Abstract
Despite the availability of highly effective vaccines, Bordetella pertussis incidence has been rapidly rising in highly vaccinated populations. Recent outbreaks have received media attention, feeding concerns about the emergence of dangerous new strains with increased virulence or that escape vaccine-induced immunity. To accelerate the study of this reemerging pathogen, we sequenced the genomes of 28 B. pertussis strains isolated during outbreaks from 2010 through 2012, making both strains and sequence data available to the scientific community.
GENOME ANNOUNCEMENT
The Centers for Disease Control and Prevention classifies whooping cough as a reemerging disease, documenting increasing numbers of cases nearly every year, from hundreds per year in the 1970s to >41,000 in 2012 (1). The recent high-profile epidemics in California (in 2010) and Washington (in 2012) contribute to growing concerns and feed speculation about the ongoing evolution of Bordetella pertussis. To address these concerns, we collected 28 strains of B. pertussis from these and other outbreaks and made them available at the Biodefense and Emerging Infections Research Resources Repository for further study by others.
Here, we report the genome sequences of these 28 clinical isolates derived from whooping cough hospital cases that occurred between 2010 and 2012. Genomic DNA was prepared using a phenol-chloroform extraction method and ethanol precipitation (2). A combination of 3- or 5-kb mate pair (~30× coverage) and 100-bp Illumina paired-end reads (~50× coverage) were used for genome sequence determination. After quality trimming, all reads were used to generate assemblies with Celera assembler 6.1 (3) or Velvet assembler (4). After improvement, all genomes had between 4 and 186 scaffolds containing 25 to 285 contigs. Underlying consensus sequences and gaps were improved using custom scripts developed at the J. Craig Venter Institute (JCVI). The overall G+C content in all cases was ~67%, with genome sizes ranging from 3.83 Mb to 4.15 Mb (average, 4.0 Mb). Up to 218 copies of insertion element IS481 and 95 tripartite transcarboxylate transporter (TTT) element were found in any one B. pertussis genome, amounting to >215 kb on average. All of the B. pertussis isolates, irrespective of geographic location, belong to the same multilocus sequence type and are nearly identical to each other at the protein level (average 99% identity) in conserved regions of the chromosome. However, the B. pertussis genomes were subject to massive genome rearrangements and different gene losses that account for the majority of the diversity between strains. All the genomes were annotated using JCVI’s annotation pipeline (http://www.jcvi.org) and were predicted to have between 3,750 and 4,193 genes. As expected, mobile elements were overrepresented in these genomes compared to in published Bordetella bronchiseptica genomes due to the expansion of the repetitive elements. Over 1,000 core B. bronchiseptica genes were absent in all of the B. pertussis genomes. Many of these genes are involved in capsule biosynthesis, alternate respiration, nutrient acquisition, type VI secretion, and antibiotic resistance. All B. pertussis isolates encoded pertussis toxin, filamentous hemagglutinin, type III secretion system, adenylate cyclase, and other virulence factors.
The findings from this study suggest that currently circulating B. pertussis isolates in the United States are derived from a single genetic background. A full analysis of the virulence genes and evolution of B. pertussis is under way and will be published in a subsequent report.
Nucleotide sequence accession numbers.
The B. pertussis whole-genome shotgun projects have been deposited for each isolate at DDBJ/EMBL/GenBank as described in Table 1. The version described in this paper is the first version.
Table 1.
