PreprintArticleVersion 1This version is not peer-reviewed
Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments
Version 1
: Received: 11 July 2024 / Approved: 12 July 2024 / Online: 15 July 2024 (11:06:33 CEST)
How to cite:
Gonzalez-Escalona, N.; Kwon, H. J.; Chen, Y. Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments. Preprints2024, 2024071026. https://doi.org/10.20944/preprints202407.1026.v1
Gonzalez-Escalona, N.; Kwon, H. J.; Chen, Y. Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments. Preprints 2024, 2024071026. https://doi.org/10.20944/preprints202407.1026.v1
Gonzalez-Escalona, N.; Kwon, H. J.; Chen, Y. Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments. Preprints2024, 2024071026. https://doi.org/10.20944/preprints202407.1026.v1
APA Style
Gonzalez-Escalona, N., Kwon, H. J., & Chen, Y. (2024). Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments. Preprints. https://doi.org/10.20944/preprints202407.1026.v1
Chicago/Turabian Style
Gonzalez-Escalona, N., Hee Jin Kwon and Yi Chen. 2024 "Nanopore sequencing allows recovery of high-quality completely closed genomes of all Cronobacter species from powdered infant formula overnight enrichments" Preprints. https://doi.org/10.20944/preprints202407.1026.v1
Abstract
Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of Escherichia coli O157:H7 from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (>90%). In this study, we aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. qPCR was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the spiked PIF samples after the overnight enrichment have high levels of Cronobacter (107 to 109 CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly two weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks.
Biology and Life Sciences, Food Science and Technology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
