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PMID: 15908377 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Identification, distribution, and expression of novel genes in 10 clinical isolates of nontypeable Haemophilus influenzae.

Infection and immunity ·Vol. 73 ·No. 6 ·2005-06-00 ·Pages 3479-91

Shen K, Antalis P, Gladitz J, Sayeed S, Ahmed A, Yu S, Hayes J, Johnson S, Dice B, Dopico R, Keefe R, Janto B, Chong W, Goodwin J, Wadowsky RM, Erdos G, Post JC, Ehrlich GD, Hu FZ

Abstract

We hypothesize that Haemophilus influenzae, as a species, possesses a much greater number of genes than that found in any single H. influenzae genome. This supragenome is distributed throughout naturally occurring infectious populations, and new strains arise through autocompetence and autotransformation systems. The effect is that H. influenzae populations can readily adapt to environmental stressors. The supragenome hypothesis predicts that significant differences exist between and among the genomes of individual infectious strains of nontypeable H. influenzae (NTHi). To test this prediction, we obtained 10 low-passage NTHi clinical isolates from the middle ear effusions of patients with chronic otitis media. DNA sequencing was performed with 771 clones chosen at random from a pooled genomic library. Homology searching demonstrated that approximately 10% of these clones were novel compared to the H. influenzae Rd KW20 genome, and most of them did not match any DNA sequence in GenBank. Amino acid homology searches using hypothetical translations of the open reading frames revealed homologies to a variety of proteins, including bacterial virulence factors not previously identified in the NTHi isolates. The distribution and expression of 53 of these genes among the 10 strains were determined by PCR- and reverse transcription PCR-based analyses. These unique genes were nonuniformly distributed among the 10 isolates, and transcription of these genes in planktonic cultures was detected in 50% (177 of 352) of the occurrences. All of the novel sequences were transcribed in one or more of the NTHi isolates. Seventeen percent (9 of 53) of the novel genes were identified in all 10 NTHi strains, with each of the remaining 44 being present in only a subset of the strains. These genic distribution analyses were more effective as a strain discrimination tool than either multilocus sequence typing or 23S ribosomal gene typing methods.

MeSH Terms
Base Sequence DNA, Bacterial/chemistry Genome, Bacterial Genomic Islands Haemophilus influenzae/classification,genetics,pathogenicity Humans Molecular Sequence Data Phylogeny RNA, Ribosomal, 23S/genetics Repetitive Sequences, Amino Acid Virulence
Chemicals
DNA, Bacterial RNA, Ribosomal, 23S
Authors & Affiliations
19 authors, click to expand affiliations / ORCID
Shen Kai
Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, 320 East North Ave., 11th Floor South Tower, Pittsburgh, PA 15212, USA.
Antalis Patricia
Gladitz John
Sayeed Sameera
Ahmed Azad
Yu Shujun
Hayes Jay
Johnson Sandra
Dice Bethany
Dopico Richard
Keefe Randy
Janto Benjamin
Chong William
Goodwin Joseph
Wadowsky Robert M
Erdos Geza
Post J Christopher
Ehrlich Garth D
Hu Fen Z
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Article Info
Journal
Infection and immunity
Abbr.
Infect Immun
ISSN
0019-9567
DOI
10.1128/IAI.73.6.3479-3491.2005
Published
2005-06-00
Pages
3479-91
Language
English
Region
United States
NLM ID
0246127
PMCID
PMC1111819
Subset
IM
Grants
NIDCD NIH HHS · R01 DC002148 · United States
NIDCD NIH HHS · R01 DC004173 · United States
NIDCD NIH HHS · DC 02148 · United States
NIDCD NIH HHS · DC 04173 · United States
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PubMed source DOI: 10.1128/IAI.73.6.3479-3491.2005 PMC Full Text View journal details
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