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. 2017 Jan 5;5(1):e00925-16. doi: 10.1128/genomeA.00925-16

Large-Scale Release of Campylobacter Draft Genomes: Resources for Food Safety and Public Health from the 100K Pathogen Genome Project

Allison M Weis a,e, Bihua C Huang a,e, Dylan B Storey a,e,*, Nguyet Kong a,e, Poyin Chen a,e, Narine Arabyan a,e, Brent Gilpin b, Carl Mason c, Andrea K Townsend d,*, Woutrina A Smith a, Barbara A Byrne a, Conor C Taff d,*, Bart C Weimer a,e,
PMCID: PMC5255908  PMID: 28057746

ABSTRACT

Campylobacter is a food-associated bacterium and a leading cause of foodborne illness worldwide, being associated with poultry in the food supply. This is the initial public release of 202 Campylobacter genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Campylobacter genus.

GENOME ANNOUNCEMENT

Campylobacter is the most common foodborne pathogen worldwide in humans and animals (1). Approximately 1.3 million people are infected in the United States yearly (2). Despite control efforts, outbreaks are increasing (2). Symptoms include fever, abdominal cramping, and bloody diarrhea, and in rare cases, infection leads to autoimmune disorders, such as Guillain-Barré syndrome (8). Infection is primarily from poultry but is also associated with domesticated livestock (3, 4) and wildlife (57).

The 100K Pathogen Genome Project (http://www.100kgenomes.org) is a large-scale sequencing effort for worldwide isolates with a genome repository at the 100K Project BioProject at the NCBI (PRJNA186441). This project included the three most commonly identified species of Campylobacter: C. jejuni, C. lari, and C. coli. For an in-depth review of Campylobacter molecular biology and pathogenesis, see the papers by Silva et al. (9) and Young et al. (10).

All Campylobacter isolates from the 100K Pathogen Genome Project were collected and banked in the laboratory of Bart Weimer (University of California, Davis, Davis, CA). Isolates were checked for purity and stored in liquid nitrogen (11). Genomic DNA (gDNA) was extracted from cultures grown on 5% blood agar plates (UC Davis, VetMed Biological Services) for one to two days, lysed (12), purified with a Qiagen QIAamp DNA minikit (catalog no. 51306), and analyzed on Agilent 2200 TapeStation system with the Genomic DNA ScreenTape assay for integrity of gDNA (13). After isolation, gDNA was fragmented using Diagenode Bioruptor next-generation sequencer (NGS) or Covaris E220 (14). Fragmented gDNA (1 μg) was used for library construction with the Kapa high-throughput (HTP) library preparation kit (catalog no. KK8234; Kapa Biosystems, Boston, MA), using the Agilent Bravo NGS workstation (Santa Clara, CA). Fragmented double-strand gDNA molecules were end-repaired (5′), adenylated (3′), and ligated with double-stranded DNA (dsDNA) adapters, either NEXTflex-96 DNA barcode (Bioo Scientific, Austin, TX), and multiplexed up to 96 isolates, or using Integrated DNA Technologies, Inc. Weimer 384 TS-LT DNA barcodes that allowed multiplexing up to 384 genomes. The standard Kapa protocol with dual-SPRI size selection was used for 250- to 500-bp fragments. Library amplification was done for eight cycles using the Kapa HiFi HotStart ReadyMix, followed by a 1× SPRI bead cleanup step. Size distribution of libraries was confirmed using Agilent 2100 Bioanalyzer system with high-sensitivity DNA kit (15, 16), and indexed libraries were quantified with quantitative PCR (qPCR)-based Kapa library quantification kit (catalog no. KK4824) prior to pooling for sequencing either on the Illumina HiSeq 2000 with PE100 plus index read at BGI@UCD (Sacramento, CA) or PE150 on the Illumina HiSeq 3000 at the UC Davis Genome Center (Davis, CA). Paired-end reads were assembled using ABySS 1.5.2 using k = 64 (17).

All sample sequences are publicly available on the NCBI’s Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra), and genome assemblies can be found in NCBI GenBank. Here, the 100K Pathogen Genome Project has assembled 202 genomes from different isolates of Campylobacter identified as C. jejuni (167 genomes), C. coli (32 genomes), and C. lari (3 genomes) (Table 1).

TABLE 1 .

