DR. AMADIN A. OLOTU

LECTURER/CONSULTANT CLINICAL MICROBIOLOGIST

BOWEN UNIVERSITY/BOWEN UNIVERSITY TEACHING HOSPITAL OGBOMOSO

▪ Introduction to Taxonomy

▪ Examples of Classification Schemes for Organisms

▪ Classification of Bacteria

▪ Classification of Fungi

▪ Classification of Viruses

▪ Classification of Helminths

▪ Classification of Protozoa

▪ The science of taxonomy involves not just naming organisms, but grouping them with other organisms that share common properties.

▪ It is the classification of organisms in an ordered system that indicates a natural relationship

▪ A taxon is a collection of related organisms grouped together for purposes of classification. Thus, genus, family, etc. are taxons.

▪ The Swedish botanist Linnaeus introduced the ´ binomial systemof nomenclature, by which each organism was assigned a genus and a species.

▪ The ranks commonly used are kingdom, phylum, class, order, family, genus, and species

▪ family, genus, and species are the most useful to us.

▪ The first letter in the genus name is always written as a capital letter and the other letters as small letters while all the letters in the species name are written as smallletters.

▪ The genus and species name are italicised, or, if this isn’t possible, underlined

▪ Homo sapiens

▪ Escherichia coli

▪ In the past bacteria have been grouped and named primarily based on their morphology, staining reactions, biochemical properties, nutritional requirements and antigenic differences.

▪ So there was a reliance on phenotype or observable characteristics.

▪ More recently classification has relied more on genotype or genetic make up.

▪ Comparison of nucleic acid sequences, notably those of 16S ribosomal RNA genes, has led to a new, phylogenetically based scheme of classification, that is, one based on how closely, different groups of bacteria are thought to be related, rather than what morphological or physiological features they may share.

▪ This has led to reclassification of some organisms.

▪ Different schemes for classification of organisms have been proposed over the years

▪ One of the most widely accepted of these was the five kingdom system proposed by Robert Whittaker in 1969

▪ Monera

▪ Protista

▪ Fungi

▪ Plantae

▪ Animalia

Whittaker’s five-kingdom system of classification

Examples of Classification Schemes for Organisms

EXAMPLES OF CLASSIFICATION SCHEMES FOR ORGANISMS

▪ Monera: This kingdom included all prokaryotic organisms. Unicellular microorganism such as bacteria and archaebacteria were grouped under kingdom Monera.

▪ Protista: This kingdom included eukaryotic unicellular protozoans, slime molds and algae. Organisms with a typical eukaryotic cell organization.

▪ Fungi: This kingdom included non green, non photosynthetic eukaryotic fungi. Molds, mushroom, toad stools, puffballs and bracket fungi were grouped under this kingdom. They are multicellular and consist of specialized eukaryotic cells arranged in a filamentous form.

▪ Plantae: It included all multicellular plants of land and water which use photosynthesis to synthesize their organic molecules.

▪ Animalia: This kingdom included all multicellular eukaryotic animals.

PROPERTIES OF THE FIVE KINGDOMS IN WHITTAKER’S CLASSIFICATION

Kingdom Monera Protista Fungi Plantae Animalia

Cell type Prokaryotic Eukaryotic Eukaryotic Eukaryotic Eukaryotic

Cell

organization

Unicellular Unicellular Multicellular/uni

cellular

Multicellular Multicellular

Cell Wall Mostly present Present/absent Present Present Absent

Nutritional

class

Phototrophic/heterot

rophic/chemoautotro

phic

Heterotrophic/ph

ototrophic

Heterotrophic Phototrophic Heterotrophic

Mode of

nutrition

Absorptive Absorptive/inges

tive

Absorptive Mostly

Absorptive

Mostly

ingestive

Examples of Classification Schemes for Organisms

Note!!!!

Phototrophic organisms use light as their source of energy

Heterotrophic organisms can only obtain carbon from organic compounds and therefore use them as their

carbon source.

Chemotrophic organisms use chemical compounds as their source of energy

Autotrophic organisms can obtain carbon from carbon dioxide which is an inorganic source of carbon

Chemoautotrophic organisms are organisms that obtain energy from chemical compounds and obtain

carbon from carbon dioxide an inorganic source

▪ However molecular studies in the 1970s revealed that the Archaea differed from all other bacteria in their 16S rRNA sequences, as well as in their cell wall structure, membrane lipids

▪ These differences were seen as sufficiently important for the recognition of a third basic cell type to add to the procaryotes and eucaryotes.

