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J Clin Microbiol. 2020 Feb 24;58(3). pii: e01591-19. doi: 10.1128/JCM.01591-19. Print 2020 Feb 24.

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

Author information

1
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.
2
Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA.
3
Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, Virginia, USA.
4
Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John's, New Foundland and Labrador, Canada.
5
Department of Medicine, Division of Gastroenterology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA.
6
Department of Pediatrics, Division of Gastroenterology and Nutrition, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA.
7
Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA wszymcza@montefiore.org.
#
Contributed equally

Abstract

The emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using H. pylori 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 23S rRNA (A2142G/A2143G) for clarithromycin (kappa coefficient, 0.84; 95% confidence interval [CI], 0.67 to 1.0) and gyrA (N87I/N87K/D91Y/D91N/D91G/D99N) for levofloxacin (kappa coefficient, 0.90; 95% CI, 0.77 to 1.0). Phenotypic resistance to amoxicillin in three isolates correlated with mutations in pbp1, pbp2, and/or pbp3 within coding regions near known amoxicillin binding motifs. All isolates were phenotypically susceptible to tetracycline, although four bore a mutation in 16S rRNA (A926G). For metronidazole, nonsense mutations and R16H substitutions in rdxA correlated with phenotypic resistance (kappa coefficient, 0.76; 95% CI, 0.56 to 0.96). Previously identified mutations in the rpoB rifampin resistance-determining region (RRDR) were not present, but 14 novel mutations outside the RRDR were found in rifampin-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 H. pylori isolates, and our findings support the use of WGS for the 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 rdxA gene truncations and R16H mutations have utility for determining metronidazole resistance.

KEYWORDS:

Helicobacter pylori ; amoxicillin; antimicrobial susceptibility testing; clarithromycin; levofloxacin; lineage; metronidazole; rifampin; tetracyclines; whole-genome sequencing

PMID:
31801839
PMCID:
PMC7041580
[Available on 2020-08-24]
DOI:
10.1128/JCM.01591-19

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