Campylobacter jejuni is the pathogen most commonly associated with Guillain-Barré syndrome (GBS). The present work describes the draft genome sequences of 3 C. jejuni strains, BD39, BD67, and BD75, isolated from stool specimens of C. jejuni-triggered patients with GBS using Illumina technologies.
ABSTRACT
Campylobacter jejuni is the pathogen most commonly associated with Guillain-Barré syndrome (GBS). The present work describes the draft genome sequences of 3 C. jejuni strains, BD39, BD67, and BD75, isolated from stool specimens of patients with C. jejuni-triggered GBS using Illumina technologies.
ANNOUNCEMENT
Campylobacter jejuni is one of the prevailing diarrheal pathogens worldwide and causes Guillain-Barré syndrome (GBS) as a postinfection sequel (1, 2). Molecular mimicry between C. jejuni outer membrane lipooligosaccharides and host peripheral nerve gangliosides is widely postulated as the mechanism that triggers this autoimmunity (3–5). The interrelation between the microbial factors and host immunity that trigger autoreactivity is still unclear. Genome profiling of C. jejuni isolated from fecal samples from patients with GBS can unfold its genetic information and create a platform for comparison with other C. jejuni strains causing campylobacteriosis, which will help to reveal the detailed mechanisms and pathogenesis of GBS and other sequelae of Campylobacter-associated diarrhea. The study was approved by the institutional review board (IRB) of icddr,b, Bangladesh.
C. jejuni strains BD39, BD67, and BD75 were isolated from stool specimens from GBS patients using standard microbiological procedures (3). The C. jejuni isolates were enriched at 42°C for 48 h in blood agar with 5% sheep blood, and genomic DNA was extracted from the C. jejuni strains using the Wizard genomic DNA purification kit (Promega) following the manufacturer’s instructions (3). The DNA quality was determined using a NanoDrop spectrophotometer (Thermo Scientific, USA) and quantified using a Quantus fluorometer with the QuantiFluor ONE double-stranded DNA (dsDNA) system in order to fulfill sample quality requirements (quantity, 10 μg; concentration, N50, <200 ng/μg). Next-generation genome sequencing of the three C. jejuni strains was performed using the NextSeq 500 system (Illumina platform). The Illumina Nextera XT DNA library preparation kit (catalog number FC-131-1024) was used to prepare the sequencing library, and the NextSeq v2.5 reagent kit was used for sequencing. Quality checks on the paired-end sequencing reads (150 bp) were performed using FastQC v0.11.5 (6). Trimmomatic v0.36 was used for adapter trimming based on quality scores of Q30 with the following parameters applied: SLIDINGWINDOW:4:15, HEADGROUP:15, TRAILING:3, and MINLEN:36 (7). De novo assembly was performed using SPAdes v3.9.0 (8). Genome annotation was accomplished by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v5.1 (9). CRISPRCasFinder (https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index) and the CRISPRTarget Web tool (http://crispr.otago.ac.nz/CRISPRTarget/crispr_analysis.html) were used to find and analyze clustered regularly interspaced short palindromic repeats (CRISPR) arrays. Default parameters were applied for all software unless otherwise specified.
The obtained genomic sequences had coverages of >200 for each strain. The guanine and cytosine (G+C) contents and genome sizes for these strains were found to be 31.8% to 32.3% and 1.59 Mbp to 1.77 Mbp (Table 1). From PGAP annotation, the C. jejuni strains have a total of 1,660 to 1,866 genes, including 46 RNAs for each strain. Moreover, CRISPR arrays were found in C. jejuni strains BD-39 and BD-67. The spacer sequences of these two strains target the protospacers of different plasmids and phages, but Campylobacter phage DA10 (GenBank accession number MN530981) was the common phage targeted by both strains (three protospacers targeted by one spacer sequence of BD-39 and two spacer sequences of BD-67). It is possible that the pathophysiology of C. jejuni is affected by the CRISPR-cas9 system, which distinctively links C. jejuni bacteriophage defense, virulence, and GBS (11, 12).
TABLE 1.
Genome features and accession numbers for Campylobacter jejuni strains BD-39, BD-67, and BD-75
| PGAPa annotation |
Read information |
||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Strain | LOSb,c | Penner typec,d | GenBank assembly accession no. | Genome size (bp) | G+C content (mol%) | No. of contigs | N50 (bp) | GenBank accession no. | Total no. of genes | No. of rRNAs |
No. of tRNAs | SRAe accession no. | No. of reads | Avg length (bp) | Genome coverage (×) | ||
| 5S | 16S | 23S | |||||||||||||||
| BD-39 | A | HS:19 | GCA_003048165.1 | 1,599,909 | 32.3 | 35 | 145,897 | NGUG00000000 | 1,660 | 1 | 1 | 1 | 40 | SRR5363131 | 5,030,760 | 300 | 393 |
| BD-67 | B | HS:23 | GCA_003048115.1 | 1,778,638 | 31.8 | 62 | 129,048 | NGUF00000000 | 1,866 | 1 | 1 | 1 | 40 | SRR5363132 | 11,984,930 | 300 | 842 |
| BD-75 | A | HS:55 | GCA_003048185.1 | 1,651,474 | 32.0 | 18 | 183,845 | NGUI00000000 | 1,734 | 1 | 1 | 1 | 40 | SRR5363133 | 6,078,678 | 300 | 460 |
PGAP, NCBI Prokaryotic Genome Annotation Pipeline.
LOS, lipooligosaccharide.
This information comes from Islam et al. (10).
Penner heat-stable (HS) serotypes.
SRA, Sequence Read Archive.
Data availability.
All accession numbers are provided in Table 1.
ACKNOWLEDGMENTS
This research activity was funded by the Fogarty International Center, National Institute of Neurological Disorders and Stroke of the National Institutes of Health (USA), under award number K43TW011447. icddr,b acknowledges with gratitude the commitment of the Government of Bangladesh to its research efforts and gratefully acknowledges the unrestricted support provided by the governments of the People’s Republic of Bangladesh, Canada, Sweden, and the United Kingdom.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
All accession numbers are provided in Table 1.