Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Haemophilus appears to be metabolically adapted for existence in a nitrogenrich, microanaerobic environment. We found a high level of 16s rrna sequence heterogeneity up to 2. Wholegenome random sequencing and assembly of haemophilus. Oct 12, 2019 haemophilus influenzae hi can cause invasive diseases such as meningitis, pneumonia, or sepsis. Jan 22, 2002 a highdensity transposon mutagenesis strategy was applied to the haemophilus influenzae genome to identify genes required for growth or viability. Wholegenome random sequencing and assembly of haemophilus influenzae. Help pages, faqs, uniprotkb manual, documents, news archive and biocuration projects. Significantly, this nonpathogenic laboratory strain does not contain certain dna sequences present in diseaseassociated haemophilus isolates. The life styles of the two bacteria are very different h. Pdf first wholegenome sequence of a haemophilus influenzae.
Our study combines a number of bioinformatics tools for function predictions of. A highdensity transposon mutagenesis strategy was applied to the haemophilus influenzae genome to identify genes required for growth or viability. After 5000 cycles, the evolved intergenic sequence genome had a slightly lower score 0. Furthermore, excluding the antibiotic resistance transposons, the gc content of the other accessory genes is similar to that of the h. The capsule, encoded by the genes within the capsule locus, is a major virulence factor of typeable hi. Haemophilus example of sequence statistics and gene. Batch sequence query query multiple sequences in fasta format. Complete genome sequence of encapsulated haemophilus. Sequence attribute search find alleles by matching criteria all loci together locusspecific sequence attribute search select, analyse and download specific alleles. Haemophilus influenzae is an important cause of childhood invasive diseases, including meningitis and septicemia, in many parts of the world. Venters grant proposal for the project was rejected. Genomic characterization of haemophilus influenzae. The genome sequence of haemophilus influenzae springerlink. Nontypeable nthi does not express capsule and is associated with invasive and noninvasive.
Complete genome sequence of haemophilus somnus histophilus. Oct 01, 2010 the complexity of the uss matrix derived from the h. In this context, it is of interest to determine which words oligonucleotides andor peptides in the sequence occur with unusually high or low frequencies and to identify anomalies in their distribution over. To see whether the buchnera genome is small because the genome of the last common ancestor lca of buchnera, e. Draft genome sequence of an isolate of nontypeable. For gene detection, the cds complete coding sequences were downloaded. Analysis of the genetics of biosynthesis and biology of lps lipopolysaccharide in h influenzae indicated shows that lps has complex cell surface glycolipid. This genomic information will enable further investigations on encapsulated nontype b h. The data is available for searching on our blast server or for download from our ftp site and from emblgenbank with accession number fq312006. Comparisons between complete genomes defined a subset of these proteins in h. Sequenced using the whole genome shotgun wgs method.
Haemophilus somnus can be either a commensal of bovine mucosal surfaces or an opportunistic pathogen. Citeseerx genomic sequence of an otitis media isolate of. Haemophilus influenzae hi can cause invasive diseases such as meningitis, pneumonia, or sepsis. This sequence, though extremely useful in understanding the basic biology of h.
The availability of a complete microbial genome sequence enormously facilitates computerbased and experimental investigations of the respective organism by providing complete lists. Frequent oligonucleotides and peptides of the haemophilus. Partial analysis of the genomes of two nontypeable. Highquality draft genome sequence and description of. Here, we present draft genomes of strains from five brazilian purpuric fever cases and one conjunctivitis case. Functional annotation of conserved hypothetical proteins from. A genomescale analysis for identification of genes required. Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. In conventional sequencing, genomes were laboriously broken down into ordered, overlapping segments physical maps before sequencing. Sequencing and analysis of bacterial genomes sciencedirect. A multilocus sequence typing mlst scheme has been developed for the unambiguous characterization of encapsulated and noncapsulated haemophilus influenzae isolates. Despite its clinical significance, accurate identification of h. Pdf an approach for genome analysis based on sequencing and assembly of unselected pieces of dna from. Whole genome sequencing is ostensibly the process of determining the complete dna sequence of an organisms genome at a single time.
Jul 28, 1995 this approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. Tracking insertion mutants within libraries by deep. Frontiers genomescale approaches to identify genes. Investigations into genome diversity of haemophilus influenzae. Nucleotide sequence analysis of hypervariable junctions of. High level of sequence diversity in the 16s rrna genes of. The complete genome sequence of the gastric pathogen. Haemophilus influenzae formerly called pfeiffers bacillus or bacillus influenzae is a gramnegative, coccobacillary, facultatively anaerobic pathogenic bacterium of the family pasteurellaceae.
The complexity of the uss matrix derived from the h. Here, we report the first wholegenome sequence of an invasive h. Whole genome sequencing to study the phylogenetic structure. Haemophilus influenzae is a nonmotile, gramnegative bacterium that is an obligate resident of the human respiratory mucosa. Genome sequence of the endocellular bacterial symbiont of. Here, we report the first whole genome sequence of an invasive h. The genome map, a pictorial representation of genomic sequence data and its bioinformatics analysis, were downloaded for available h. Investigations into genome diversity of haemophilus. Dec 01, 2014 the genome map, a pictorial representation of genomic sequence data and its bioinformatics analysis, were downloaded for available h. The fluenzae genome provides opportunities for characterizing genomic inhomogeneities and detecting distinctive sequence patterns.
