| Table 5A. Emerging Infectious Diseases (Cellular) | ||||||||||||
| Phylogeny | Family | Genus | NCBI Name | Common Name / Disease | Accession | |||||||
| Fungi | Ascomycota | Ajellomyces | Ajellomyces capsulatus | histoplasmosis 28 | ||||||||
| Ajellomyces | Histoplasma capsulatum var. duboisii | histoplasmosis 28 | ||||||||||
| Candida | Candida spp. | candidiasis | NC_005967 | |||||||||
| Coccidioides | Coccidioides immitis | coccidioidomycosis 28 | ||||||||||
| Fusarium | Fusarium oxysporum | fusariosis 28 | ||||||||||
| Fusarium | Fusarium solani | fusariosis 28 | ||||||||||
| Pneumocystis | Pneumocystis jirovecii | Pneumocystis pneumonia (human genotype) 114 | ||||||||||
| Basidiomycota | Filobasidiella | Filobasidiella neoformans | cryptococcosis 28 | |||||||||
| Microsporidia | microsporidial infections | |||||||||||
| Protists | Acanthamoebidae | Acanthamoeba | Acanthamoeba castellanii | amoebic keratitis or chronic granulomatous amoebic meningoencephalitis 28 | ||||||||
| Acanthamoeba | Acanthamoeba polyphaga | amoebic keratitis or chronic granulomatous amoebic meningoencephalitis 28 | ||||||||||
| Alveolata | Cryptosporidium | Cryptosporidium parvum | cryptosporidiosis (human genotype), cryptosporidiosis (calf genotype 2) 115 | http://www.parvum.mic.vcu.edu/ | ||||||||
| Cryptosporidium | Cryptosporidium hominis | cryptosporidiosis (human genotype) 115 | ||||||||||
| Plasmodium vivax | malaria | |||||||||||
| Plasmodium | Plasmodium falciparum | malaria | NC_004325 | |||||||||
| Diplomonadida | Giardia | Giardia intestinalis | giardiasis (human genotype) 116 | |||||||||
| Heterolobosea | Naegleria | Naegleria fowleri | primary amebic meningoencephalitis 28 | |||||||||
| Bacteria | Actinobacteria | Corynebacterium | Corynebacterium diphtheriae | diphtheria | NC_002935 | |||||||
| Corynebacterium | Corynebacterium xerosis | corynebacterial endocarditis 28 | ||||||||||
| Corynebacterium | Corynebacterium amycolatum | corynebacterial endocarditis 28 | ||||||||||
| Mycobacterium | Mycobacterium tuberculosis | tuberculosis (multidrug-resistant strains) | NC_002755 | NC_000962 | ||||||||
| Mycobacterium | Mycobacterium avium | avian tuberculosis | NC_002944 | |||||||||
| Mycobacterium | Mycobacterium bovis | bovine tuberculosis 117 | NC_002945 | |||||||||
| Mycobacterium | Mycobacterium ulcerans | Buruli ulcer disease | ||||||||||
| Mycobacterium | Mycobacterium kansasii | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Mycobacterium | Mycobacterium xenopi | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Mycobacterium | Mycobacterium marinum | mycobacterial diseases other than tuberculosis 28 | NC_004506* | |||||||||
| Mycobacterium | Mycobacterium haemophilum | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Mycobacterium | Mycobacterium fortuitum | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Mycobacterium | Mycobacterium scrofulaceum | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Mycobacterium | Mycobacterium abscessus | mycobacterial diseases other than tuberculosis 28 | ||||||||||
| Rhodococcus | Rhodococcus equi | rhodococcosis 28 | ||||||||||
| Alphaproteobacteria | Anaplasma | Anaplasma phagocytophilum | human granulocytic ehrlichiosis 103, 104 | NC_004351* | ||||||||
| Bartonella | Bartonella quintana | trench fever 118 | NC_005955 | |||||||||
| Bartonella | Bartonella henselae | cat-scratch fever 118 | NC_005956 | |||||||||
| Brucella | Brucella melitensis | brucellosis 105 | NC_003317 | NC_003318 | ||||||||
| Brucella | Brucella melitensis biovar Abortus | brucellosis 105 | ||||||||||
| Brucella | Brucella melitensis biovar Suis | brucellosis 105 | NC_004310 | NC_004311 | ||||||||
