areas that they exist in within the human body. this bacterium can exist in the nasal passages (especially the nasopharynx), the ear canal, and the lungs. the bacterium's presence in these areas can lead to some conditions such as otitis media (which is the inflammation of the middle ear), chronic obstructive pulmonary disorder, which causes decreased air flow to the lungs, epiglotitis (which is the swelling of the epiglottis) and asthma which can become severe. metabolism h. influenzae uses the embden–meyerhof–parnas (emp) pathway for glycolysis and the pentose phosphate pathway, which is anabolic rather than catabolic. the citric acid cycle is incomplete and lacks several enzymes that are found in a fully functioning cycle. this partially functional cycle is not unique to the h. influenzae. the enzymes missing from the tca cycle are citrate synthase, aconitate hydratase, and isocitrate dehydrogenase. haemophilus influenzae has been found in both aerobic, and anaerobic environments, as well as environments with different ph's. prevention acthib (hib-vaccine) effective vaccines for haemophilus influenzae serotype b have been available since the early 1990s, and are recommended for children under age 5 and asplenic patients. the world health organization recommends a pentavalent vaccine, combining vaccines against diphtheria, tetanus, pertussis, hepatitis b and hib. there is not yet sufficient evidence on how effective this pentavalent vaccine is in relation to the individual vaccines. hib vaccines cost about seven times the total cost of vaccines against measles, polio, tuberculosis, diphtheria, tetanus, and pertussis. consequently, whereas 92% of the populations of developed countries were vaccinated against hib as of 2003, vaccination coverage was 42% for developing countries, and only 8% for least-developed countries. the hib vaccines do not provide cross-protection to any other haemophilus influenzae serotypes like hia, hic, hid, hie or hif. an oral vaccination has been developed for non-typeable haemophilus influenzae (nthi) for patients with chronic bronchitis but it has not shown to be effective in reducing the number and severity of copd exacerbations. however, there is no effective vaccine for the other types of capsulated haemophilus inflenzae or haemophilus inflenzae nontypeable. genome h. influenzae was the first free-living organism to have its entire genome sequenced. completed by craig venter and his team at the institute for genomic research, now part of the j. craig venter institute. haemophilus was chosen because one of the project leaders, nobel laureate hamilton smith, had been working on it for decades and was able to provide high-quality dna libraries. the sequencing method used was whole-genome shotgun, which was completed and published in science in 1995. the genome of strain rd kw20 consists of 1,830,138 base pairs of dna in a single circular chromosome that contains 1604 protein-coding genes, 117 pseudogenes, 57 trna genes, and 23 other rna genes. about 90% of the genes have homologs in e. coli, another gamma-proteobacterium. in fact, the similarity between genes of the two species ranges from 18% to 98% protein sequence identity, with the majority sharing 40-80% of their amino acids (with an average of 59%). conjugative plasmids (dna molecules that are capable of horizontal transfer between different species of bacteria) can frequently be found in h. influenzae. it is common that the f+ plasmid of a competent escherichia coli bacterium conjugates into the h. influenzae bacterium, which then allows the plasmid to transfer among h. influenzae strands via conjugation. likely protective role of transformation unencapsulated h. influenzae is often observed in the airways of patients with chronic obstructive pulmonary disease (copd). neutrophils are also observed in large numbers in sputum from patients with copd. the neutrophils phagocytize h. influenzae, thereby activating an oxidative respiratory burst. however instead of killing the bacteria the neutrophils are themselves killed (though such an oxidative burst likely causes dna damage in the h. influenzae cells). dearth of killing the bacteria appears to explain the persistence of infection in copd. h. influenzae mutants defective in the rec1 gene (a homolog of reca) are very sensitive to killing by the oxidizing agent hydrogen peroxide. this finding suggests that rec1 expression is important for h. influenzae survival under conditions of oxidative stress. since it is a homolog of reca, rec1 likely plays a key role in recombinational repair of dna damage. thus h. influenzae may protect its genome against the reactive oxygen species produced by the host's phagocytic cells through recombinational repair of oxidative dna damages. recombinational repair of a damaged site of a chromosome requires, in addition to rec1, a second homologous undamaged dna molecule. individual h. influenzae cells are capable of taking up homologous dna from other cells by the process of transformation. transformation in h. influenzae involves at least 15 gene products, and is likely an adaptation for repairing dna damage in the resident chromosome. vaccines that target unencapsulated h. influenzae serotypes are in development.