Diagnostic role of stool TB-PCR in suspected tuberculous colitis patient at Dr Cipto Mangunkusumo National Central General Hospital: a cross-sectional study.

Introduction: the signs and symptoms of tuberculous (TB) colitis were similar with other diseases, such as inflammatory bowel disease. Therefore, finding the diagnostic modality to help differentiate TB colitis with other diseases was a challenge. In this study we aimed to find the proportion of positive stool TB-PCR in suspected TB colitis subjects and also the diagnostic value of the stool TB-PCR if compared to colonoscopy, histopathology and clinical evaluation. Methods: a cross-sectional study was done on subjects suspected to have TB colitis who undergone colonoscopy and histopathology examination between February-April 2019. Stool samples from those subjects were collected and extracted with the QIAamp® Fast Stool DNA Mini Kit. The TB-PCR was done using artus® M. tuberculosis RG PCR kit, which targeted on 16s rRNA gene. The results of stool TB-PCR then were compared with the combination of colonoscopy, histopathology and clinical evaluation as the gold standard. Results: from sixty subjects who were recruited, there were 26/60 (43.3%) subjects with positive stool TB-PC. It was consisted of 7/8 TB colitis subjects and 19/52 non-TB colitis subjects. The diagnostic value of the stool TB-PCR was: sensitivity 87.5%, specificity 63.5%, positive predictive value 26.9% and negative predictive value 97.1%. Conclusion: stool TB-PCR has good sensitivity but low specificity for diagnosing TB colitis. Therefore, stool TB-PCR could be utilized as a screening test for TB colitis.

Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia.

Background: Thus far, Indonesia has recorded over 4,000,000 confirmed COVID-19 cases and 144,000 fatalities; 12.8% of cases have been in children under 18 years. Whole-genome viral sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been demonstrated to help differentiate hospital-acquired infection from community-acquired coronavirus disease 2019 (COVID-19) infection. Our study highlighted the use of WGS to investigate the origin of infection among pediatric oncology patients in Jakarta. The aim of our study was to evaluate clinical and laboratory characteristics and also the efficacy of using WGS to confirm hospital-acquired COVID-19 infection in a cluster of immunocompromised children within a single ward of a tertiary hospital in metropolitan Jakarta based on quasispecies, viral load, and admission dates. Method: Real-time reverse-transcription polymerase chain reaction (RT-PCR) from nasopharyngeal (NP) swabs was used to diagnose the patients and also guardians and healthcare workers (HCWs) in the ward, followed by WGS of RT-PCR positive cases to establish their phylogenetic relationships. Result: Using WGS, we showed that SARS-CoV-2 transmission in a cluster of children with underlying malignancy was characterized by high similarity of whole virus genome, which suggests nosocomial transmission.