Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430

Lennard Epping; Julia C Golz; Marie-Theres Knüver; Charlotte Huber; Andrea Thürmer; Lothar H Wieler; Kerstin Stingl; Torsten Semmler

doi:10.1186/s13099-019-0340-7

Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430

Gut Pathog. 2019 Dec 16:11:59. doi: 10.1186/s13099-019-0340-7. eCollection 2019.

Authors

Lennard Epping¹, Julia C Golz², Marie-Theres Knüver², Charlotte Huber³, Andrea Thürmer⁴, Lothar H Wieler⁴, Kerstin Stingl², Torsten Semmler¹

Affiliations

¹ 1NG1-Microbial Genomics, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
² 2National Reference Laboratory for Campylobacter, Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany.
³ 3Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany.
⁴ 4Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany.

Abstract

Background: Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION.

Results: In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones.

Conclusion: The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.

Keywords: Antibiotic resistance; Assembler comparison; Campylobacter jejuni; Hybrid assemblies; Long read sequencing.