Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae

Kevin C. Ma, Tatum D. Mortimer, Marissa A. Duckett, Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó and Yonatan H. Grad ()
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Kevin C. Ma: Harvard T.H. Chan School of Public Health
Tatum D. Mortimer: Harvard T.H. Chan School of Public Health
Marissa A. Duckett: Harvard T.H. Chan School of Public Health
Allison L. Hicks: Harvard T.H. Chan School of Public Health
Nicole E. Wheeler: Wellcome Sanger Institute, Wellcome Genome Campus
Leonor Sánchez-Busó: Wellcome Sanger Institute, Wellcome Genome Campus
Yonatan H. Grad: Harvard T.H. Chan School of Public Health

Nature Communications, 2020, vol. 11, issue 1, 1-8

Abstract: Abstract The emergence of resistance to azithromycin complicates treatment of Neisseria gonorrhoeae, the etiologic agent of gonorrhea. Substantial azithromycin resistance remains unexplained after accounting for known resistance mutations. Bacterial genome-wide association studies (GWAS) can identify novel resistance genes but must control for genetic confounders while maintaining power. Here, we show that compared to single-locus GWAS, conducting GWAS conditioned on known resistance mutations reduces the number of false positives and identifies a G70D mutation in the RplD 50S ribosomal protein L4 as significantly associated with increased azithromycin resistance (p-value = 1.08 × 10−11). We experimentally confirm our GWAS results and demonstrate that RplD G70D and other macrolide binding site mutations are prevalent (present in 5.42% of 4850 isolates) and widespread (identified in 21/65 countries across two decades). Overall, our findings demonstrate the utility of conditional associations for improving the performance of microbial GWAS and advance our understanding of the genetic basis of macrolide resistance.

Date: 2020
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DOI: 10.1038/s41467-020-19250-6

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