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 (5–7). 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.

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.