Campylobacter jejuni is the leading cause of bacterial foodborne disease worldwide. Here, we report the complete annotated genomes and plasmid sequences of 17 Campylobacter jejuni strains isolated from patients with gastroenteritis in Santiago, Chile.
ABSTRACT
Campylobacter jejuni is the leading cause of bacterial foodborne disease worldwide. Here, we report the complete annotated genomes and plasmid sequences of 17 Campylobacter jejuni strains isolated from patients with gastroenteritis in Santiago, Chile.
ANNOUNCEMENT
Campylobacter spp. are now considered the most common bacterial cause of human gastroenteritis worldwide. Of the 25 Campylobacter species, Campylobacter jejuni is the most common species associated with human disease (1–3). In Chile, Campylobacter jejuni infections are emerging as an important cause of foodborne illnesses (4–7). In this study, we obtained the complete genome sequences of 17 C. jejuni strains using a combination of long (Oxford Nanopore) and short (Illumina) reads.
These 17 strains, all belonging to different sequence types, were selected for genome closing out of 81 total strains. These strains were isolated in the laboratory from stool samples from patients with gastroenteritis as previously described (6, 8). These strains were exempt from institutional review board (IRB) review. Strains were grown overnight in Mueller-Hinton 5% sheep blood agar plates at 42°C under microaerobic conditions, and genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen). DNA quality and quantity were assessed using a NanoDrop spectrophotometer and a Qubit fluorometer (Thermo Scientific, Waltham, MA, USA), respectively, following the manufacturer’s instructions. The long reads for each strain were generated in a MinION sequencer (Nanopore Technologies, Oxford, UK). The sequencing library was prepared using the rapid barcoding sequencing kit (SQK-RBK004). Every 10 libraries were pooled and run in a FLO-MIN106 (R9.4.1) flow cell, according to the manufacturer’s instructions, for 48 h. The run was base called live using default settings (MinKNOW v19.06.8, Guppy v3.0.7). Default parameters were used for all software unless otherwise specified. In total, we conducted 2 Nanopore runs. The sequencing outputs for each of the 2 runs were 2.50 Gb (quality score, 12.41; N50, 3,957 bp; total reads, 300,000) and 7.2 Gb (quality score, 11.46; N50, 6,000 bp; total reads, 569,349), for an estimated average genome coverage of 60 to 90×. Reads of <5,000 bp and with a quality score of <7 were discarded for downstream analysis.
The short-read sequencing libraries for each strain were prepared using 100 ng DNA per strain according to the manufacturer’s instructions using the Nextera DNA flex kit (Illumina, San Diego, CA, USA) for the MiSeq sequencing and 1 ng DNA for the Nextera XT kit for the NextSeq sequencing. Strains were sequenced using a MiSeq sequencer and a NextSeq sequencer (Illumina). For the MiSeq sequencing, we used a MiSeq v3 kit using 2 × 250-bp paired-end chemistry, according to the manufacturer’s instructions, with >100× average coverage. For the NextSeq sequencing, we used a NextSeq 500/550 high-output kit v2.5 (300 cycles) using 2 × 150-bp paired-end chemistry, according to the manufacturer’s instructions, with >300× average coverage. The reads were trimmed with Trimmomatic v0.36 (9).
The final complete genome sequence (comprising the chromosome and plasmid, when present) for each strain was obtained using a previously described pipeline (10), except that Flye v2.6 (11) was used instead of Canu v1.7 (12) for long-read de novo assembling. The genomes were confirmed as circular closed by finding the contig end overlap, which was then manually trimmed. Each closed genome was rotated to start at the dnaA gene.
Data availability.
The complete genome sequences reported here have been deposited in NCBI GenBank under the accession numbers listed in Table 1.
TABLE 1.
