Table 1.
Different subtyping methods of Salmonella Typhimurium strains and respectively discriminatory index.
| Source | Number of strains | Serotype | Phenotype methods | DI (95% CI) | Genotype methods | DI (95% CI) | References | |
|---|---|---|---|---|---|---|---|---|
| Swine | 32 | Typhimurium DT104 | PP | 0.76 |
SpeI-PFGE Xbal-PFGE BlnI-PFGE 3enz.PFGE PP-SpeI-PFGE PP-XbaI-PFGE PP-BlnI-PFGE PP-3enz.PFGE RAPD (23L/OPB15/B) RAPD (12 primers) |
0.520 0.332 0.599 0.796 0.853 0.794 0.893 0.909 0.673 0.778 |
Malorny et al., 2001 | |
| Swine | 40 | Typhimurium | PT AMR |
0.628 0.579 |
AFLP Xbal-PFGE Rep PCR |
0.939 0.925 0.421 |
Gebreyes et al., 2006 | |
| Swine Asymptomatic (85) Swine Disease-associated (44) |
129 | Typhimurium DT 104 |
AMR | 0.77 0.80 |
Xbal-PFGE SpeI-PFGE Xbal-SpeI PFGE Xbal-PFGE SpeI-PFGE Xbal-SpeI PFGE |
0.87 0.89 0.96 0.72 0.85 0.93 |
Perron et al., 2007 | |
| Animals | 78 | 41 37 |
Typhimurium Non-DT 126 Typhimurium DT 126 |
– | – | 10-loci MLVA MAPLT 10-loci MLVA MAPLT |
0.913 0.880 0.829 0.405 |
Ross et al., 2009 |
| Egg | 54 | Typhimurium | – | – |
Xbal-PFGE SpeI-PFGE |
0.60 0.71 |
Rivoal et al., 2009 | |
| Human | 183 203 |
Typhimurium Typhimurium (closely related) |
– | – |
Xbal-PFGE 4-loci MLVA 5-loci MLVA 8-loci MLVA 16-loci MLVA Xbal-PFGE 4-loci MLVA 5-loci MLVA 8-loci MLVA 16-loci MLVA |
0.995 (0.992–0.998) 0.997 (0.995–0.999) 0.997 (0.996–0.999) 0.997 (0.996–0.999) 0.997 (0.996–0.999) 0.846 (0.825–0.866) 0.976 (0.966–0.985) 0.977 (0.968–0.986) 0.980 (0.972–0.988) 0.981 (0.973–0.989) |
Chiou et al., 2010 | |
| Human Bovine Human (120) Bovine (62) |
28 182 |
4,5,12:i:_ Typhimurium |
– | – | 4-loci MLVA Xbal-PFGE MLVA- PFGE PFGE-AMR 4-loci MLVA Xbal-PFGE MLVA- PFGE PFGE-AMR 4-loci MLVA Xbal-PFGE MLVA- PFGE PFGE-AMR |
0.910 (0.843–0.977) 0.833 (0.711–0.955) 0.971 (0.940–1.000) 0.844 (0.717–0.971) 0.994 (0.990–0.999) 0.975 (0.960–0.990) 0.997 (0.994–1.000) 0.990 (0.979–0.997) 0.976 (0.959–0.993) 0.938 (0.910–0.966) 0.992 (0.984–0.999) 0.980 (0.967–0.994) |
Hoelzer et al., 2010 | |
| Human outbreaks | 100 | DT 101 | – | – | STTR9 STTR5 STTR6 STTR10 STTR3 |
0.131 (0.044–0.219) 0.797 (0.757–0.836) 0.059 (0.000–0.122) 0.078 (0.005–0.150) 0.131 (0.044–0.219) |
Dyet et al., 2011 | |
| 37 |
DT 104 |
STTR9 STTR5 STTR6 STTR10 STTR3 |
0.000 (0.000–0.172) 0.653 (0.515–0.791) 0.849 (0.816–0.892) 0.885 (0.831–0.940) 0.200 (0.030–0.371) |
|||||
| 96 | DT 160 | STTR9 STTR5 STTR6 STTR10 STTR3 |
0.000 (0.000–0.073) 0.301 (0.194–0.409) 0.157 (0.059–0.256) 0.429 (0.376–0.607) 0.042 (0.000–0.096) |
