Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus

Jordan, I. King; Conley, Andrew B.; Antonov, Ivan; Arthur, Robert A.; Cook, Erin D.; Cooper, Guy P.; Jones, Bernard L.; Knipe, Kristen; Lee, Kevin J.; Liu, Xing; Mitchell, Gabriel; Pande, Pushkar R.; Petit, Robert A.; Qin, Shaopu; Rajan, Vani; Sarda, Shrutii; Sebastian, Aswathy; Tang, Shiyuyun; Thapliyal, Racchit; Varghese, Neha; Ye, Tianjun; Katz, Lee S.; Wang, Xin; Rowe, Lori A.; Frace, Michael; Mayer, Leonard W.

doi:10.1128/jb.05863-11

Cited by 20 publications

(17 citation statements)

References 11 publications

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“…However, genes encoding factors for colonization and invasion such as pili and IgA1 protease are present in these strains. (18). Comparative analysis revealed several H. haemolyticus-specific genes, including the purT gene; these genes were found to be present exclusively among 5 H. haemolyticus genomes and absent from 20 H. influenzae genomes.…”

Section: Discussionmentioning

confidence: 99%

“…Genome sequences of the five H. haemolyticus strains were used for comparison with those of H. influenzae. Details of whole-genome sequencing of the strains and the assembled sequences have been reported previously (18). Twenty complete and draft H. influenzae (19 NT H. influenzae and 1 H. influenzae b genome) genome sequences were downloaded from the NCBI RefSeq and Shotgun Assembly Sequence database (19) ( Table 1).…”

Section: Methodsmentioning

confidence: 99%

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Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

Rishishwar

Sivadas

et al. 2016

J Clin Microbiol

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g Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae. Haemophilus haemolyticus is a human commensal that colonizes the respiratory tract. It shares high similarities in morphology, biochemistry, and genetics with nontypeable Haemophilus influenzae (NT H. influenzae) (1-3). NT H. influenzae has emerged as the major cause of invasive H. influenzae disease since the implementation of H. influenzae serotype b (H. influenzae b) vaccine (4). NT H. influenzae infections such as childhood otitis media and respiratory tract infections in adults with chronic obstructive pulmonary disease (COPD) result in an enormous social and economic burden to societies (5). H. haemolyticus was recently reported to cause invasive disease (1). These cases were previously misidentified as NT H. influenzae due to the lack of proper identification methods to discriminate between the two species (6). Reevaluation of NT H. influenzae cases from previous years revealed that about 2% (7/374) of the NT H. influenzae invasive cases reported from Active Bacterial Core surveillance (ABCs) were in fact caused by H. haemolyticus (1).Misidentification of H. haemolyticus as NT H. influenzae has been repeatedly reported by multiple research groups, with up to 40% of isolates being misidentified as NT H. influenzae using classical phenotypic methods in clinical microbiology laboratories (1, 7-11). The misidentification of H. haemolyticus has a potential impact on accurate assessment of the prevalence of antibioticresistant NT H. influenzae (12). Therefore, a rapid and accurate method is needed to distinguish H. haemolyticus from NT H. influenzae and to better understand the epidemiology of H. haemolyticus infections....

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

Rishishwar

Sivadas

et al. 2016

J Clin Microbiol

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“…genomes were available for this study: 316 H. influenzae (145 generated in the current study, 19 unpublished and 152 published elsewhere [6,[18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]), 59 H. haemolyticus (44 generated in the current study, one unpublished and 14 published elsewhere [6,26,28,[35][36] Table 1). The hypD assay differentiates H. haemolyticus (red) from all other species and the siaT assay differentiates H. influenzae (blue), 'Clade I' H. influenzae (purple) and fucose operon-negative H. influenzae strains (green) from all other species.…”

Section: • Haemophilus Genomesmentioning

confidence: 99%

“…Following phylogenetic reconstruction, SPANDx was rerun with the inclusion of the H. parainfluenzae genomes to identify genetic loci specific to H. influenzae, including the fucP-negative clade, and to H. haemolyticus, as described previously [6]. Reads were mapped against the closed reference genome H. influenzae 86-028NP (GenBank ref: NC_007146) [22] and the draft H. haemolyticus genome M19501 (GenBank ref: NZ_AFQN00000000) [35].…”

Section: • Haemophilus Genomesmentioning

confidence: 99%

Simultaneous Identification of Haemophilus Influenzae and Haemophilus Haemolyticus using Real-Time PCR

et al. 2017

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Aim: To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic nearneighbor Haemophilus haemolyticus. Materials & methods: A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed. Results & discussion: PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT. These two assays were multiplexed with the recently described fucP assay for further differentiation among H. influenzae. Conclusion: The triplex assay provides rapid, unambiguous, sensitive and highly specific genotyping results for the simultaneous detection of hypD and siaT, including fucose-positive H. influenzae (fucP), in a single PCR.

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“…Based on the profile of these phenotypic and genotypic laboratory tests, the seven isolates from cases 1 to 7 were identified as H. haemolyticus. Genome sequences of isolates from case 6 (AFQR00000000) and 7 (AFQQ00000000) have recently been published (9). The fucK gene is missing, but the hpd gene is present in these two isolates, suggesting that the PCR target region of the hpd gene is species specific.…”

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confidence: 99%

Haemophilus haemolyticus Isolates Causing Clinical Disease

et al. 2012

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We report seven cases of Haemophilus haemolyticus invasive disease detected in the United States, which were previously misidentified as nontypeable Haemophilus influenzae. All cases had different symptoms and presentations. Our study suggests that a testing scheme that includes reliable PCR assays and standard microbiological methods should be used in order to improve H. haemolyticus identification.

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Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus

Cited by 20 publications

References 11 publications

Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

Simultaneous Identification of Haemophilus Influenzae and Haemophilus Haemolyticus using Real-Time PCR

Haemophilus haemolyticus Isolates Causing Clinical Disease

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