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High prevalence of Klebsiella pneumoniae in European food products: a multicentric study comparing culture and molecular detection methods

By Carla Rodrigues, Kathrin Hauser, Niamh Cahill, Malgorzata Ligowska-Marzeta, Gabriella Centorotola, Alessandra Cornacchia, Raquel Garcia Fierro, Marisa Haenni, Eva Moller Nielsen, Pascal Piveteau, Elodie Barbier, Dearbhaile Morris, Francesco Pomilio, Sylvain Brisse

Posted 24 Nov 2021
bioRxiv DOI: 10.1101/2021.11.24.469859

Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices, and to characterize food isolates phenotypically and genotypically. Chicken meat (n=160) and salad (n=145) samples were collected in five European countries and screened for KpSC presence using culture-based and ZKIR qPCR methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44C/48h) was defined as the most suitable selective culture method for KpSC recovery. High prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples: same food type and same country (15 cases); different food types and same country (1); same food type and two countries (1), suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans.

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