Script_diagnostic_tools.R.

Animal African trypanosomosis is an important vector-borne disease of livestock in sub-Saharan Africa. Pigs seem relatively tolerant to trypanosome infection and could act as a reservoir of trypanosomes affecting animals and humans. Our ability to reliably detect trypanosome infection in pigs depends on the performance of diagnostic tools, which is not well known. In pigs experimentally infected with Trypanosoma brucei brucei, we evaluated the performance of parasitological Buffy Coat Technique (BCT), two molecular (TBR and 5.8S PCR) and four serological tests (CATT, HAT Sero-K-Set rapid diagnostic test–RDT, indirect ELISA, immune trypanolysis). Most diagnostic tests showed high specificity, estimated at 100% (95% CI = 74–100%) with the exception of CATT and RDT whose specificity varied between 100% (95% CI = 74–100%) to 50% (95% CI = 7–93%) during the experiment. The sensitivity of each test fluctuated over the course of the infection. The percentage of positive BCT over the infection (30%) was lower than of positive PCR (56% and 62%, depending on primers). Among the serological tests, the percentage of positive tests was 97%, 96%, 86% and 84% for RDT, ELISA, immune trypanolysis and CATT, respectively. Fair agreement was observed between both molecular tests (κ = 0.36). Among the serological tests, the agreement between the ELISA and the RDT was substantial (κ = 0.65). Our results on the T.b. brucei infection model suggest that serological techniques are efficient in detecting the chronic phase of infection, PCR is able to detect positive samples several months after parasites inoculation while BCT becomes negative. BCT examination and RDT are useful to get a quick information in the field, and BCT can be used for treatment decision. ELISA appears most suited for epidemiological studies. The selection of diagnostic tests for trypanosomosis in pigs depends on the context, the objectives and the available resources.</div

diagnostic_PCR.csv.

Raw data for PCR tests. Columns header: Index (index line), Date: date of sampling; Group: group C for the control group, I for infected group; Pig: pig identifier; Test: molecular test (TBR PCR, 5.8S PCR); Result: result of the PCR test 0 for negative, 1 for positive; DPI: Date Post-Infection; Phase: pre_inf for before infection; inf for from infection; Status: healthy or infected status of pigs. (CSV)</p

diagnostic_Serologic.csv.

Raw data for serological tests. Columns header: Index (index line), Date: date of sampling; Group: group C for the control group, I for infected group; Pig: pig identifier; Test: serolgoical test (CATT, RDT, ELISA, TL LiTat1.6); Result: result of the serological test 0 for negative, 1 for positive; DPI: Date Post-Infection; Phase: pre_inf for before infection; inf for from infection; Status: healthy or infected status of pigs. (CSV)</p

Specificity and sensitivity of different diagnostic tests.

Specificity and the percentage of negative tests were estimated during the experiment in non-infected animals (all animals before infection and in the control group), the first one was assessed overtime and the last one averaged on all the samples. Sensitivity and the percentage of positive tests were estimated during the experiment in the infected group from 7 DPI, the first one was assessed overtime and the last one averaged on all the samples. Regarding specificity and sensitivity, minimal and maximal values observed during the experiment are shown on the first and second lines respectively, if they are different. 95% confidence intervals are indicated in brackets.</p

Consensus intensity and intensity scores given by 3 readers to the test lines in HAT Sero-<i>K</i>-Set and SD Bioline HAT (line 1 and 2).

<p>In case of a negative (N) consensus intensity the test line intensity was considered negative, the test line was interpreted positive if the consensus test line intensity was faint or stronger. N: negative, F: faint, W: weak, M: Medium, S: strong.</p><p>Consensus intensity and intensity scores given by 3 readers to the test lines in HAT Sero-<i>K</i>-Set and SD Bioline HAT (line 1 and 2).</p

Number of positive test results combining RDTs with trypanolysis, by type of study participant.

<p>Number of positive test results combining RDTs with trypanolysis, by type of study participant.</p

Individual result of all pigs to the four serological tests (ELISA, TL LiTat 1.6, RDT and CATT).

Large points: positive test; small points: negative test. Pigs of the infected group are indicated in red, pigs of the control group in green. DPI: days post infection.</p

Number of positive test results by type of study participant.

<p>Number of positive test results by type of study participant.</p