Genome AnnouncGenome AnnouncgagaGAGenome Announcements2169-8287American Society for Microbiology1752 N St., N.W., Washington, DC249487544064020genomeA00438-1410.1128/genomeA.00438-14ProkaryotesGenome Sequences of Nine Bordetella holmesii Strains Isolated in the United StatesHarvillEric T.aGoodfieldLaura L.aIvanovYuryaSmallridgeWilliam E.aMeyerJessica A.aCassidayPamela K.bTondellaMaria L.bBrinkacLaurencSankaRavicKimMariacLosadaLilianacThe Pennsylvania State University, University Park, Pennsylvania, USACenters for Disease Control and Prevention, Atlanta, Georgia, USAJ. Craig Venter Institute, Rockville, Maryland, USAAddress correspondence to Liliana Losada, llosada@jcvi.org.1962014May-Jun201423e00438-142242014662014Copyright © 2014 Harvill et al.2014Harvill et al.This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

An increasing number of pertussis-like cases are attributed to the emergent pathogen Bordetella holmesii. The genomes of 9 clinical isolates show that they are clonal, lack the virulence factors encoded by B. pertussis, and are more similar to nonpertussis bordetellae. New markers for B. holmesii can be developed using these sequences.

cover-dateMay/June 2014access-typefree
GENOME ANNOUNCEMENT

An increasing number of pertussis-like cases in the United States and Europe are attributed to the emergent pathogen Bordetella holmesii (1, 2). An analysis of the 2010-2011 outbreak in Ohio showed that B. holmesii was detected in nearly 20% of pertussis-like illnesses (1), up from ~1% in the 1990s (3, 4). Only three whole-genome sequences are available for this group of pathogens (57). B. holmesii genomes do not encode known Bordetella pertussis virulence factors, though they share a genomic island that contains the IS481 insertion element (7) commonly used to diagnose B. pertussis infections and leading to common misidentifications. More specific diagnostic tests were developed using the B. holmesii-specific IS1001 element (4), but it is unclear whether this marker is sufficient due to sparse genomic data.

Here, we report the genome sequences of 9 clinical isolates obtained between 2004 and 2011: six from patients with bacteremia (five from blood and one from synovial fluid) and three respiratory isolates from patients with pertussis-like symptoms. A respiratory isolate was from an infant who had a coinfection with B. pertussis. Genomic DNA was prepared (8) and sequenced using a combination of 3- or 5-kb mate-pair (~30× coverage) and 100-bp Illumina paired-end reads (~50× coverage). After quality trimming, all reads were used in assemblies with Celera Assembler 6.1 (9) or Velvet Assembler. Underlying consensus sequences and gaps were improved using custom scripts. All genomes had between 119 and 213 contigs (Table 1). The overall G+C content was ~62.6%, with genome sizes ranging from 3.55 Mb to 3.59 Mb.

Isolate characteristics and accession numbers

B. holmesii isolate IDStateYr isolatedSourceGenome length (bp)Total no. of contigsGenBank accession no.
H572Colorado2010Synovial fluid3,585,459119JFZY00000000
H585Minnesota2010Blood3,587,402150JFZZ00000000
H629New York2010Blood3,475,248190JGVZ00000000
H635California2010Respiratory fluid3,569,022173JGAA00000000
H643Pennsylvania2010Blood3,614,976193JGWD00000000
H719Minnesota2011Blood3,578,998149JGWA00000000
H785Oregon2011Respiratory fluid3,565,090161JGWB00000000
H809New York2011Blood3,584,230153JMGZ00000000
04P3421Massachusetts2004Respiratory fluid3,595,240213JGWC00000000

B. holmesii isolates belonged to the same multilocus sequencing type (MLST), as seen in B. pertussis strains (10), suggesting that the B. holmesii isolates were also clonal. The genomes were annotated and predicted to have between 3,118 and 3,285 genes. The genomic content of the B. holmesii strains was more similar to those of Bordetella avium and Bordetella petrii than to those of B. pertussis or B. bronchiseptica. However, nearly 66% of the genes were shared with B. pertussis or Bordetella bronchiseptica. Almost 400 genes were shared by all B. holmesii isolates but were not present in any other bordetellae, likely due to acquisition via horizontal transfer. Many of these genes were involved in the transport and detoxification of organic compounds and antibiotics. Each strain had between 24 and 114 unique genes, including one strain that had residual members of a degraded type III secretion system, as seen in Escherichia coli (11). As expected, the IS481 element was present in all genomes (32 to 65 copies), as was BhlIS1001 (5 to 21 copies). The acellular vaccine targets of pertussis toxin, pertactin, and fimbriae were not present, while filamentous hemagglutinin was encoded by all B. holmesii genomes.