|||||
| Swine | 301 | Typhimurium | PT AMR |
0.7651 0.7378 |
STTR10 STTR5 STTR6 STTR3 STTR9 |
0.875 (0.858–0.892) 0.868 (0.848–0.888) 0.875 (0.854–0.895) 0.558 (0.522–0.595) 0.538 (0.485–0.591) |
Prendergast et al., 2011 | |
| Cattle | 544 29 |
116 178 276 5 6 18 |
Typhimurium 4,5,12:i:_ |
– | – |
Xbal-PFGE 5-loci MLVA PFGE-MLVA Xbal-PFGE 5-loci MLVA PFGE-MLVA |
0.842 (0.813–0.871) 0.981 (0.977–0.985) 0.991 (0.989–0.993) 0.660 (0.466–0.854) 0.797 (0.681–0.913) 0.797 (0.681–0.913) |
Kurosawa et al., 2012 |
| Human | 50 5 |
Typhimurium MDR DT104 |
PT | 0.74 | CRISPR1 CRISPR2 Xbal-PFGE CRISPR1-2 CRISPR1-2 Xbal-PFGE 5-loci MLVA |
0.84 0.84 0.87 0.88 0.64 0.38 1 |
Fabre et al., 2012 | |
| Human | 1,415 | Typhimurium | AMR PP |
0.88 0.88 |
5loci-MLVA | 0.98 | Wuyts et al., 2013 | |
| Human | 86 | 45 37 |
Typhimurium | – | – |
Xbal-PFGE CRISPR-MVLST |
0.948 0.941 |
Shariat et al., 2013 |
| Human (63) Animal (119) Human (205) Animal (206) |
182 411 |
Typhimurium 4,[5],12:i:- |
– | – | STTR6 STTR5 STTR10 STTR3 STTR9 STTR6 STTR5 STTR10 STTR3 STTR9 |
0.87 (0.84–0.89) 0.82 (0.79–0.86) 0.60 (0.52–0.69) 0.51 (0.44–0.58) 0.37 (0.28–0.45) 0.78 (0.75–0.80) 0.72 (0.70–0.75) 0.06 (0.03–0.09) 0.13 (0.09–0.18) 0.02 (0.00–0.04) |
Barco et al., 2015 | |
| Chicken | 71 | Typhimurium | PP | 0.969 | Xbal-PFGE | 0.974 | Wang et al., 2015 | |
| Human | 375 | Typhimurium | PT | 0.749 |
Xbal-PFGE 5-loci MLVA |
0.829 0.867 |
Lienemann et al., 2015 | |
| Human (43) Food (49) |
92 | Typhimurium | – | – | 5-loci MLVA Xbal-PFGE ERIC |
0.976 0.993 0.983 |
Almeida et al., 2015 | |
| Health swine (22) Environment (5) Human (43) |
70 | Typhimurium | – | – | 5-loci MLVA Xbal-PFGE ERIC |
0.957 0.996 0.983 |
Almeida et al., 2016 | |
| Human (43) Food (49) |
92 | Typhimurium | – | – | CRISPR1-2 CRISPR-MVLST | 0.906 0.906 |
Almeida et al., 2017 | |
AFLP, Amplified fragment length polymorphism; CRISPR-MVLST, Clustered Regularly Interspaced Short Palindromic Repeats-multi-virulence locus sequence typing; ERIC, Enterobacterial repetitive intergenic consensus; MLVA, Multilocus variable-number tandem repeat analysis; MAPLT, multiple amplification of phage locus typing; PFGE, Pulsed-field gel electrophoresis; RAPD, Random amplification of polymorphic DNA; Rep PCR, Repetitive palindromic extragenic–PCR; DI, Simpson's diversity index; 95% CI, Confidence Interval, precision of the diversity index, expressed as 95%; PT, Phage typing; AMR, Antimicrobial Resistance Profile; PP, Plasmid profiling; MDR DT104, Multi drug resistance ST DT04.