Metadata for the 17 C. jejuni strains reported in this studya
| CFSAN no.b | GenBank accession no. for: |
GC content (%) | Hybrid assembly genome coverage (×) | Nanopore sequencing depth (×) | MiSeq sequencing depth (×) | Illumina SRA no. (no. of reads) | Nanopore SRA no. (no. of reads) | Yr of isolation | STc | |
|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | Plasmid | |||||||||
| CFSAN093260 | CP040618 (1,627,779) | 30.56 | 70 | 72 | 145 | SRR10860968 (1,022,308) | SRR11620707 (4,572) | 2018 | 52 | |
| CFSAN093259 | CP040617 (1,688,111) | 30.51 | 64 | 31 | 135 | SRR10860969 (981,408) | SRR11620706 (5,234) | 2018 | 50 | |
| CFSAN093257 | CP040616 (1,720,666) | 30.47 | 76 | 20 | 168 | SRR10860971 (1,250,338) | SRR11620698 (2,472) | 2018 | 1359 | |
| CFSAN093256 | CP040615 (1,653,603) | 30.53 | 84 | 95 | 184 | SRR10860973 (1,334,060) | SRR11620697 (9,032) | 2018 | 10196 | |
| CFSAN093246 | CP040613 (1,680,823) | CP040614 (71,914) | 30.54 | 73 | 20 | 150 | SRR10860981 (1,224,214) | SRR11620696 (2,637) | 2018 | 8938 |
| CFSAN093241 | CP040612 (1,662,100) | 30.51 | 66 | 90 | 140 | SRR10860987 (995,550) | SRR11620695 (9,485) | 2018 | 475 | |
| CFSAN093238 | CP040611 (1,745,502) | 30.35 | 76 | 54 | 160 | SRR10860990 (1,187,310) | SRR11620694 (5,587) | 2018 | 353 | |
| CFSAN093227 | CP040610 (1,824,459) | 30.16 | 66 | 46 | 133 | SRR10860972 (1,072,404) | SRR11620693 (4,855) | 2017 | 607 | |
| CFSAN093226 | CP040608 (1,681,003) | CP040609 (39,913) | 30.52 | 71 | 60 | 149 | SRR10860983 (1,086,354) | SRR11620692 (7,883) | 2018 | 21 |
| CFSAN093224 | CP040607 (1,625,593) | 30.56 | 88 | 78 | 187 | SRR10860995 (1,288,270) | SRR11620691 (7,887) | 2018 | 6091 | |
| CFSAN096296d | CP047484 (1,635,710) | 30.54 | 296 | 20 | 675 | SRR10859473 (7,707,678) | SRR11620705 (2,243) | 2019 | 50 | |
| CFSAN096297d | CP047482 (1,664,471) | CP047483 (48,209) | 30.42 | 210 | 79 | 424 | SRR10859482 (5,183,902) | SRR11620704 (7,953) | 2018 | 257 |
| CFSAN096301d | CP047481 (1,661,307) | 30.48 | 271 | 200 | 553 | SRR10859574 (6,233,036) | SRR11620703 (48,095) | 2019 | 52 | |
| CFSAN096302d | CP047480 (1,721,182) | 30.47 | 249 | 97 | 510 | SRR10859489 (5,972,014) | SRR11620702 (11,058) | 2018 | 1359 | |
| CFSAN096305d | CP047479 (1,721,265) | 30.44 | 260 | 58 | 520 | SRR10859603 (6,157,576) | SRR11620701 (6,781) | 2019 | 222 | |
| CFSAN096306d | CP047478 (1,650,107) | 30.51 | 139 | 267 | 285 | SRR10859609 (3,157,756) | SRR11620700 (47,192) | 2019 | 50 | |
| CFSAN096307d | CP047477 (1,720,216) | 30.42 | 81 | 30 | 165 | SRR10859583 (1,902,526) | SRR11620699 (3,198) | 2018 | 1359 | |
All strains were isolated in Santiago de Chile, Chile, from stools of patients with gastroenteritis.
CFSAN, Center for Food Safety and Applied Nutrition.
ST, sequence type (https://pubmlst.org/campylobacter/).
Sequenced using NextSeq.
ACKNOWLEDGMENTS
This study was supported by funding from the MCMi Challenge Grants Program proposal number 2018-646 (N.G.-E.), the FDA Foods Program Intramural Funds (N.G.-E.), and REDI170269 from CONICYT (C.J.B.). C.J.B. is a Howard Hughes Medical Institute (HHMI)-Gulbenkian international research scholar (grant number 55008749).
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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
The complete genome sequences reported here have been deposited in NCBI GenBank under the accession numbers listed in Table 1.