▪ This led to the proposal of a three-domain scheme of classification:

▪ Archaea, Bacteria and Eucarya

▪ The Three-Domain System was first proposed by Carl Woese in 1990.

▪ This classification system divides life forms into three domains and six kingdoms.

▪ The three-Domains are Archaea, Bacteria, Eukarya

▪ The six kingdoms are:

▪ under the Domain Archaea - Kingdom Archaebacteria

▪ under the Domain Bacteria – Kingdom Eubacteria

▪ under the Domain Eukarya – Kingdom Protista, Kingdom Fungi, Kingdom Plantae, Kingdom Animalia.

▪ This classification system divides the life based on the differences in the 16S ribosomal RNA (rRNA) structure and as well as the cell’s membrane lipid structure and its sensitivity to antibiotics.

▪Domain Archaea▪ The organisms in the Domain Archaea (Kingdom Archaebacteria) possess the following

characteristics:

▪ Archaea are prokaryotic cells.

▪ Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains) attached to glycerol by ether linkages.

▪ The cell walls of Archaea contain no peptidoglycan.

▪ Archaea are not sensitive to some antimicrobials that affect the Bacteria, but are sensitive to some antimicrobials that affect the Eukarya.

▪ Archaea contain rRNA that is unique to the Archaea this is demonstrated by the presence of molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

▪Domain Bacteria▪ The organisms in Domain Bacteria (Kingdom Eubacteria) possess the following

characteristics:

▪ Bacteria are prokaryotic cells.

▪ Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages

▪ The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan.

▪ Bacteria are sensitive to antibiotics which are antibacterial antimicrobials but are resistant to most antimicrobials that affect Eukarya.

▪ Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

▪Domain Eukarya▪ The organisms in the Domain Eukarya possess the following characteristics:

▪ Eukarya have eukaryotic cells.

▪ Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages

▪ Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.

▪ Eukarya are mostly resistant to traditional antibacterial antimicrobials but are sensitive to various antimicrobials that affect eukaryotic cells.

▪ Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Bacteria.

▪Domain Eukarya▪ The Eukarya are divided into four kingdoms:

▪ Kingdom Protista: Protista also called protists are unicellular eukaryotic organisms. Examples are slime molds, algae, and protozoans.

▪ Kingdom Fungi: Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples are yeasts, and molds.

▪ Kingdom Plantae: Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include ferns, and flowering plants.

▪ Kingdom Animalia: Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include worms, insects, and vertebrates.

▪ Using the 3 domain system of classification the bacterium: Escherichia coli would be classified scientifically as;

▪ Domain: Bacteria

▪ Kingdom: Eubacteria

▪ Phylum: Proteobacteria

▪ Class: Gammaproteobacteria

▪ Order: Enterobacteriales

▪ Family: Enterobacteriaceae

▪ Genus: Escherichia

▪ Species: Escherichia coli

▪ However what is more useful to us clinically is a classification based on certain characteristics especially characteristics that can be used in identification

▪ The simplest and most useful classification of bacteria is based on their gram stain reaction and morphology

▪ Gram stain reaction

▪ Developed by Hans Christian Gram

▪ Based on cell wall differences

▪ Enables us view bacteria from specimens or culture under the microscope

▪ Gram stain Method:

▪ 1 Fix the dried smear with heat or alcohol

▪ 2 Cover the fixed smear with Crystal violet stain for 30–60 seconds.3 Rapidly wash off the stain with clean water.4 Tip off all the water, and cover the smear with Lugol’s iodine for 30–60 seconds.5 Wash off the iodine with clean water.6 Decolorize rapidly (few seconds) with acetone. Wash immediately with clean water.7 Cover the smear with Safranin stain for 1-2 minutes.8 Wash off the stain with clean water.9 Wipe the back of the slide clean, and place it in a draining rack for the smear to air-dry.10 Examine the smear microscopically, first with the 40x objective to check the staining and to see the distribution of material, and then with the oil immersion or 100x objective to report the bacteria and cells

Gram negative bacilli Gram positive cocci

Classification of Bacteria

▪ Principle of the gram stain

▪ – Gram positive bacteria have a thick layer of peptidoglycan and when acetone is applied in the decolorization step in the gram stain they retain the complex of crystal violet and lugols iodine because of the thick peptidoglycan layer and so do not take up the counterstain safranin and so look purple or dark blue under the microscope.

