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Table 1 Comparison of conventional methods and Sanger sequencing for the detection of individual DPs

From: Clinical application of a multiplex genetic pathogen detection system remaps the aetiology of diarrhoeal infections in Shanghai

Bacteria Culture Sequencing Sensitivity Specificity PPV NPV Accuracy
+
Vibrio + 23 0 0.575 1.000 1.000 0.971 0.972
17 573
S. typhimurium + 17 0 0.415 1.000 1.000 0.960 0.961
24 572
S. enteritis + 2 0 0.333 1.000 1.000 0.993 0.993
4 607
Shigella + 3 0 0.333 1.000 1.000 0.990 0.990
6 604
C. difficile + 6 0 0.214 1.000 1.000 0.964 0.964
22 585
C. jejuni + 12 0 0.267 1.000 1.000 0.946 0.947
33 578
Y. enterocolitica + 0 0 0.000 1.000 0.998 0.998
1 612
EPEC + 49 0 0.325 1.000 1.000 0.819 0.834
102 462
ETEC + 11 0 0.379 1.000 1.000 0.970 0.971
18 584
EAEC + 8 0 0.296 1.000 1.000 0.969 0.969
19 586
EIEC + 2 0 0.250 1.000 1.000 0.990 0.990
6 605
EHEC + 0 0 0.000 1.000 0.993 0.993
4 609
E. coli O157 + 1 0 0.167 1.000 1.000 0.992 0.992
5 607
Viruses Singleplex real-time PCR
 Norovirus + 31 2 1.000 0.997 0.939 1.000 0.997
0 580
 Rotavirus + 55 3 1.000 0.995 0.948 1.000 0.995
0 555
 Adenovirus + 8 1 1.000 0.998 0.888 1.000 0.995
0 604
 Astrovirus + 4 0 1.000 1.000 1.000 1.000 0.997
0 609
  1. Outcomes of conventional detection methods: the results of culture-based methods for bacteria and singleplex real-time PCR for viruses were compared to those of Sanger sequencing. Sensitivity = TP/(TP + FN) × 100, Specificity = TN/(TN + FP) × 100; PPV and NPV were calculated as follows: PPV = TP/P, NPV = TN/N. Notably, the sensitivity of the culture-based method was very low and highly variable for various species, while the outcomes of PCR-based detection of viruses were consistent with the sequencing method
  2. DP-HMGS diarrheal pathogens high-throughput multiple genetic detection system, PPV positive predict value, NPV negative predict value