Comparison of Culture With Antibiogram to Next-Generation Sequencing Using Bacterial Isolates and Formalin-Fixed, Paraffin-Embedded Gastric Biopsies

• Published in: Gastroenterology (New York, N.Y. 1943) Vol. 161; no. 5; pp. 1433 - 1442.e2
• Main Authors: Hulten, Kristina G., Genta, Robert M., Kalfus, Ira N., Zhou, Yi, Zhang, Hongjun, Graham, David Y.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.11.2021
• Subjects: Anti-Bacterial Agents - therapeutic use; Bacterial Resistance; Biopsy; Culture; Drug Resistance, Bacterial; Fixatives; Formaldehyde; Formalin-Fixed Tissue; Gastric Mucosa - microbiology; Helicobacter Infections - diagnosis; Helicobacter Infections - microbiology; Helicobacter pylori; Helicobacter pylori - drug effects; Helicobacter pylori - genetics; Helicobacter pylori - isolation & purification; High-Throughput Nucleotide Sequencing; Humans; Microbial Sensitivity Tests; Next-Generation Sequencing; Paraffin Embedding; Ribotyping; Tissue Fixation; Helicobacter pylori; FFPE; NPV; MIC; PPV; PPI; Bacterial Resistance; NGS; Next-Generation Sequencing; Culture; Formalin-Fixed Tissue; PCR
• ISSN: 0016-5085; 1528-0012
• DOI: 10.1053/j.gastro.2021.07.012

The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics. Traditional antibiotic susceptibility testing is often not available for testing for Helicobacter pylori. This study compared one of the new techniques, next-generation sequencing, to traditional culture-based testing and found that there was good agreement for the commonly used antibiotics clarithromycin and levofloxacin.