Species, isolate name, assembly data, and accession numbers of 202 Campylobacter genomes

GenBank accession no. Isolate name Speciesa No. of contigs Total genome size (bp) No. of CDSsb
MJWB00000000 BCW_4453 C. coli 34 1,746,170 1,766
MJVZ00000000 BCW_4454 C. coli 46 1,983,591 2,062
MJWE00000000 BCW_4455 C. coli 43 1,872,803 1,937
MJWC00000000 BCW_4457 C. coli 37 1,834,436 1,893
MKAY00000000 BCW_4724 C. coli 31 1,711,767 1,724
MKCC00000000 BCW_5137 C. coli 25 1,725,970 1,742
MKAO00000000 BCW_5818 C. coli 48 1,837,036 1,907
MJYL00000000 BCW_5914 C. coli 53 1,819,402 1,890
MJWD00000000 BCW_5916 C. coli 32 1,828,621 1,894
MJWF00000000 BCW_5917 C. coli 37 1,823,469 1,893
MJVY00000000 BCW_5918 C. coli 40 1,964,242 2,043
MJWL00000000 BCW_6447 C. coli 32 1,861,852 1,912
MJWM00000000 BCW_6448 C. coli 31 1,857,061 1,912
MJWA00000000 BCW_6450 C. coli 48 1,983,760 2,061
MJYP00000000 BCW_6860 C. coli 48 1,731,589 1,766
MJZG00000000 BCW_6913 C. coli 41 1,812,371 1,882
MJZH00000000 BCW_6914 C. coli 43 1,827,738 1,884
MKEX00000000 BCW_6946 C. coli 46 1,828,827 1,893
MJZK00000000 BCW_6948 C. coli 35 1,740,538 1,767
MJZJ00000000 BCW_6949 C. coli 43 1,823,646 1,888
MJZL00000000 BCW_6950 C. coli 34 1,740,481 1,766
MJZM00000000 BCW_6951 C. coli 57 1,966,450 2,056
MJZP00000000 BCW_6955 C. coli 41 1,818,341 1,886
MJZR00000000 BCW_6957 C. coli 47 1,868,605 1,928
MJZS00000000 BCW_6958 C. coli 40 1,738,043 1,774
MJZU00000000 BCW_7432 C. coli 35 1,874,299 1,934
MJZV00000000 BCW_7433 C. coli 41 1,813,482 1,882
MJZW00000000 BCW_7434 C. coli 48 1,848,847 1,926
MJZX00000000 BCW_7435 C. coli 62 1,967,893 2,051
MJZY00000000 BCW_7437 C. coli 41 1,829,683 1,892
MKAA00000000 BCW_7460 C. coli 36 1,629,723 1,686
MKAB00000000 BCW_7692 C. coli 51 1,785,336 1,805
MEIB00000000 BCW_3781 C. jejuni 59 1,803,513 1,853
MJYK00000000 BCW_3782 C. jejuni 41 1,669,259 1,677
MEIC00000000 BCW_3784 C. jejuni 30 1,748,672 1,864
MJWO00000000 BCW_3785 C. jejuni 28 1,731,393 1,759
MJWP00000000 BCW_3786 C. jejuni 76 1,808,881 1,856
MJVF00000000 BCW_3787 C. jejuni 75 1,805,330 1,856
MJVG00000000 BCW_3788 C. jejuni 28 1,673,630 1,695
MJVH00000000 BCW_3789 C. jejuni 31 1,681,150 1,765
MJVI00000000 BCW_3790 C. jejuni 75 1,809,651 1,836
MJVJ00000000 BCW_3791 C. jejuni 141 2,006,566 2,034
MJVK00000000 BCW_3792 C. jejuni 74 1,809,576 1,833
MJVL00000000 BCW_3794 C. jejuni 63 1,759,193 1,775
MJVM00000000 BCW_3797 C. jejuni 31 1,699,040 1,676
MJVN00000000 BCW_3798 C. jejuni 53 1,744,518 1,751
MJVO00000000 BCW_3799 C. jejuni 55 1,768,431 1,783
MJVP00000000 BCW_3800 C. jejuni 70 1,832,983 1,840
MJVQ00000000 BCW_3802 C. jejuni 64 1,836,234 1,848
MJVR00000000 BCW_3803 C. jejuni 19 1,693,605 1,689
MKAL00000000 BCW_3804 C. jejuni 42 1,700,860 1,688
MJVS00000000 BCW_3805 C. jejuni 74 1,807,158 1,832
MJVT00000000 BCW_3807 C. jejuni 95 1,997,747 2,027
MJVU00000000 BCW_3810 C. jejuni 67 1,827,740 1,836
MJVV00000000 BCW_4216 C. jejuni 29 1,689,963 1,694