TABLE 1.
Metadata for the 17 C. jejuni strains reported in this studya
| CFSAN no.b | GenBank accession no. for: |
GC content (%) | Hybrid assembly genome coverage (×) | Nanopore sequencing depth (×) | MiSeq sequencing depth (×) | Illumina SRA no. (no. of reads) | Nanopore SRA no. (no. of reads) | Yr of isolation | STc | |
|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | Plasmid | |||||||||
| CFSAN093260 | CP040618 (1,627,779) | 30.56 | 70 | 72 | 145 | SRR10860968 (1,022,308) | SRR11620707 (4,572) | 2018 | 52 | |
| CFSAN093259 | CP040617 (1,688,111) | 30.51 | 64 | 31 | 135 | SRR10860969 (981,408) | SRR11620706 (5,234) | 2018 | 50 | |
| CFSAN093257 | CP040616 (1,720,666) | 30.47 | 76 | 20 | 168 | SRR10860971 (1,250,338) | SRR11620698 (2,472) | 2018 | 1359 | |
| CFSAN093256 | CP040615 (1,653,603) | 30.53 | 84 | 95 | 184 | SRR10860973 (1,334,060) | SRR11620697 (9,032) | 2018 | 10196 | |
| CFSAN093246 | CP040613 (1,680,823) | CP040614 (71,914) | 30.54 | 73 | 20 | 150 | SRR10860981 (1,224,214) | SRR11620696 (2,637) | 2018 | 8938 |
| CFSAN093241 | CP040612 (1,662,100) | 30.51 | 66 | 90 | 140 | SRR10860987 (995,550) | SRR11620695 (9,485) | 2018 | 475 | |
| CFSAN093238 | CP040611 (1,745,502) | 30.35 | 76 | 54 | 160 | SRR10860990 (1,187,310) | SRR11620694 (5,587) | 2018 | 353 | |
| CFSAN093227 | CP040610 (1,824,459) | 30.16 | 66 | 46 | 133 | SRR10860972 (1,072,404) | SRR11620693 (4,855) | 2017 | 607 | |
| CFSAN093226 | CP040608 (1,681,003) | CP040609 (39,913) | 30.52 | 71 | 60 | 149 | SRR10860983 (1,086,354) | SRR11620692 (7,883) | 2018 | 21 |
| CFSAN093224 | CP040607 (1,625,593) | 30.56 | 88 | 78 | 187 | SRR10860995 (1,288,270) | SRR11620691 (7,887) | 2018 | 6091 | |
| CFSAN096296d | CP047484 (1,635,710) | 30.54 | 296 | 20 | 675 | SRR10859473 (7,707,678) | SRR11620705 (2,243) | 2019 | 50 | |
| CFSAN096297d | CP047482 (1,664,471) | CP047483 (48,209) | 30.42 | 210 | 79 | 424 | SRR10859482 (5,183,902) | SRR11620704 (7,953) | 2018 | 257 |
| CFSAN096301d | CP047481 (1,661,307) | 30.48 | 271 | 200 | 553 | SRR10859574 (6,233,036) | SRR11620703 (48,095) | 2019 | 52 | |
| CFSAN096302d | CP047480 (1,721,182) | 30.47 | 249 | 97 | 510 | SRR10859489 (5,972,014) | SRR11620702 (11,058) | 2018 | 1359 | |
| CFSAN096305d | CP047479 (1,721,265) | 30.44 | 260 | 58 | 520 | SRR10859603 (6,157,576) | SRR11620701 (6,781) | 2019 | 222 | |
| CFSAN096306d | CP047478 (1,650,107) | 30.51 | 139 | 267 | 285 | SRR10859609 (3,157,756) | SRR11620700 (47,192) | 2019 | 50 | |
| CFSAN096307d | CP047477 (1,720,216) | 30.42 | 81 | 30 | 165 | SRR10859583 (1,902,526) | SRR11620699 (3,198) | 2018 | 1359 | |
All strains were isolated in Santiago de Chile, Chile, from stools of patients with gastroenteritis.
CFSAN, Center for Food Safety and Applied Nutrition.
ST, sequence type (https://pubmlst.org/campylobacter/).
Sequenced using NextSeq.