) |
mdtK
| 43/43 (100) (99.79) | 48/48 (100) (99.79) | 26/26 (100) (99.16–99.79) |
emrA
| 43/43 (100) (99.92–100) | 48/48 (100) (100) | 26/26 (72–100) (98.40–100) |
emrB
| 43/43 (100) (95.7) | 48/48 (100) (95.7) | 26/26 (99.80–100) (95.7) |
emrR
| 43/43 (100) (93.14) | 48/48 (100) (93.14) | 26/26 (100) (93.14) |
tolC
| 43/43 (99–100) (100) | 48/48 (100) (100) | 26/26 (100) (98.78–100) |
mdsA
| 43/43 (100) (99.75–100) | 48/48 (100) (100) | 18/26 (100) (100) |
mdsB
| 43/43 (100) (100) | 48/48 (100) (100) | 18/26 (100) (100) |
mdfA
| 18/43 (100) (87.93) | 39/48 (100) (87.93) | 26/26 (100) (87.93) |
cmlA1
| Not detected | Not detected | 05/26 (100) (99.76) |
Discussion
Conclusions
Methods
Bacterial strains
CFSAN nº | Isolate name | Source | State | Year of isolation | Sequence type (ST) |
---|---|---|---|---|---|
CFSAN033848 | STm01 | Human feces | SP | 1983 | 19 |
CFSAN033849 | STm02 | Human feces | SP | 1983 | 19 |
CFSAN033850 | STm03 | Human feces | SP | 1983 | 19 |
CFSAN033851 | STm04 | Human feces | SP | 1983 | 19 |
CFSAN033852 | STm05 | Human feces | SP | 1983 | 19 |
CFSAN033853 | STm06 | Human feces | SP | 1983 | 1649 |
CFSAN033854 | STm07 | Human feces | SP | 1983 | 19 |
CFSAN033855 | STm08 | Human feces | SP | 1983 | 19 |
CFSAN033856 | STm09 | Human feces | SP | 1984 | 19 |
CFSAN033857 | STm10 | Human feces | SP | 1984 | 19 |
CFSAN033858 | STm11 | Human feces | SP | 1984 | 19 |
CFSAN033859 | STm12 | Human feces | SP | 1984 | 19 |
CFSAN033860 | STm13 | Human feces | SP | 1984 | 19 |
CFSAN033861 | STm14 | Human feces | SP | 1984 | 19 |
CFSAN033862 | STm15 | Human feces | SP | 1985 | 3343 |
CFSAN033863 | STm16 | Human feces | SP | 1985 | 19 |
CFSAN033864 | STm17 | Human feces | SP | 1985 | 19 |
CFSAN033865 | STm18 | Human feces | SP | 1985 | 19 |
CFSAN033866 | STm19 | Human feces | SP | 1986 | 19 |
CFSAN033867 | STm20 | Human feces | SP | 1986 | 19 |
CFSAN033868 | STm21 | Human feces | SP | 1986 | 19 |
CFSAN033869 | STm22 | Human feces | SP | 1986 | 19 |
CFSAN033870 | STm23 | Human feces | SP | 1986 | 19 |
CFSAN033871 | STm24 | Human feces | SP | 1986 | 19 |
CFSAN033872 | STm25 | Human feces | SP | 1986 | 19 |
CFSAN033873 | STm26 | Human feces | SP | 1986 | 19 |
CFSAN033874 | STm27 | Human feces | SP | 1986 | 19 |
CFSAN033875 | STm28 | Human feces | SP | 1988 | 3343 |
CFSAN033876 | STm29 | Human feces | SP | 1989 | 313 |
CFSAN033877 | STm30 | Human feces | SP | 1990 | 313 |
CFSAN033878 | STm31 | Human feces | SP | 1991 | 19 |
CFSAN033879 | STm32 | Human feces | SP | 1992 | 19 |
CFSAN033880 | STm33 | Human feces | SP | 1992 | 19 |
CFSAN033881 | STm34 | Human feces | SP | 1993 | 313 |
CFSAN033882 | STm35 | Human feces | SP | 1995 | 313 |
CFSAN033883 | STm36 | Cold chicken | SP | 1995 | 19 |
CFSAN033884 | STm37 | Raw pork sausage | SP | 1996 | 313 |
CFSAN033885 | STm38 | Human feces | SP | 1997 | 19 |
CFSAN033886 | STm39 | Human feces | SP | 1998 | 313 |
CFSAN033887 | STm40 | Lettuce | SP | 1998 | 313 |
CFSAN033888 | STm41 | Raw kafta | SP | 1998 | 19 |
CFSAN033889 | STm42 | Human feces | SP | 1999 | 19 |
CFSAN033890 | STm43 | Human feces | SP | 2000 | 19 |
CFSAN033891 | STm44 | Blood | SP | 2000 | 313 |
CFSAN033892 | STm45 | Raw pork sausage | SP | 2000 | 19 |
CFSAN033893 | STm46 | Raw tuscan sausage | SP | 2002 | 19 |
CFSAN033894 | STm47 | Human feces | SP | 2003 | 313 |
CFSAN033895 | STm48 | Brain abscess | SP | 2005 | 19 |
CFSAN033896 | STm49 | Human feces | SP | 2010 | 19 |
CFSAN033897 | 702/99 | Final product | SC | 1999 | 19 |
CFSAN033898 | 12,288/06 | Swine | SC | 2006 | 19 |
CFSAN033899 | 12,278/06 | Swine | SC | 2006 | 19 |
CFSAN033900 | 12,290/06 | Swine | SC | 2006 | 19 |
CFSAN033901 | 12,268/06 | Swine | SC | 2006 | 19 |