MKAM00000000 BCW_4218 C. jejuni 36 1,688,993 1,707
MJXR00000000 BCW_4219 C. jejuni 29 1,689,256 1,693
MJXS00000000 BCW_4220 C. jejuni 71 1,812,101 1,834
MJWI00000000 BCW_4221 C. jejuni 33 1,660,182 1,633
MJXT00000000 BCW_4222 C. jejuni 76 1,812,008 1,832
MJXU00000000 BCW_4223 C. jejuni 73 1,792,952 1,790
MJWH00000000 BCW_4224 C. jejuni 29 1,680,989 1,689
MJXV00000000 BCW_4225 C. jejuni 72 1,808,664 1,827
MJXW00000000 BCW_4226 C. jejuni 29 1,693,524 1,706
MJXX00000000 BCW_4228 C. jejuni 74 1,776,092 1,777
MJXY00000000 BCW_4229 C. jejuni 76 1,777,005 1,776
MJWJ00000000 BCW_4230 C. jejuni 34 1,670,410 1,639
MJXZ00000000 BCW_4231 C. jejuni 66 1,833,811 1,842
MKAW00000000 BCW_4317 C. jejuni 87 1,729,089 1,758
MKAQ00000000 BCW_4319 C. jejuni 18 1,662,736 1,639
MJYA00000000 BCW_4321 C. jejuni 67 1,840,105 1,882
MJYB00000000 BCW_4322 C. jejuni 67 1,806,657 1,837
MJYC00000000 BCW_4323 C. jejuni 88 1,736,882 1,756
MKET00000000 BCW_4324 C. jejuni 56 1,804,461 1,856
MJYD00000000 BCW_4325 C. jejuni 88 1,733,375 1,755
MJYE00000000 BCW_4326 C. jejuni 90 1,732,137 1,750
MKAN00000000 BCW_4328 C. jejuni 63 1,854,445 1,889
MJYF00000000 BCW_4332 C. jejuni 70 1,739,132 1,764
MJYG00000000 BCW_4333 C. jejuni 81 1,874,835 1,927
MJYH00000000 BCW_4335 C. jejuni 91 1,725,603 1,756
MJYI00000000 BCW_4337 C. jejuni 68 1,806,323 1,836
MJYJ00000000 BCW_4338 C. jejuni 66 1,807,200 1,840
MKAH00000000 BCW_4341 C. jejuni 55 1,773,112 1,773
MJWG00000000 BCW_4452 C. jejuni 25 1,800,178 1,850
MKAI00000000 BCW_4456 C. jejuni 30 1,724,619 1,726
MJWN00000000 BCW_4459 C. jejuni 55 1,942,729 2,031
MKAJ00000000 BCW_4460 C. jejuni 25 1,601,734 1,576
MKAK00000000 BCW_4461 C. jejuni 22 1,604,851 1,577
MKAZ00000000 BCW_4727 C. jejuni 13 1,678,985 1,684
MKBA00000000 BCW_4728 C. jejuni 41 1,712,512 1,743
MKBB00000000 BCW_4731 C. jejuni 32 1,698,127 1,731
MKBC00000000 BCW_4734 C. jejuni 34 1,684,111 1,732
MKBD00000000 BCW_4735 C. jejuni 35 1,837,130 1,892
MKBE00000000 BCW_4737 C. jejuni 36 1,642,302 1,692
MKBF00000000 BCW_4738 C. jejuni 40 1,748,256 1,788
MKBG00000000 BCW_4741 C. jejuni 172 1,819,989 1,970
MKBH00000000 BCW_4743 C. jejuni 18 1,644,315 1,648
MKBI00000000 BCW_4744 C. jejuni 61 1,654,980 1,715
MKBL00000000 BCW_4747 C. jejuni 22 1,718,223 1,720
MKBJ00000000 BCW_4748 C. jejuni 49 1,747,262 1,782
MKBK00000000 BCW_4749 C. jejuni 48 1,704,441 1,757
MKBM00000000 BCW_4753 C. jejuni 60 1,661,715 1,720
MKBN00000000 BCW_4755 C. jejuni 27 1,687,997 1,681
MKBO00000000 BCW_4757 C. jejuni 51 1,645,272 1,708
MKBP00000000 BCW_5121 C. jejuni 52 1,891,211 1,916
MKBQ00000000 BCW_5122 C. jejuni 94 1,846,320 1,949
MKBR00000000 BCW_5123 C. jejuni 60 1,722,506 1,797
MKBS00000000 BCW_5124 C. jejuni 66 1,673,066 1,727
MKBT00000000 BCW_5125 C. jejuni 49 1,774,518 1,808
MKBU00000000 BCW_5126 C. jejuni 69 1,815,843 1,883
MKBV00000000 BCW_5128 C. jejuni 116 1,797,324 1,868
MKBW00000000 BCW_5129 C. jejuni 58 1,703,448 1,777
MKBX00000000 BCW_5131 C. jejuni 120 1,775,968 1,880