Most systemic haemophilus infections are associated with encapsulated strains, and h. Role of horizontal gene transfer in the development of. We report here the draft genome of an isolate of nthi collected from the sputum of a patient presenting with copd in tasmania, australia. Haemophilus influenzae rd was the first freeliving organism to have its genome sequenced completely. Brazilian purpuric fever is a febrile hemorrhagic pediatric disease caused by haemophilus influenzae biogroup aegyptius, a bacterium which was formerly associated with only selflimited purulent conjunctivitis. Although extremely useful in understanding the basic biology of h.
Haemophilus influenzae is a gramnegative bacterium that has no identified natural niche outside of the human host. The availability of a complete microbial genome sequence enormously facilitates computerbased and experimental investigations of the respective organism by providing complete lists of genes, their genetic contexts, and. In the united states, before the introduction of h. Genome sequencing of disease and carriage isolates of. In a collaboration with hamilton smith, of johns hopkins university medical school, who, in 1970, discovered sitespecific restriction enzymes, he decided to sequence an organism much more complex than any yet attempted, using what they called whole genome random sequencing. This strain exhibited a 16s rrna sequence similarity of 94. Characterisation of invasive clinical haemophilus influenzae. Genome scanning in haemophilus influenzae for identification. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for. Proteincoding and noncoding genes, splice variants, cdna and protein sequences, noncoding rnas. This analysis detected putative essential roles for the products of 259 orfs of unknown function.
Nontypeable haemophilus influenzae nthi is an important cause of human illness, including pneumonia and acute exacerbations of chronic obstructive pulmonary disease copd. This entails sequencing all of an organisms chromosomal dna as well as dna contained in the mitochondria and, for plants, in the chloroplast. Sequencing the genome of bacterium haemophilus influenzae, reported in may 1995, demonstrated for the first time that random shotgun sequencing could be applied to whole genomes with speed and accuracy. Gnn genetics and genomics timeline genome news network. Draft wholegenome sequences of haemophilus influenzae.
The 2 phylogenetic populations of the canadian hia isolates are similar to the 2 clonal divisions described for serotype b h. Nontypeable nthi does not express capsule and is associated with invasive and non. First complete genome sequence of haemophilus influenzae. It primarily colonizes the nasopharyngeal mucosa in an asymptomatic mode, but has the ability to disseminate to other anatomical sites to cause otitis media, upper, and lower respiratory tract infections, septicemia, and meningitis. Haemophilus influenzae is an important humanspecific pathogen colonizing the mucosa of the upper respiratory tract. The details of the library construction, the insert mapping strategy, and the analysis used for identification of previously unknown essential genes. Haemophilus influenzae nthi lies in the genetic diversity of the species, which. The sanger institute has been funded by the wellcome trust to sequence the genomes of. Genetics and genomics timeline genome news network.
Resistance to extendedspectrum cephalosporins in h. Metabolism and evolution of haemophilus influenzae deduced. Systems used to automatically annotate proteins with high accuracy. Genomic dna sequence was obtained from 85 strains of h. These genome maps were incorporated in higdb under search menu. To gain insight in to the activity of several classes of antibiotics against five wellcharacterized unencapsulated h. Singlestrain infections in the pulmonary clearance model. Unirule expertly curated rules saas system generated rules.
Typeable hi includes six serotypes a through f, each expressing a unique capsular polysaccharide. Research into haemophilus influenzae, a commensal and pathogen of humans, has resulted in major scientific contributions to biology. A molecular typing method based on the 16s rrna sequence diversity was developed for haemophilus influenzae isolates. Highthroughput dna sequencing was used to investigate differences in genome content within this species. Haemophilus influenzae is a pathogen restricted to humans, and it resides in the upper respiratory tract, causing airway infections and, occasionally, invasive disease. The haemophilus influenzae genome was the first to be sequenced and assembled in a freeliving organism. Strain ff7t was isolated from the peritoneal fluid of a 44yearold woman who suffered from pelvic peritonitis. Genes encoding three enzymesaconitase, citrate synthetase, and isocitrate dehydrogenasein the. The first endonucleases restriction enzymes, which paved the way for the new genetics, and the dna used to obtain the first complete genome sequence of a freeliving organism were obtained from h. An approach for genome analysis based on sequencing and assembly of unselected pieces of dna from the whole chromosome has been applied to obtain the complete nucleotide sequence 1,830,7 base pairs of the genome from the bacterium haemophilus influenzae rd. Apr 14, 2016 strain ff7t was isolated from the peritoneal fluid of a 44yearold woman who suffered from pelvic peritonitis. Characterization of encapsulated and noncapsulated. Combining mlst, core snvphyl, and hitabc gene sequence alignment showed that most 99.