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. 2020 Apr 30;9(18):e00072-20. doi: 10.1128/MRA.00072-20

Draft Whole-Genome Sequences of 51 Campylobacter jejuni and 12 Campylobacter coli Clinical Isolates from Chile

Verónica Bravo a, Carmen Varela b, Lorena Porte b, Thomas Weitzel b,c, George J Kastanis d, Maria Balkey d, Carlos J Blondel e,f, Narjol Gonzalez-Escalona d,✉
Editor: David Raskog
PMCID: PMC7193920  PMID: 32354965

Campylobacter species are the leading cause of gastroenteritis worldwide and an emerging threat in developing countries. Here, we report the draft whole-genome sequences of 51 Campylobacter jejuni and 12 Campylobacter coli strains isolated from patients with gastroenteritis in Santiago, Chile.

ABSTRACT

Campylobacter species are the leading cause of gastroenteritis worldwide and an emerging threat in developing countries. Here, we report the draft whole-genome sequences of 51 Campylobacter jejuni and 12 Campylobacter coli strains isolated from patients with gastroenteritis in Santiago, Chile.

ANNOUNCEMENT

Human campylobacteriosis has been recognized as an important public health problem worldwide (1, 2). In developing countries such as Chile, diarrheal illness caused by Campylobacter species are emerging as an important cause of childhood morbidity (3–5). Over a 2-year period (2017 to 2019), 51 Campylobacter jejuni and 12 Campylobacter coli strains were isolated from acquired enteric infections by the clinical laboratory of Clinica Alemana in Santiago, Chile. The samples consisted of fresh stool, transported at room temperature and processed within 2 h of collection. Sample swabs were plated onto Campylobacter selective chromogenic (CASA) medium (bioMérieux, Marcy-l’Étoile, France), streaked into 4 quadrants with a sterile loop, and incubated for 48 h at 42°C under microaerobic conditions (Anaerocult C; Merck, Darmstadt, Germany). Campylobacter plates were analyzed after 48 h, and suspicious colonies were further identified through matrix-assisted laser desorption–ionization time of flight (MALDI-TOF) mass spectrometry using a Vitek MS instrument (bioMérieux). Following surveillance regulations, Campylobacter strains were sent to the National Reference Laboratory at the Chilean Institute of Public Health for further confirmation.

The Campylobacter strains were grown overnight on 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, Hilden, Germany). The 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. Sequencing libraries 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 instrument and 1 ng DNA for the Nextera XT kit for the NextSeq instrument. The strains were sequenced using both the MiSeq and NextSeq sequencers (Illumina). For the MiSeq, we used a MiSeq v3 kit with 2 × 250-bp paired-end chemistry, according to the manufacturer’s instructions, with >100× average coverage. For the NextSeq, we used a NextSeq 500/550 high-output kit v2.5 (300 cycles) with 2 × 150-bp paired-end chemistry, according to the manufacturer’s instructions, with >300× average coverage. Default parameters were used for all software unless otherwise specified. The Illumina reads were managed with the CLC Genomics Workbench v9.5.2 (Qiagen), assessed for quality (Q, >30) with the quality control tool, and trimmed (adapter trimming, quality trimming, and length trimming) with the trim sequences tool. The trimmed data for each strain were de novo assembled using CLC Genomics Workbench and a minimum contig size threshold of 500 bp.

The assembly and annotation metrics of the draft whole-genome sequences are listed in Table 1. This study reports the draft genomes of 51 C. jejuni and 12 C. coli strains from Chile. Currently, there are only 3 draft genomes of C. jejuni from this country available at NCBI (6); thus, this release increases by 17-fold the number of available C. jejuni genomes from Chile. In silico multilocus sequence typing (MLST) analysis using the MLST Campylobacter jejuni/coli database (http://pubmlst.org/campylobacter) identified that clonal complex 21 (CC-21) was the most common among the reported C. jejuni strains (35.3%). In the case of C. coli, 66.7% of strains belonged to CC-828. Our study presents genomic data that will be useful for understanding the genetic diversity, virulence potential, and antimicrobial resistance of clinical Campylobacter strains from Chile and the region.

TABLE 1.