Characteristics of the 28 B. pertussis strains
| B. pertussis strain name | NCBI accession no. | No. of contigs | N50 (bp) | Total length (bp) | G+C % |
|---|---|---|---|---|---|
| 2250905 | AXSU00000000 | 285 | 20,908 | 3,940,180 | 67.76 |
| 2356847 | AXST00000000 | 179 | 31,198 | 3,907,019 | 67.86 |
| 2371640 | AXSS00000000 | 193 | 33,462 | 3,904,605 | 67.88 |
| STO1-SEAT-0006 | AXSR00000000 | 49 | 139,362 | 4,028,421 | 67.77 |
| STO1-SEAT-0007 | AXSQ00000000 | 26 | 343,155 | 4,053,851 | 67.78 |
| STO1-CHLA-0011 | AXSP00000000 | 25 | 419,274 | 4,083,349 | 67.69 |
| H897 | AXSO00000000 | 173 | 36,602 | 3,938,675 | 67.81 |
| H918 | AXSN00000000 | 60 | 150,397 | 4,073,712 | 67.71 |
| H921 | AXSM00000000 | 48 | 164,785 | 4,064,086 | 67.73 |
| H939 | AXSL00000000 | 43 | 177,196 | 4,018,810 | 67.74 |
| H973 | AXSK00000000 | 62 | 112,367 | 4,014,250 | 67.81 |
| STO1-SEAT-0004 | AXSJ00000000 | 121 | 52,170 | 3,839,596 | 67.9 |
| I002 | AXSI00000000 | 63 | 102,522 | 4,047,567 | 67.74 |
| I036 | AXSH00000000 | 46 | 189,616 | 4,057,285 | 67.74 |
| I176 | AXSG00000000 | 33 | 266,526 | 4,045,246 | 67.78 |
| STO1-CHLA-0006 | AXSF00000000 | 65 | 134,387 | 4,044,283 | 67.79 |
| CHLA-15 | AXSD00000000 | 138 | 46,158 | 3,844,206 | 67.89 |
| CHLA-13 | AXSE00000000 | 95 | 74,009 | 4,029,822 | 67.79 |
| CHLA-20 | AXSC00000000 | 131 | 46,140 | 3,828,499 | 67.9 |
| CHLA-26 | AXSB00000000 | 41 | 264,509 | 4,045,408 | 67.8 |
| STO1-CHOC-0016 | AXSA00000000 | 54 | 122,855 | 4,033,849 | 67.79 |
| STO1-CHOC-0017 | AXRZ00000000 | 108 | 45,197 | 4,050,208 | 67.8 |
| STO1-CHOC-0018 | AXRY00000000 | 127 | 43,391 | 4,051,577 | 67.81 |
| STO1-CHOC-0019 | AXRX00000000 | 120 | 52,255 | 4,150,262 | 67.72 |
| STO1-CHOC-0021 | AXRW00000000 | 56 | 115,723 | 4,027,480 | 67.8 |
| STO1-CHOC-0008 | AXRV00000000 | 124 | 50,507 | 3,834,602 | 67.9 |
| STO1-CHOM-0012 | AXRU00000000 | 37 | 222,972 | 4,065,443 | 67.71 |
| STO1-CNMC-0004 | AXSV00000000 | 149 | 46,159 | 3,855,042 | 67.88 |
ACKNOWLEDGMENTS
We acknowledge the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Collaborative Pediatric Critical Care Research Network (CPCCRN) for assisting in collecting B. pertussis isolates.
This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN272200900007C, and by cooperative agreements from the Eunice Kennedy Shriver National Institute of Child Health and Human Development, Department of Health and Human Services (no. U10HD050096, U10HD049981, U10HD049983, U10HD050012, U10HD063108, U10HD063106, U10HD063114, U10HD049945, U10HD050009, and U01HD049934), and the National Vaccine Program Office at the United States Department of Health and Human Services. All B. pertussis isolates were collected in agreement with each institution’s IRB requirements for patient safety and confidentiality.
Footnotes
Citation Harvill ET, Goodfield LL, Ivanov Y, Meyer JA, Newth C, Cassiday P, Tondella ML, Liao P, Zimmerman J, Meert K, Wessel D, Berger J, Dean JM, Holubkov R, Burr J, Liu T, Brinkac L, Kim M, Losada L. 2013. Genome sequences of 28 Bordetella pertussis U.S. outbreak strains dating from 2010 to 2012. Genome Announc. 1(6):e01075-13. doi:10.1128/genomeA.01075-13.
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