▪ Gram negative bacteria on the other hand when decolorized by acetone do not retain the crystal violet – lugols iodine complex because they have a thin layer of peptidoglycan so they take up the counterstain safranin and appear red or pink under the microscope.

▪ Based on gram stain and morphology some common genera of medically important bacteria are:

▪ Gram positive cocci:

▪ Staphylococci

▪ Streptococci

▪ Gram positive bacilli

▪ Bacillus (spore forming)

▪ Clostridium (spore forming)

▪ Corynebacterium ( non spore forming)

▪ Listeria (non spore forming)

▪ Gram negative cocci

▪ Neisseria

▪ Moraxella

▪ Gram negative bacilli

▪ Escherichia

▪ Klebsiella

▪ Enterobacter

▪ Citrobacter

▪ Proteus

▪ Shigella

▪ Salmonella

Morphology Gram positive Gram negative

Coccus/cocci (spherical) Streptococcus

Staphylococcus

Neisseria

Bacillus/bacilli (rod shaped) Listeria

Corynebacterium

Bacillus

Clostridium

Escherichia coli

Klebsiella

Enterobacter

Citrobacter

Proteus

Salmonella

Shigella

Yersinia

Pseudomonas

Vibrio

Campylobacter

Helicobacter

Spiral Spirochetes

Treponema

Borrelia

Leptospira

Branching filamentous growth Actinomyces

Norcardia (partially acid fast)

Pleomorphic Chlamydia

Rickettsiae

Absence of a cell wall Mycoplasma ( cannot be classified as gram positive or gram negative)

Acid fast – Mycobacterium cannot be stained using the gram stain rather Ziehl Neelson is used

▪ One important property that can be used to classify bacteria is:

▪ How the organism deals with oxygen:

▪ Molecular oxygen is very reactive, and when it snatches up electrons, it can form hydrogen peroxide (H2O2),

▪ superoxide radicals (02-), and a

▪ hydroxyl radical (OH-).

▪ All of these are toxic unless broken down

▪ There are 3 enzymes that some bacteria possess to break downthese oxygen products:

▪ Catalase breaks down hydrogen peroxide

▪ Peroxidase also breaks down hydrogen peroxide

▪ Superoxide dismutase breaks down the superoxide radical

▪ Bacteria with these enzymes can survive in the presence of oxygen while bacteria without these enzymes will not survive in the presence of oxygen so based on this we can classify bacteria as:

▪ Obligate aerobes

▪ Facultative anaerobes

▪ Microaerophilic

▪ Obligate anaerobes

Staining

Reacttion

Obligate

aerobes

Facultative

Anaerobes

Microaerophill

ic

Obligate

anaerobes

Gram positive Nocardia

(weakly acid

fast)

Bacillus cereus

Staphycoccus

Bacillus anthracis

Corynebacterium

Listeria

Actinomyces

Clostridium

Gram negative Neisseria

Pseudomonas

Bordetella

Legionella

Brucella

Enterobacteriacea

e

Spirochaetes

Treponema

Borrelia

Leptospira

Campylobacter

Bacteroides

Acid fast Mycobacterium

Norcardia

No cell wall

Mycoplasma

▪ Fungi are

▪ Nonmotile eukaryotic organisms, with cell walls and which produce filamentous structures and spores.

▪ They exist as unicellular forms called yeasts or multicellular filamentous forms called moulds

▪ They are considered saprophytes

▪Two kinds of classification commonly used

▪Morphologic classification and Clinical classification

▪Morphologic Classification▪Yeasts (unicellular forms) eg Candida spp.

▪Moulds (multicellular filamentous forms) eg Aspergillus spp.