Metadata for the Campylobacter jejuni and Campylobacter coli strains reported in this study

Strain no.a Species SRA accession no. GenBank accession no. CCb STc Genome size (bp) GC content (%) No. of contigs No. of reads Coverage (×)
CFSAN093225 C. jejuni SRR10860994 JAAMXD000000000 48 475 1,680,704 30.35 29 1,324,624 180
CFSAN093228 C. jejuni SRR10860964 JAAMXC000000000 21 1359 1,781,797 30.32 39 1,057,805 140
CFSAN093229 C. jejuni SRR10860963 JAAMXB000000000 468 1,587,226 30.39 27 1,133,889 137
CFSAN093231 C. jejuni SRR10860962 JAAMXA000000000 21 1359 1,697,519 30.37 31 1,475,962 162
CFSAN093232 C. jejuni SRR10860961 JAAMWZ000000000 52 52 1,595,492 30.49 25 1,465,907 196
CFSAN093233 C. jejuni SRR10860960 JAAMWY000000000 257 257 1,773,175 30.24 21 1,205,773 148
CFSAN093234 C. jejuni SRR10860959 JAAMWX000000000 21 1359 1,760,698 31.06 60 882,983 23
CFSAN093235 C. jejuni SRR10860993 JAAMWW000000000 21 1359 1,695,455 30.38 31 1,045,271 141
CFSAN093236 C. jejuni SRR10860992 JAAMWV000000000 353 10197 1,698,351 30.25 39 1,023,125 141
CFSAN093237 C. jejuni SRR10860991 JAAMWU000000000 206 10193 1,671,646 30.35 29 1,121,441 155
CFSAN093239 C. jejuni SRR10860989 JAAMWT000000000 353 10198 1,681,217 30.28 28 1,329,238 179
CFSAN093240 C. jejuni SRR10860988 JAAMWS000000000 21 1359 1,744,288 30.36 32 1,255,094 148
CFSAN093242 C. jejuni SRR10860986 JAAMWR000000000 21 1359 1,658,077 30.37 33 1,073,048 108
CFSAN093243 C. jejuni SRR10860985 JAAMWQ000000000 52 52 1,636,882 30.41 26 1,115,084 159
CFSAN093244 C. coli SRR10860984 JAAMWP000000000 828 829 1,672,819 31.36 21 1,254,542 155
CFSAN093245 C. jejuni SRR10860982 JAAMWO000000000 206 10193 1,672,029 30.35 30 1,125,976 159
CFSAN093247 C. jejuni SRR10860980 JAAMWN000000000 52 52 1,604,559 30.48 26 1,375,114 195
CFSAN093249 C. jejuni SRR10860979 JAAMWM000000000 443 51 1,626,108 30.33 19 1,091,724 153
CFSAN093250 C. jejuni SRR10860978 JAAMWL000000000 48 475 1,712,809 31.08 30 1,002,658 53
CFSAN093251 C. coli SRR10860977 JAAMWK000000000 828 1173 1,748,418 31.24 40 1,013,159 135
CFSAN093253 C. coli SRR10860976 JAAMWJ000000000 1150 10203 1,786,483 31.16 29 993,128 101
CFSAN093254 C. coli SRR10860975 JAAMWI000000000 828 1173 1,690,423 31.27 27 1,287,195 175
CFSAN093255 C. jejuni SRR10860974 JAAMWH000000000 21 883 1,670,465 30.45 33 1,015,414 140
CFSAN093258 C. jejuni SRR10860970 JAAMWG000000000 48 475 1,645,019 30.41 27 1,065,408 148
CFSAN093261 C. jejuni SRR10860967 JAAMWF000000000 353 10198 1,682,616 30.28 28 1,056,783 142
CFSAN093262 C. coli SRR10860966 JAAMWE000000000 828 10201 1,678,889 31.36 26 1,055,784 147
CFSAN093263 C. coli SRR10860965 JAAMWD000000000 828 829 1,672,987 31.37 23 1,251,285 172
CFSAN096299 C. jejuni SRR10859487 AANORF000000000 464 464 1,718,277 30.2 43 5,476,280 465
CFSAN096304 C. jejuni SRR10868852 AANHWB000000000 21 883 1,671,524 30.43 36 4,419,880 381
CFSAN096308 C. jejuni SRR10859598 AANOWN000000000 49 3720 1,601,057 30.41 19 5,861,201 361
CFSAN096310 C. jejuni SRR10859577 AANOUI000000000 48 475 1,674,594 30.35 66 1,753,261 155
CFSAN096311 C. jejuni SRR10859580 AANCIZ000000000 508 508 1,647,086 30.44 33 4,708,076 423
CFSAN096312 C. jejuni SRR10859610 AANOQP000000000 45 137 1,633,626 30.41 18 5,353,374 483
CFSAN096313 C. jejuni SRR10859488 AANOPZ000000000 21 883 1,620,403 30.46 34 3,177,773 287
