NAT | Bacteria | Target | Sample type | Duration numeric (minutes) | Detection Limit (Unit) | Detection Limit | Sensitivity % | Specificity % | Reference |
RT-PCR | S. typhi | prg K | Blood | Not specified | Not reported | Not reported | 83.33 | 73.68 | |
Multiplex three colour RT-PCR | S. typhi, S. paratyphi A | STY0201, | Blood, Bone Marrow | ~100 (PCR only) | copies/ml | 250 | 42 | 100 | |
Multiplex three colour RT-PCR | S. paratyphi A | SSPA2308 | Blood | ~100 (PCR only) | copies/ml | 250 | 39 | 100 | |
Multiplex three colour RT-PCR | S.typhi | STY0201 | Bone Marrow | ~100 (PCR only) | Not reported | Not reported | 100 | 100 | |
Multiplex three colour RT-PCR | S. paratyphi A | SSPA2308 | Bone Marrow | ~100 (PCR only) | Not reported | Not reported | 100 | 100 | |
RT-PCR | S.typhi | clyA | Blood | 154 ± 15 | cfu/ml | 0.01 | 40 | 90 | |
RT-PCR | S. paratyphi A | clyA | Blood | 154 ± 15 | cfu/ml | 0.01 | 40 | 90 | |
RT-PCR | S.typhi | clyA | Blood | 154 ± 15 | Not reported | Not reported | Not reported | 96 | |
RT-PCR | S. paratyphi A | clyA | Blood | 154 ± 15 | Not reported | Not reported | Not reported | 96 | |
Multiplex PCR | S.typhi | rfb, tyv, vi, prt, H antigen typing, dT fermentation | Blood culture isolates | 30-60 (PCR only) | Not reported | Not reported | 100 | 100 | |
Multiplex PCR | S. paratyphi A | rfb, tyv, vi, prt, H antigen typing, dT fermentation | Blood culture isolates | 30-60 (PCR only) | Not reported | Not reported | 100 | 100 | |
Multiplex PCR | S. paratyphi B | rfb, tyv, vi, prt, H antigen typing, dT fermentation | Blood culture isolates | 30-60 (PCR only) | Not reported | Not reported | 100 | 100 | |
Multiplex PCR | S.typhi | fliC-d, tyv, prt, Via B | Bacterial strains | 75 (PCR only) | Not reported | Not reported | Not Reported | Not Reported | |
Multiplex PCR | S. paratyphi A | fliC-a, prt | Bacterial strains | 75 (PCR only) | Not reported | Not reported | Not Reported | Not Reported | |
PCR | S.typhi | STY0312, STY0313 to STY0316 | Blood | 210 (PCR only) | cfu/ml | 4 | 95 | Not Reported | |
PCR | S. paratyphi A | SPA2476 | Blood | 210 (PCR only) | cfu/ml | 4 | 95 | Not Reported | |
Nested PCR | S. typhi | fliC | Blood | 617 (PCR only) | cfu/ml | 0.01 | 100 | 97.3 | |
Nested PCR | S. typhi | H1-d | Blood | 137 (PCR only) | Not reported | Not reported | 92.8 | Not Reported | |
PCR | S. typhi | fliC-d | Blood | 1445 (PCR only) | Not reported | Not reported | Not Reported | Not Reported | |
Blood culture PCR | S. typhi | fliC-d | Blood | Not specified | cfu/ml | 0.75 | NA | NA | |
Nested multiplex PCR | S. typhi | fliC, tviA, tviB | Blood | 70 (PCR only) | cfu/ml | 5 | Not Reported | Not Reported | |
PCR | S. typhi | STY1599 | Blood | 107 (PCR only) | Not reported | Not reported | 89 | Not Reported | |
Multiplex PCR | S. typhi | invA, fliC | Blood | Not reported | Not reported | 100 | 86.49 | ||
Nested PCR | S. typhi | fliC | Urine | 117 (PCR only) | Not reported | Not reported | 95.5 | 100 | |
Nested PCR | S. typhi | fliC | Blood | 117 (PCR only) | Not reported | Not reported | 90.9 | 100 | Kumar et al., 2012 |