MKBY00000000 BCW_5132 C. jejuni 38 1,694,325 1,735
MKBZ00000000 BCW_5133 C. jejuni 140 1,858,971 1,987
MKCA00000000 BCW_5135 C. jejuni 105 1,776,102 1,902
MKCB00000000 BCW_5136 C. jejuni 52 1,780,266 1,796
MKCD00000000 BCW_5140 C. jejuni 42 1,691,709 1,726
MKCE00000000 BCW_5141 C. jejuni 73 1,701,529 1,760
MKCF00000000 BCW_5143 C. jejuni 95 1,795,032 1,848
MKCG00000000 BCW_5144 C. jejuni 95 1,787,787 1,880
MKCH00000000 BCW_5145 C. jejuni 65 1,752,372 1,798
MKCI00000000 BCW_5146 C. jejuni 60 1,764,810 1,832
MKCJ00000000 BCW_5147 C. jejuni 130 1,721,583 1,824
MKCK00000000 BCW_5148 C. jejuni 42 1,670,278 1,703
MKCL00000000 BCW_5150 C. jejuni 98 1,794,347 1,876
MKCM00000000 BCW_5151 C. jejuni 53 1,683,276 1,727
MKEY00000000 BCW_5152 C. jejuni 41 1,685,669 1,721
MKEZ00000000 BCW_5154 C. jejuni 65 1,741,318 1,809
MKFA00000000 BCW_5155 C. jejuni 67 1,722,407 1,807
MKFB00000000 BCW_5156 C. jejuni 85 1,817,799 1,814
MKFC00000000 BCW_5157 C. jejuni 88 1,810,646 1,803
MKFD00000000 BCW_5158 C. jejuni 26 1,643,431 1,670
MKFE00000000 BCW_5159 C. jejuni 40 1,633,952 1,655
MKFF00000000 BCW_5160 C. jejuni 54 1,824,739 1,887
MKHS00000000 BCW_5161 C. jejuni 56 1,770,897 1,786
MKHT00000000 BCW_5162 C. jejuni 34 1,771,963 1,791
MKHU00000000 BCW_5166 C. jejuni 47 1,880,441 1,915
MKHV00000000 BCW_5167 C. jejuni 32 1,715,657 1,746
MKHW00000000 BCW_5170 C. jejuni 68 1,803,925 1,863
MKHX00000000 BCW_5171 C. jejuni 117 1,764,157 1,809
MKHY00000000 BCW_5172 C. jejuni 64 1,695,537 1,706
MKHZ00000000 BCW_5174 C. jejuni 98 1,757,175 1,779
MKES00000000 BCW_5913 C. jejuni 80 1,829,124 1,791
MJXA00000000 BCW_6451 C. jejuni 23 1,658,447 1,671
MJXB00000000 BCW_6452 C. jejuni 25 1,657,388 1,670
MJXC00000000 BCW_6453 C. jejuni 73 1,870,366 1,907
MJXD00000000 BCW_6454 C. jejuni 78 1,839,000 1,885
MJXE00000000 BCW_6456 C. jejuni 47 1,738,922 1,802
MJXF00000000 BCW_6457 C. jejuni 66 1,820,178 1,841
MJXG00000000 BCW_6458 C. jejuni 48 1,770,748 1,779
MJXH00000000 BCW_6459 C. jejuni 91 1,873,732 1,895
MJXI00000000 BCW_6460 C. jejuni 42 1,743,085 1,756
MJXJ00000000 BCW_6461 C. jejuni 28 1,724,268 1,755
MJXK00000000 BCW_6462 C. jejuni 45 1,762,804 1,774
MJXL00000000 BCW_6463 C. jejuni 80 1,810,501 1,847
MJXM00000000 BCW_6464 C. jejuni 89 1,874,875 1,906
MJXN00000000 BCW_6465 C. jejuni 113 1,898,179 1,918
MJXO00000000 BCW_6466 C. jejuni 75 1,856,101 1,908
MJXP00000000 BCW_6467 C. jejuni 52 1,706,044 1,706
MJXQ00000000 BCW_6468 C. jejuni 44 1,745,966 1,746
MJYM00000000 BCW_6475 C. jejuni 133 1,715,549 1,732
MJYN00000000 BCW_6476 C. jejuni 49 1,750,597 1,751
MJWQ00000000 BCW_6871 C. jejuni 83 1,838,932 1,893
MJWR00000000 BCW_6872 C. jejuni 38 1,727,268 1,728
MJWS00000000 BCW_6873 C. jejuni 114 1,864,402 1,881
MJWT00000000 BCW_6874 C. jejuni 116 1,864,348 1,871
MJWU00000000 BCW_6875 C. jejuni 40 1,737,054 1,756
MJWV00000000 BCW_6876 C. jejuni 39 1,798,356 1,914
MJWW00000000 BCW_6877 C. jejuni 65 1,866,607 1,905
