Table 2

Kappa agreement values stratified by country and case/control status

OrganismaKappa agreement valueb for organisms detected in:Overall kappa value
The GambiaMaliKenyaBangladeshCasesControls
Aeromonas
    16S survey∗Micro0.12900.1806−0.02340.1014
    16S survey∗Illumina−0.0056−0.01960.4439−0.02310.18140.18590.1827
    Illumina∗Micro0.07350.02160.08160.0587
Campylobacter
    16S survey∗Micro0.08430.00600.13990.44820.22290.03560.1538
    16S survey∗Illumina0.58120.57220.53150.53380.59200.48460.5574
    16S survey∗Ibis0.0189−0.00960.02290.00000.00480.01910.0106
    Illumina∗Micro0.08640.03560.33630.54930.37150.17990.2711
    Ibis∗Micro−0.0059−0.00630.05810.03540.1023−0.00320.0421
    Ibis∗Illumina0.0083−0.01150.05170.06520.04020.01250.0271
Salmonella
    16S survey∗Micro0.15000.19310.2207−0.02780.2245−0.01770.1603
    16S survey∗Illumina0.02790.55880.5007−0.03860.31030.07750.2379
    16S survey∗Ibis0.03380.15630.09510.04460.1449−0.00410.0778
        Illumina∗Micro0.15770.39320.59030.53760.52460.12420.3691
    Ibis∗Micro0.03440.06250.09570.01280.14190.02520.0725
    Ibis∗Illumina−0.00620.41820.1589−0.01830.18700.00380.0855
Shigella spp.
    16S survey∗Micro0.10800.0280−0.01080.09210.00570.00020.0311
    16S survey∗Illumina0.03610.04990.03830.11670.0004−0.0190.0303
    16S survey∗Ibis0.33720.28570.21920.0770.27230.13450.2487
    Illumina∗Micro0.25190.14920.34580.56720.46460.19690.3835
    Ibis∗Micro0.16340.09220.14690.41290.22800.13250.2027
    Ibis∗Illumina0.51190.49040.50240.61120.55480.47900.5388
EPEC
    Illumina∗Micro0.06200.31550.47830.19700.31560.15730.2341
    Ibis∗Micro0.18580.21280.21640.33570.27780.18560.2247
    Ibis∗Illumina0.36920.68560.49910.22760.54380.32060.4278
ETEC
    Illumina∗Micro0.08300.12230.05200.07290.09640.06860.0811
    Ibis∗Micro0.05470.07320.07960.11730.08820.06370.0753
    Ibis∗Illumina0.56420.58840.61750.56960.56140.61650.5909
EAEC
    Illumina∗Micro0.00130.12800.02450.02160.01930.00760.0129
    Ibis∗Micro0.05650.02580.04390.07260.03020.06530.0514
    Ibis∗Illumina0.30640.32840.42790.43530.35230.38200.3689
  • a Micro, microbiology; 16S survey, 16S rRNA gene survey; Illumina, Illumina GoldenGate assay; Ibis, Ibis Universal Biosensor assay. ∗, pairs of methods were compared.

  • b Agreement: fair, 0.21 to 0.40 (underlined); moderate, >0.40 (bold). Cells without data indicate a zero cell count.