Nested PCR | S. typhi | fliC | Stool | 117 (PCR only) | Not reported | Not reported | 68.1 | 85 | Kumar et al., 2012 |
Nested PCR | S. typhi | fliC | Blood | 117 (PCR only) | Not reported | Not reported | Not Reported | 100 | |
MIOD | S. typhi | STY2879 | Blood | Not specified | cfu/ml | 5 | 100 | 100 | |
rtLAMP | S. typhi | STY1607, | Blood | cfu/ml | 3 | 100 | 100 | ||
rtLAMP | S. typhi | STY1607, | stool | cfu/ml | 3 | 100 | 100 | ||
Blood culture multiplex PCR | S. typhi | STY0201, SSPA2308 | Blood | 53 55.5 (only PCR) | cfu/reaction | 1 | 95 | 95 | |
Blood culture multiplex PCR | S. paratyphi | SSPA2308 | Blood | 53 55.5 (only PCR) | cfu/reaction | 1 | 95 | 95 | |
LAMP | S. typhi | STBHUCCB_38510 | Blood culture isolates | 62 (LAMP only) | cfu/reaction | 20 | 100 | 100 | |
Magneto-DNA nanoparticle system | S. typhi | staG, SPA2472, sopB, sipC | Blood | 210 | cfu/ml | 1 | NA | NA | |
Magneto-DNA nanoparticle system | S. paratyphi A | hsdR, sopB, sipC | Blood | 210 | cfu/ml | 1 | NA | NA | |
SMOL | S. typhi | STY2879 | Blood culture isolates | Not specified | cfu/ml | 5 | 100 | 100 | |
SMOL | S. paratyphi A | SPA2539 | Blood culture isolates | Not specified | cfu/ml | 5 | 100 | 100 | |
Enrichment Broth Culture-Multiplex PCR | Samonella serovars | invA, spvC | Stool | 92 (PCR only) | bacteria | 200 | Not Reported | Not Reported | |
PCR | S. Typhi | dH flagellin gene of S typhi. | Blood | Not specified | pg/DNA | 28 | 100 | 93.7 | |
Multiplex PCR | S. typhi | STY4220, stg, SSPAI, OmpC | Bacterial strains | 130 (PCR only) | pg/DNA | 1 | 100 | 100 | |
Multiplex PCR | S. typhi | STY4220, stg, SSPAI, OmpC | Bacterial strains | 130 (PCR only) | pg/DNA | 1 | 100 | 100 | |
Nested PCR | S. typhi | fliC | Blood | 210 (PCR only) | Not reported | Not reported | 84.5 | Not reported | |
Nested PCR | S.typhi | fliC | Urine | 210 (PCR only) | Not reported | Not reported | 46.9 | 70 | |
Nested PCR | S.typhi | fliC | Stool | 210 (PCR only) | Not reported | Not reported | 69.3 | 70 | |
PCR | S.typhi | fliC | Blood | Not specified | pg/DNA | 0.00891 | Not reported | 100 | |
Nested PCR | S.typhi | fliC | Blood | 95 (PCR only) | Not reported | Not reported | Not reported | Not reported | |
PCR | Salmonella sp. | hilA | Blood | 103 (PCR only) | cfu/ml | 10 | 100 | 100 | |
PCR | Salmonella sp. | hilA | Stool | 103 (PCR only) | cfu/ml | 400 | 97 | 100 | |
Nested PCR | S.typhi | staA | Blood | 117 (PCR only) | cfu/ml | 30000 | 92.7 | 100 | |
Nested PCR | S.typhi | staA | Stool | 117 (PCR only) | cfu/ml | 30000 | 62.2 | 100 | Pratap et al., 2013 |
Nested PCR | S.typhi | staA | Urine | 117 (PCR only) | cfu/ml | 30000 | 96.5 | 100 | Pratap et al., 2013 |
Nested PCR | S.typhi | staA | Gall bladder stone | 117 (PCR only) | Not reported | Not reported | 73.9 | 100 | Pratap et al., 2013 |
Nested PCR | S.typhi | staA | Gall bladder wall | 117 (PCR only) | Not reported | Not reported | 20.9 | 100 | Pratap et al., 2013 |
Nested PCR | S.typhi | staA | Carcinoma gallbladder tissue | 117 (PCR only) | Not reported | Not reported | 78.3 | 100 | Pratap et al., 2013 |