These findings suggest that circulating B. holmesii isolates in the United States emerged from a single genetic background more similar to nonpertussis bordetellae. The genomes are a resource for understanding the pathogenicity and evolution of B. holmesii and for further developing detection and differentiation strategies.

Nucleotide sequence accession numbers.

The B. holmesii whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. described in Table 1. The version described in this paper is the first version.

Citation Harvill ET, Goodfield LL, Ivanov Y, Smallridge WE, Meyer JA, Cassiday PK, Tondella ML, Brinkac L, Sanka R, Kim M, Losada L. 2014. Genome sequences of nine Bordetella holmesii strains isolated in the United States. Genome Announc. 2(3):e00438-14. doi:10.1128/genomeA.00438-14.

ACKNOWLEDGMENTS

We acknowledge the participants of the Enhanced Pertussis Surveillance of the Emerging Infections Program Network (Minnesota and Oregon) for their contribution of the isolates included in this study.

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 HHSN272200900007C.

REFERENCES RodgersLMartinSWCohnABuddJMarconMTerranellaAMandalSSalamonDLeberATondellaM-LTattiKSpicerKEmanuelAKochEMcGloneLPawloskiLLeMaile-WilliamsMTuckerNIyerRClarkTADiOrioM 2013 Epidemiologic and laboratory features of a large outbreak of pertussis-like illnesses associated with cocirculating Bordetella holmesii and Bordetella pertussis—Ohio, 2010-2011. Clin. Infect. Dis. 56:322331. 10.1093/cid/cis88823087388 NjamkepoEBonacorsiSDebruyneMGibaudSAGuillotSGuisoN 2011 Significant finding of Bordetella holmesii DNA in nasopharyngeal samples from French patients with suspected pertussis. J. Clin. Microbiol. 49:43474348. 10.1128/JCM.01272-1122012009 YihWKSilvaEAIdaJHarringtonNLettSMGeorgeH 1999 Bordetella holmesii-like organisms isolated from Massachusetts patients with pertussis-like symptoms. Emerg. Infect. Dis. 5:441443. 10.3201/eid0503.99031710341183 AntilaMHeQde JongCAartsIVerbakelHBruistenSKellerSHaanperäMMäkinenJEerolaEViljanenMKMertsolaJvan der ZeeA 2006 Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis. J. Med. Microbiol. 55:10431051. 10.1099/jmm.0.46331-016849724 PlanetPJNarechaniaAHymesSRGagliardoCHuardRCWhittierSDella-LattaPRatnerAJ 2013 Bordetella holmesii: initial genomic analysis of an emerging opportunist. Pathog. Dis. 67:132135. 10.1111/2049-632X.1202823620158 TattiKMLoparevVNRanganathanGanakammalSChangayilSFraceMWeilMRSammonsSMacCannellDMayerLWTondellaML 2013 Draft genome sequences of Bordetella holmesii strains from blood (F627) and nasopharynx (H558). Genome Announc. 1(2):e00056-13. 10.1128/genomeA.00056-1323405310 DiavatopoulosDACummingsCAvan der HeideHGvan GentMLiewSRelmanDAMooiFR 2006 Characterization of a highly conserved island in the otherwise divergent Bordetella holmesii and Bordetella pertussis genomes. J. Bacteriol. 188:83858394. 10.1128/JB.01081-0617041054 ChomczynskiPSacchiN 1987 Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162:156159. 10.1006/abio.1987.99992440339 MillerJRDelcherALKorenSVenterEWalenzBPBrownleyAJohnsonJLiKMobarryCSuttonG 2008 Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:28182824. 10.1093/bioinformatics/btn54818952627 HarvillETGoodfieldLLIvanovYMeyerJANewthCCassidayPTondellaMLLiaoPZimmermanJMeertKWesselDBergerJDeanJMHolubkovRBurrJLiuTBrinkacLKimMLosadaL 2013 Genome sequences of 28 Bordetella pertussis U.S. outbreak strains dating from 2010 to 2012. Genome Announc. 1(6):e01075-13. 10.1128/genomeA.01075-1324356839 RenCPChaudhuriRRFivianABaileyCMAntonioMBarnesWMPallenMJ 2004 The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J. Bacteriol. 186:35473560. 10.1128/JB.186.11.3547-3560.200415150243