Genomic resistance determinants imperfectly explain phenotypic resistance to ciprofloxacin and azithromycin among Campylobacter spp. isolated from pediatric patients

Authors: SCHIAFFINO, FRANCESCA - Universidad Peruana; Parker, Craig; PAREDES-OLORTEGUI, MARIBEL - Prisma Charitable Association; PASCOE, BEN - University Of Oxford; VILLANUEVA-MANZANARE, KATIA - Prisma Charitable Association; GARCIA-BARDALES, PAUL - Prisma Charitable Association; MOURKAS, EVANGELOS - University Of Oxford; Huynh, Steven; PENATARO-YORI, PABLO - University Of Virginia; ROMAINA-CACHIQUE, LUCERO - Prisma Charitable Association; GRAY, HANNAH - Johns Hopkins University; SALVATIERRA, GUILLERMO - Universidad Peruana; DIAZ-VASQUEZ, ARTUR - Prisma Charitable Association; SILVA-DELGADO, HERMANN - National University Of The Peruvian Amazon; SHEPPARD, SAMUEL - University Of Oxford; COOPER, KERRY - University Of Arizona; KOSEK, MARGARET - University Of Virginia

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2024
Publication Date: 1/24/2024
Citation: Schiaffino, F., Parker, C.T., Paredes-Olortegui, M., Pascoe, B., Villanueva-Manzanare, K., Garcia-Bardales, P.F., Mourkas, E., Huynh, S., Penataro-Yori, P., Romaina-Cachique, L., Gray, H.K., Salvatierra, G., Diaz-Vasquez, A.N., Silva-Delgado, H., Sheppard, S.K., Cooper, K.K., Kosek, M.N. 2024. Genomic resistance determinants imperfectly explain phenotypic resistance to ciprofloxacin and azithromycin among Campylobacter spp. isolated from pediatric patients. Journal of Global Antimicrobial Resistance. 36:309-318. https://doi.org/10.1016/j.jgar.2024.01.009.
DOI: https://doi.org/10.1016/j.jgar.2024.01.009

Interpretive Summary: Antimicrobial resistant (AMR) Campylobacter is a rapidly emerging health threat in Peru and other low- and middle-income countries (LMIC) where Campylobacter is the leading cause of bacterial foodborne illness and also associated with deficits in early childhood development. With the increase in whole genome sequencing, AMR genotyping has become a possibly affordable option for tracking AMR among Campylobacter as compared to phenotypic assays. Using a collection of Campylobacter jejuni and C. coli isolates from infants in Amazonian Peru, we evaluated the accuracy of existing AMR genotypic databases in predicting observed phenotypic resistances. The gyrA point mutation leading to Thr86Ile was found in nearly all ciprofloxacin resistant C. coli (96.2%; 50/52), but in a lower percentage of C. jejuni isolates (75.0%; 51/68). The negative predictive value (NPV) that corresponds to a ciprofloxacin sensitive genotype from the databases with a ciprofloxacin resistance phenotype was 81.3% for C. coli and 59.5% for C. jejuni. The A2075G mutation in 23S rRNA was present in 90.0% (27/30) of azithromycin resistant C. coli isolates and in 31.3% (5/16) of azithromycin resistant C. jejuni isolates. Three other 23S rRNA mutations previously associated with macrolide resistance were not identified in any isolates. The NPV of genotype-based predictions for macrolide resistance was 91.2% for C. coli and 87.9% for C. jejuni. A previously described cmeABC efflux pump genotype (RE-cmeABC) present in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes was associated with a multidrug resistant genotype but did not alone account for the observed discordance in ciprofloxacin and azithromycin resistance genotypes and phenotypes among the C. jejuni or C. coli isolates. Improved databases are needed before genotypic resistome monitoring of Campylobacter isolates are used as a substitute for phenotypic resistance due to poor accuracy of genomic determinants in predicting AMR phenotypes.

Technical Abstract: Objectives Antimicrobial resistant (AMR) Campylobacter is a global health threat, however there is limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated genomic determinants of AMR using a collection of whole genome sequenced Campylobacter jejuni and C. coli isolates from Iquitos, Peru. Methods Campylobacter isolates from two pediatric cohort studies enriched with isolates that demonstrated resistance to ciprofloxacin and azithromycin were sequenced and mined for AMR determinants. Results The gyrA mutation leading to the Thr86Ile amino acid change was the only gyrA mutation associated with fluoroquinolone resistance identified. The A2075G mutation in 23S rRNA was present but three other 23S rRNA mutations previously associated with macrolide resistance were not identified. A resistant-enhancing variant of the cmeABC efflux pump genotype (RE-cmeABC) was identified in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes. Mutations identified in the CmeR-binding site, an inverted repeat sequence in the cmeABC promoter region which increase expression of the operon, were identified in 24/97 C. jejuni and 14/67 C. coli genomes. The presence of these variants, in addition to RE-cmeABC was noted in 18 of the 24 C. jejuni and 9 of the 14 C. coli genomes. Conclusions Both RE-cmeABC, and mutations in the CmeR-binding site were strongly associated with MDR phenotype in C. jejuni and C. coli. This is the first report of RE-cmeABC in Peru and suggests it is a major driver of resistance to the principal therapies used to treat human campylobacteriosis in this setting.