MJWX00000000 BCW_6878 C. jejuni 114 1,862,090 1,875
MJWY00000000 BCW_6879 C. jejuni 31 1,633,912 1,684
MJYO00000000 BCW_6880 C. jejuni 40 1,684,005 1,685
MJYQ00000000 BCW_6881 C. jejuni 90 1,789,448 1,773
MJYR00000000 BCW_6882 C. jejuni 85 1,886,467 1,891
MJYS00000000 BCW_6883 C. jejuni 82 1,870,773 1,908
MKEW00000000 BCW_6884 C. jejuni 111 1,874,853 1,925
MJYT00000000 BCW_6885 C. jejuni 85 1,745,151 1,777
MJYU00000000 BCW_6886 C. jejuni 114 1,737,339 1,758
MKEV00000000 BCW_6887 C. jejuni 141 1,802,256 1,801
MJYV00000000 BCW_6888 C. jejuni 81 1,676,843 1,691
MJWZ00000000 BCW_6889 C. jejuni 81 1,944,460 2,003
MJYW00000000 BCW_6891 C. jejuni 83 1,751,933 1,778
MJYX00000000 BCW_6893 C. jejuni 57 1,770,259 1,778
MJYY00000000 BCW_6896 C. jejuni 120 1,625,057 1,606
MJYZ00000000 BCW_6897 C. jejuni 27 1,713,241 1,717
MJZA00000000 BCW_6898 C. jejuni 36 1,668,807 1,665
MJZB00000000 BCW_6899 C. jejuni 35 1,674,680 1,665
MJZC00000000 BCW_6900 C. jejuni 60 1,839,405 1,838
MJZD00000000 BCW_6901 C. jejuni 172 1,671,632 1,678
MKEU00000000 BCW_6902 C. jejuni 37 1,706,600 1,714
MJZE00000000 BCW_6904 C. jejuni 71 1,719,544 1,739
MKAP00000000 BCW_6907 C. jejuni 55 1,829,263 1,849
MJZF00000000 BCW_6910 C. jejuni 47 1,817,981 1,839
MJZN00000000 BCW_6953 C. jejuni 40 1,700,213 1,723
MJZO00000000 BCW_6954 C. jejuni 81 1,881,118 1,881
MJZQ00000000 BCW_6956 C. jejuni 57 1,783,446 1,795
MJZT00000000 BCW_6959 C. jejuni 48 1,699,337 1,726
MJZZ00000000 BCW_7438 C. jejuni 73 1,950,893 2,009
MJVX00000000 BCW_3783 C. lari 23 1,493,439 1,495
MJVW00000000 BCW_3793 C. lari 25 1,492,968 1,492
MJWK00000000 BCW_4217 C. lari 21 1,491,293 1,492
a

The average number of contigs, genome size, and number of coding sequences were 41.4, 1,828,002.30 bp, and 1,884 for C. coli; 63.8, 1,764,345.40 bp, and 1,792 for C. jejuni; and 23, 1,492,566.50 bp, and 1,493 for C. lari, respectively.

b

CDSs, coding sequences.

Accession number(s).

Sequences can be found in the 100K Project BioProject at the NCBI SRA BioProject and in the NCBI Genbank. Accession numbers are presented in Table 1.

ACKNOWLEDGMENTS

We thank Whitney Ng and Kao Thao for their effort in isolate logistics and technical assistance and all of the collaborators to the 100K Pathogen Genome Project.

This project was funded by 100K Pathogen Genome Project, with initial funding from the FDA, and Agilent Technologies, to produce these sequences.

Footnotes

Citation Weis AM, Huang BC, Storey DB, Kong N, Chen P, Arabyan N, Gilpin B, Mason C, Townsend AK, Smith WA, Byrne BA, Taff CC, Weimer BC. 2017. Large-scale release of Campylobacter draft genomes: resources for food safety and public health from the 100K Pathogen Genome Project. Genome Announc 5:e00925-16. https://doi.org/10.1128/genomeA.00925-16.

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Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)

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