Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing

Emergence of drug resistance in has resulted in a greater need for susceptibility-guided treatment. While alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding molecular mechanisms underlying resistance to other antimicrobials. Using isolates from 42 clinical specimens, we compared phenotypic and whole genome sequencing (WGS)-based detection of resistance. Phenotypic resistance correlated with the presence of alleles of (A2142G/A2143G) for clarithromycin (kappa 0.84, 95% CI: 0.67-1.0) and (N87I/N87K/D91Y/D91N/D91G/D99N) for levofloxacin (kappa 0.90, 95% CI: 0.77-1.0). Phenotypic resistance to amoxicillin in three isolates correlated with mutations in and/or within coding regions near known amoxicillin binding motifs. All isolates were phenotypically susceptible to tetracycline, although four bore a mutation in (A926G). For metronidazole, nonsense mutations and R16H substitutions in correlated with phenotypic resistance (kappa = 0.76, 95% CI: 0.56-0.96). Previously identified mutations in the rifampicin resistance-determining region (RRDR) were not present, but 14 novel mutations outside the RRDR were found in rifampicin resistant isolates. WGS also allowed for strain lineage determination, which may be important for future studies in associating precise MICs with specific resistance alleles. In summary, WGS allows for broad analyses of isolates and our findings support the use of WGS for detection of clarithromycin and levofloxacin resistance. Additional studies are warranted to better define mutations conferring resistance to amoxicillin, tetracycline, and rifampin, but combinatorial analyses for gene truncations and R16H mutations have utility for determining metronidazole resistance.