Background: Childhood tuberculosis accounts for about 10% of estimated TB cases in the world. Despite advances in diagnostics, childhood TB remains a challenge. We evaluated pooling method and testing with GeneXpert MTB/RIF in southern Ethiopia. Methods: This is a cross-sectional study in presumptive TB children < 15 years. Structured questionnaire was used to collect socio-demographic and clinical data. Two sputum or gastric aspirate sample were collected and examined by ZN and Xpert MTB/RIF for 1st, 2nd and pooled samples. Results: Of 340 presumptive TB cases enrolled, 96 and 244 children submitted gastric aspirate and sputum samples respectively. Of 1020 samples collected (282 gastric aspirate and 738 sputum samples), 38 (3.7%) were positive by Xpert (10 (3.5%) from gastric aspirate and 28 (3.8%) from sputum sample). Similarly, 8 (1.2%) of sputum samples were positive by ZN but none from gastric aspirate. Of 244 children who submitted sputum samples, 3 (1.2%) were bacteriologically positive compared to 12 (4.9%) by Xpert. Of 96 children who submitted gastric aspirate samples, none were positive by ZN while 5 (5.2%) were positive by Xpert. Of bacteriologically confirmed TB cases 0.9% was by ZN and 4.7% by Xpert, an increase of 3.8%. Pooled testing increased positivity by 0.3% for ZN and 1.5% by Xpert compared to the 1st sample. Conclusions: Xpert MTB/RIF testing increases yield compared to ZN testing for gastric aspirate samples. The same-day approach and pooling samples improves efficient use of cartridge, reduce the number of visits for seeking diagnosis and save resources.
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