CFSAN096315 C. jejuni SRR10859588 AANOQR000000000 21 50 1,695,902 30.69 42 3,791,069 300
CFSAN096316 C. jejuni SRR10859605 AANHVC000000000 443 10200 1,669,068 30.34 22 5,679,390 469
CFSAN096317 C. jejuni SRR10859607 AANHUM000000000 21 883 1,624,970 30.47 35 5,730,522 340
CFSAN096318 C. coli SRR10859593 AANHVQ000000000 828 1556 1,739,084 31.33 34 5,897,351 366
CFSAN096319 C. jejuni SRR10859596 AANORO000000000 21 8938 1,751,744 30.25 54 4,898,705 394
CFSAN096320 C. jejuni SRR10859484 AANHVM000000000 48 475 1,718,157 30.42 30 4,360,492 355
CFSAN096321 C. jejuni SRR10859579 AANOQK000000000 42 3997 1,639,939 30.5 25 4,791,209 374
CFSAN096322 C. coli SRR10859575 AANORL000000000 10202 1,686,003 31.28 19 5,638,361 435
CFSAN096323 C. jejuni SRR10859576 AANOQD000000000 45 137 1,628,880 30.51 22 5,964,128 514
CFSAN096324 C. jejuni SRR10868843 AANOFK000000000 21 883 1,617,745 30.47 45 6,814,094 608
CFSAN096325 C. jejuni SRR10859491 AANOQN000000000 21 50 1,624,655 30.43 39 5,580,427 498
CFSAN096326 C. coli SRR10859578 AANOQJ000000000 10204 1,560,320 31.79 20 5,267,801 496
CFSAN096327 C. coli SRR10859608 AANOQZ000000000 828 828 1,826,387 31.05 69 7,193,183 536
CFSAN096328 C. jejuni SRR10859486 AANHUK000000000 8941 1,573,428 30.53 25 3,972,658 371
CFSAN096329 C. jejuni SRR10859490 AANOQL000000000 6091 1,644,013 30.39 19 7,719,809 640
CFSAN096330 C. jejuni SRR10859571 AANOQF000000000 48 475 1,638,878 30.43 34 5,762,736 511
CFSAN096331 C. jejuni SRR10859601 AANHVB000000000 353 4053 1,704,061 30.32 25 4,438,611 381
CFSAN096332 C. jejuni SRR10859606 AANOQH000000000 607 1510 1,681,507 30.22 49 8,590,010 745
CFSAN096333 C. jejuni SRR10859599 AANHUZ000000000 21 50 1,700,375 30.48 38 5,241,779 288
CFSAN096334 C. jejuni SRR10859600 AANCJA000000000 48 475 1,638,392 30.44 32 7,357,763 627
CFSAN096335 C. coli SRR10868836 AANORE000000000 10204 1,561,235 31.81 21 4,668,764 410
CFSAN096336 C. jejuni SRR10859481 AANOQM000000000 353 4053 1,735,932 30.28 34 2,937,522 230
CFSAN096337 C. jejuni SRR10859483 AANOED000000000 21 1359 1,740,390 30.37 33 6,008,099 417
CFSAN096339 C. coli SRR10859485 AANOQC000000000 828 1556 1,735,795 32.79 37 7,891,488 664
CFSAN096340 C. jejuni SRR10859492 AANOEA000000000 21 1359 1,693,355 30.38 33 6,779,991 550
CFSAN096341 C. jejuni SRR10859477 AANOEB000000000 21 1359 1,696,562 30.37 53 5,452,622 456
CFSAN096343 C. jejuni SRR10859474 JAAMWC000000000 206 10192 1,746,366 30.44 37 6,525,453 549
CFSAN096344 C. jejuni SRR10859586 AANOQG000000000 3573 1,603,229 30.41 30 5,346,306 494
CFSAN096345 C. jejuni SRR10859604 AANOQO000000000 48 38 1,693,493 30.38 29 7,799,266 676
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a

Strains in bold were sequenced on the NextSeq platform.

b

CC, clonal complex.

c

ST, sequence type. Entries in bold are novel STs.

Data availability.

The SRA sequences reported here have been deposited in NCBI GenBank under the accession numbers listed in Table 1.

ACKNOWLEDGMENTS

This study was supported by funding from the MCMi Challenge Grants, program proposal number 2018-646, the FDA Foods Program Intramural Funds (FDA employees), 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 SRA sequences reported here have been deposited in NCBI GenBank under the accession numbers listed in Table 1.

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