CFSAN033902 | 12,381/06 | Swine | SC | 2006 | 19 |
CFSAN033903 | 5936/06 | Cold chicken | SC | 2006 | 19 |
CFSAN033904 | 5937/06 | Cold chicken | SC | 2006 | 19 |
CFSAN033905 | 5934/06 | Swine | SC | 2006 | 19 |
CFSAN033906 | 5961/06 | Swine | SC | 2006 | 19 |
CFSAN033907 | 5962/06 | Swine | SC | 2006 | 19 |
CFSAN033908 | 5929/06 | Poultry | SC | 2006 | 19 |
CFSAN033909 | 13,609/06 | Poultry | SC | 2006 | 19 |
CFSAN033910 | 3848/08 | Food | SC | 2008 | 19 |
CFSAN033911 | 16,238/09 | Ready-to-eat dish | MS | 2009 | 19 |
CFSAN033912 | 16,239/09 | Ready-to-eat dish | MS | 2009 | 19 |
CFSAN033913 | 16,240/09 | Ready-to-eat dish | MS | 2009 | 19 |
CFSAN033914 | 16,202/09 | Industrialized product | RS | 2009 | 19 |
CFSAN033915 | 16,251/09 | Industrialized product | GO | 2009 | 19 |
CFSAN033916 | 16,273/09 | Industrialized product | GO | 2009 | 19 |
CFSAN033917 | 17,307/09 | Industrialized product | – | 2009 | 19 |
CFSAN033918 | 9461/10 | In natura meat | SC | 2010 | 19 |
CFSAN033919 | 9479/10 | In natura meat | SC | 2010 | 19 |
CFSAN033920 | 7032/10 | Poultry | PR | 2010 | 19 |
CFSAN033921 | 3057/10 | Frozen chicken carcass | PR | 2010 | 19 |
CFSAN033922 | 6346/10 | Chicken | SP | 2010 | 19 |
CFSAN033923 | 5635/10 | Unknown | RS | 2010 | 19 |
CFSAN033924 | 9109/10 | Swine | PR | 2010 | 19 |
CFSAN033925 | 426/10 | Chicken | SC | 2010 | 19 |
CFSAN033926 | 447/10 | Chicken | SC | 2010 | 19 |
CFSAN033927 | 2452/11 | Frozen chicken carcass | SP | 2011 | 19 |
CFSAN033928 | 6709/11 | Cold chicken | RS | 2011 | 19 |
CFSAN033929 | 948/12 | Raw salad | BA | 2012 | 19 |
CFSAN033930 | 1103/12 | Swine (homemade salami) | RS | 2012 | 19 |
CFSAN033931 | 1104/12 | Swine (homemade salami) | RS | 2012 | 19 |
CFSAN033932 | 3330/12 | Roast beef | SC | 2012 | 19 |
CFSAN033933 | 994/13 | Final product sales (animal origin) | SP | 2013 | 19 |
CFSAN033934 | 374/13 | Final product sales (animal origin) | SC | 2013 | 19 |
CFSAN033935 | 465/13 | Final product sales (animal origin) | SP | 2013 | 19 |
CFSAN033937 | 622/13 | Final product sales (animal origin) | SC | 2013 | 1921 |
CFSAN033938 | 583/13 | Final product sales (animal origin) | SC | 2013 | 19 |
CFSAN033939 | 623/13 | Final product sales (animal origin) | SC | 2013 | 1921 |
CFSAN068033 | 739 | Mesenteric lymph node | SC | 2000 | 19 |
CFSAN034668 | 1030 | Swine feces | SC | 2003 | 19 |
CFSAN068028 | 22 | Inguinal lymph node | SC | 2004 | 516 |
CFSAN034669 | 29 | Swine feces | SC | 2004 | 639 |
CFSAN034670 | 51 | Swab swine carcass | SC | 2004 | 14 |
CFSAN034671 | 68 | Swine feces | SC | 2004 | 14 |
CFSAN068029 | 58 | Swine faeces | SC | 2004 | 19 |
CFSAN068040 | 1212 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068043 | 1218 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068044 | 1220 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068045 | 1221 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068046 | 1222 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068047 | 1224 | Mesenteric lymph node | SC | 2005 | 19 |
CFSAN068031 | 343 | Herd environment | SC | 2006 | 19 |
CFSAN068042 | 1214 | Herd environment | SC | 2006 | 19 |
CFSAN068041 | 1213 | Herd environment | SC | 2007 | 19 |
CFSAN068030 | 338 | Swine faeces | SC | 2008 | 19 |
CFSAN068032 | 345 | Swine faeces | SC | 2008 | 19 |
CFSAN068034 | 812 | Swine urine | SC | 2011 | 1921 |
CFSAN068035 | 824 | Swine urine | SC | 2011 | 1921 |
CFSAN068036 | 1206 | Swab drag | SC | 2011 | 19 |
CFSAN034672 | 804 | Swine urine | SC | 2011 | 1921 |
CFSAN034673 | 1209 | Swab feeder | SC | 2011 | Unknown |
CFSAN068037 | 1207 | Swab carcass | SC | 2012 | 19 |
CFSAN068038 | 1210 | Swab carcass | SC | 2012 | 64 |
CFSAN068039 | 1211 | Swab carcass | SC | 2012 | 64 |