| Rickettsia | Rickettsia conorii | African tick typhus 119 | NC_003103 | |||||||||
| Rickettsia | Rickettsia typhi | Murine typhus 120, 121 | ||||||||||
| Bacteroidetes | Chryseobacterium | Chryseobacterium meningosepticum | atypical bacterial meningitis and sepsis 28 | |||||||||
| Betaproteobacteria | Bordetella | Bordetella pertussis | whooping cough 122 | NC_002929 | ||||||||
| Burkholderia | Burkholderia cepacia | bacterial infections associated with cystic fibrosis 28 | NZ_AAEH00000000* | NZ_AAEI00000000* | ||||||||
| Burkholderia | Burkholderia pseudomallei | melioidosis 28 | NC_002930* | http://www.sanger.ac.uk/Projects/B_pseudomallei/ | ||||||||
| Neisseria | Neisseria meningitidis | meningococcal disease 109 | NC_003112 | NC_003116 | ||||||||
| Ralstonia | Ralstonia spp. | bacterial infections associated with cystic fibrosis 28 | ||||||||||
| Chlamydia | Chlamydia | Chlamydia trachomatis | chlamydial pneumonia and cardiovascular disease 123 | NC_000117 | ||||||||
| Chlamydophila psittaci | chlamydial pneumonia and cardiovascular disease 123 | |||||||||||
| Chlamydia | Chlamydophila pneumoniae | chlamydial pneumonia and cardiovascular disease 123 | NC_005043 | NC_002491 | NC_002179 | NC_000922 | ||||||
| Parachlamydia | Parachlamydia acanthamoebae | Chlamydia-like pneumonia 28 | ||||||||||
| Epsilonproteobacteria | Campylobacter | Campylobacter jejuni | campylobacterosis 64 | NC_002163 | ||||||||
| Helicobacter | Helicobacter pylori | peptic ulcer disease 124 | NC_000915 | NC_000921 | ||||||||
| Firmicutes | Bacillus | Bacillus cereus | food poisoning 28 | |||||||||
| Clostridium | Clostridium difficile | intestinal clostridiosis 28 | NC_002933* | |||||||||
| Clostridium | Clostridium perfringens | intestinal clostridiosis 28 | NC_003366 | |||||||||
| Enterococcus | Enterococcus faecium | vancomycin-resistant enterococcal disease 125, 126 | NZ_AAAK00000000* | |||||||||
| Gammaproteobacteria | Acinetobacter | Acinetobacter calcoaceticus | acinetobacter bacteremia 28 | |||||||||
| Acinetobacter | Acinetobacter baumanii | acinetobacter bacteremia 28 | ||||||||||
| Acinetobacter | Acinetobacter radioresistans | acinetobacter bacteremia 28 | ||||||||||
| Escherichia | Escherichia coli O157:H7 | hemorrhagic colitis, hemolytic uremic syndrome 127 | NC_002695 | NC_002655 | ||||||||
| Francisella | Francisella tularensis | tularemia | ||||||||||
| Haemophilus | Haemophilus influenzae | Haemophilus infections (including Brazilian purpuric fever) 128, 129 | NC_000907 | |||||||||
| Haemophilus | Haemophilus aegyptius | Haemophilus infections (including Brazilian purpuric fever) 130 | ||||||||||
| Klebsiella | Klebsiella pneumoniae | nosocomial Klebsiella pneumoniae | NC_002941 | |||||||||
| Legionella | Legionella pneumophila | legionellosis and Pontiac fever 28 | NC_002942* | http://genome3.cpmc.columbia.edu/~legion/ | ||||||||
| Legionella | Tatlockia micdadei | legionellosis and Pontiac fever 28 | ||||||||||
| Pseudomonas | Pseudomonas aeruginosa | Pseudomonas aeruginosa bacteremia (including antibiotic-resistant strains) | ||||||||||
| Salmonella enteriditis | salmonellosis 131 | |||||||||||
| Salmonella | Salmonella typhimurium | salmonellosis 131 | ||||||||||
| Vibrio | Vibrio parahaemolyticus | vibrio gastroenteritis or dermatitis 28 | NC_004603 | NC_004605 | ||||||||
| Vibrio | Vibrio vulnificus | vibrio gastroenteritis or dermatitis 28 | NC_004459 | NC_004460 | NC_005139 | NC_005140 | ||||||
| Spirochaetes | Borrelia | Borrelia burgdorferi | Lyme disease 132 | NC_001318 | ||||||||
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