Nested PCR | S.typhi | staA | Bonemarrow specimen | 117 (PCR only) | Not reported | Not reported | 23.3 | 100 | Pratap et al., 2013 |
RT-PCR | S.typhi | h1d | Blood | Not specified | copies/ml | 3.9 | 100 | 100 | |
Nested PCR | S.typhi | fliC | Blood | Not specified | Inaccessible | Inaccessible | 88.7 | 100 | |
Nested PCR | S.typhi | fliC | Blood | 130 (PCR only) | Not reported | Not reported | 100 | 35.8 | |
RT-PCR | S.typhi | clyA | Blood | Not specified | cfu/ml | 0.01 | 40.1 | 91 | |
Nested PCR | S.typhi | fliC | Blood | ~175 (PCR only) | Not reported | Not reported | 100 | 76.9 | |
LAMP | S.typhi | STBHUCCB_38510 | Blood culture isolates | Not specified | cfu/reaction | 20 | 100 | 100 | |
LAMP | S.typhi | STBHUCCB_38510 | Blood culture isolates | Not specified | cfu/reaction | 20 | 100 | 97.1 | |
LAMP | S.typhi | STBHUCCB_38510 | Blood | Not specified | cfu/reaction | 20 | 10 | 98.3 | |
LAMP | S.typhi | STBHUCCB_38510 | Blood | Not specified | Not reported | Not reported | 38 | 83.3 | |
LAMP | S.typhi | STBHUCCB_38510 | Blood culture isolates | Not specified | Not reported | Not reported | Not reported | Not reported | |
LAMP | S.typhi | STBHUCCB_38510 | Blood culture isolates | Not specified | Not reported | Not reported | Not reported | Not reported | |
TAC | S.typhi | Not reported | Blood | Not specified | Not reported | Not reported | Not reported | Not reported | |
TAC | S.typhi | Not reported | Stool | Not specified | Not reported | Not reported | Not reported | Not reported | |
PCR | S.typhi | Not reported | Not reported | Not specified | Not reported | Not reported | Not reported | 100 | |
PCR | S.typhi | fliC-d | Blood cuture isolates | ~70 (PCR only) | Not reported | Not reported | 70 | 65 | |
PCR | S.typhi | fliC-d | Blood cuture isolates | 132 (PCR only) | copies/reaction | 30000 | NA | NA | |
RT-PCR | S.typhi | fliC-d | Blood cuture isolates | 132 (PCR only) | copies/reaction | 3 | NA | NA | |
Nested PCR | S.typhi | fliC-d | Blood cuture isolates | 132 (PCR only) | copies/reaction | 3 | NA | NA | |
RT-PCR | S.typhi | fliC-d | Blood | Not specified | Not reported | Not reported | 91.4 | 100 | |
Nested PCR | S.typhi | fliC-d | Blood | Not specified | Not reported | Not reported | 81.5 | 100 | |
Electrochemical DNA Biosensor | S.typhi | STM4497 | Stool | Not specified | nM DNA | 0.94 | NA | NA | |
PCR | S.typhi | STY0201 | Blood cuture isolates | 66 (PCR only) | Not reported | Not reported | 100 | 97.2 | |
PCR | S.typhi | STY0307 | Blood cuture isolates | 67 (PCR only) | pg/DNA | 1.28 | 100 | 100 | |
PCR | S.typhi | STY0322 | Blood cuture isolates | 68 (PCR only) | pg/DNA | 32 | 100 | 100 | |
PCR | S.typhi | STY0326 | Blood cuture isolates | 69 (PCR only) | pg/DNA | 6.4 | 100 | 100 | |
PCR | S.typhi | STY2020 | Blood cuture isolates | 70 (PCR only) | pg/DNA | 6.4 | 100 | 100 | |
PCR | S.typhi | STY2021 | Blood cuture isolates | 71 (PCR only) | pg/DNA | 6.4 | 100 | 100 | |
Metal nanoparticle assisted PCR | S.typhi | fliC | Blood culture isolates | Not specified | Not reported | Not reported | NA | NA |