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Table 1 AFB smear, culture, TB identification and DST methods for each clinical study

From: Performance of the G4 Xpert® MTB/RIF assay for the detection of Mycobacterium tuberculosis and rifampin resistance: a retrospective case-control study of analytical and clinical samples from high- and low-tuberculosis prevalence settings

Study number Geographical location/collection site Xpert MTB/RIF Assay Testing Site Specimen Used for Xpert MTB/RIF Assay Testinga Specimen Processing for Smear & Culture AFB Smear Method on Processed Sputuma Culture Methoda TB Identification Methoda DST Methoda
CS1 Peru NJMS Archived (Frozen) Raw Sputum NALC-NaOH ZN LJ and MGIT CapilliaTB-Neo LJ Proportions
South Africa, Vietnam, Bangladeshb,c NJMS Archived (Frozen) Raw Sputum NALC- NaOH ZN LJ and MGIT GenoType® MTBC MGIT SIRE
CS2 New York New York Archived (4 °C) Pellet NaOH ZN 7H10 and MGIT In house RT-PCR MB Proportions
CS3 New York New York Fresh Pellet NaOH ZN 7H10 and MGIT In house RT-PCR MB Proportionsd
California California Fresh Pellet NALC- NaOH AuRho 7H10 and MGIT AccuProbe MTBC MB Proportionsd
Florida Florida Fresh Pellet or Raw Sputum NALC-NaOH    AccuProbe MB Proportionsd
AuO + ZN LJ and MGIT AccuProbe MTBC
CS4 Tijuana, Mexico California Fresh Raw Sputum NALC-NaOH AuRho LJ and MGIT AccuProbe MTBCe MB Proportionse
  1. aZN Ziehl-Neelsen, AuRho Auramine Rhodamine, AuO Auramine O, Raw Sputum direct, not decontaminated/undigested, Pellet decontaminated/digested sediment, MB Middlebrook, LJ Lowenstein-Jensen, MGIT BD BBL™ MGIT™ Mycobacteria Growth Indicator Tube, OADC Enrichment, PANTA™ Antibiotic Mixture, (Becton, Dickinson and Company, Sparks, MD), AccuProbe MTBC Mycobacterium tuberculosis Complex Culture Identification Test (Hologic, Incorporated, Marlborough MA), MGIT SIRE BD BACTEC™ MGIT™ 960 SIRE Kits For the Antimycobacterial Susceptibility Testing of Mycobacterium tuberculosis, (Becton, Dickinson and Company, Sparks, MD), Capillia TB-Neo Capilia TB Test Kit (Tauns Laboratories, Numazu, Japan), PNB – p-nitrobenzoic acid, Genotype® MTBC GenoType® MTBC (Hain Lifescience GmbH, Nehren, Germany)
  2. bSpecimens were originally cultured and identified for MTB using the following methods: Capillia TB-Neo, Hain Genotype, Niacin + PNB5 at these sites: Unit for Clinical and Biomedical TB Research, South African Medical Research Council. Durban, South Africa, Pham Ngoc Thach Hospital Laboratory. Ho Chi Minh City, Vietnam, Bangladesh: International Centre for Diarrhoeal Disease Research, Bangladesh. Dhaka, Bangladesh. Raw frozen sputum specimens were available and sent to the National Reference Center (NRC) for Mycobacteria, Supranational Reference Laboratory (SRL) of WHO, Research Center Borstel - Leibniz Center for Medicine and Biosciences, Borstel Germany for culture confirmation and DST and when appropriate bi-directional sequencing
  3. cSamples were provided by the Foundation for Innovative Diagnostics (FIND) under their study protocol. FIND staff performed all of the data collection, monitoring and auditing of the study
  4. dNew York served as the central lab for DST testing and, when appropriate, for bi-directional sequencing
  5. eUniversity of Massachusetts Medical School served as the central lab for CS4 TB identification and DST testing