▪Dimorphic fungi – can exist as yeasts and moulds at different temperatures eg Histoplasmosis spp

▪Clinical Classification▪ Superficial mycoses –fungal infection of the superficial layers

of the skin eg

▪ Cutaneous mycoses –fungal infection of keratinized tissue (skin, hair and nails)

▪ Subcutaneous mycoses –fungal infection of subcutaneous tissue

▪ Systemic mycoses –fungal infections that are systemic in nature involving deep tissue and organs.

▪ Opportunistic mycoses –fungal infections that occur mainly in the immunocompromised

Type of Mycosis Disease Causative Fungal Agents

Superficial mycoses Pityriasis versicolor Malassezia species

Tinea nigra Hortaea werneckii

White piedra Trichosporon species

Black piedra Piedraia hortae

Cutaneous mycoses Dermatophytosis Microsporum species, Trichophyton species, and Epidermophyton floccosum

Candidiasis of skin, mucosa, or nails Candida albicans and other Candida species

Subcutaneous mycoses Sporotrichosis Sporothrix schenckii

Chromoblastomycosis Phialophora verrucosa, Fonsecaea pedrosoi, and others

Mycetoma Pseudallescheria boydii, Madurella mycetomatis, and others

Phaeohyphomycosis Exophiala, Bipolaris, Exserohilum, and other dematiaceous mold

Systemic mycoses Coccidioidomycosis Coccidioides posadasii and Coccidioides immitis

Histoplasmosis Histoplasma capsulatum

Blastomycosis Blastomyces dermatitidis

Paracoccidioidomycosis Paracoccidioides brasiliensis

Opportunistic mycoses Systemic candidiasis C. albicans and many other Candida species

Cryptococcosis Cryptococcus neoformans and Cryptococcus gattii

Aspergillosis Aspergillus fumigatus and other Aspergillus species

Hyalohyphomycosis Species of Fusarium, Paecilomyces, Trichosporon, and other hyaline molds

Phaeohyphomycosis Cladophialophora bantiana; species of Alternaria, Cladosporium, Bipolaris,

Exserohilum, and numerous other dematiaceous molds

Mucormycosis Species of Rhizopus, Lichtheimia, Cunninghamella, and other members of the Order

Mucorales

Pneumocystis pneumonia Pneumocystis jiroveci

Penicilliosis Talaromyces marneffei

▪ Viruses are

▪ obligate intracellular organisms that contain either RNA or DNA but never both. They are some of the smallest infective agents, which can affect man, animals or plants. Sizes range from 10 to 300nm in diameter.

▪ Viruses depend on the metabolic machinery of the host cell for their replication

▪ Viral Structure

▪ Components of a typical virus

▪ Viral genome or Nucleic acid - RNA or DNA

▪ Capsid- The protein coat

▪ Envelope

▪ Enzymes

▪ Viruses have been separated or classed together on the basis of virion morphology, genome structure and strategies of replication into major groupings called families

▪ These virus family names have the suffix -viridae.

▪ Viruses are classified based on their:

▪ Nucleic acid:▪ Type of nucleic acid: DNA or RNA

▪ Double- or single-stranded

▪ Single or segmented pieces of nucleic acid

▪ Positive stranded (positive sense) RNA or negative stranded (negative sense) RNA

▪ Capsid:▪ Icosahedral

▪ Helical

▪ Envelope:▪ Enveloped

▪ Unenveloped (Naked)

DNA VIRUSES

Enveloped Naked

Double stranded Double stranded Single stranded

Icosahedral Icosahedral IcosahedralComplex

ParvoviridaePapillomaviridae

Polyomaviridae

Adenoviridae

PoxviridaeHepadnaviridae

Herpesviridae Families

of viruses

RNA VIRUSES

Single strandedDouble stranded

Naked

Positive stranded Negative stranded

Reoviridae

Enveloped

Bunyaviridae

Orthomyxoviridae

Paramyxoviridae

Rhabdoviridae

Arenaviridae

Filoviridae

Naked Enveloped

Picornaviridae

CaliciviridaeTogaviridae

Flaviviridae

Icosahedral Icosahedral Helical

Coronaviridae

Icosahedral Helical

Families

of

viruses

Complex

Retroviridae

Classification of viruses that cause human disease

Nucleic Acid Virus Family Examples of Specific viruses or viral diseases

DNA Hepadnaviridae Hepatitis B virus

Herpesviridae Herpes simplex viruses, Varicella zoster virus

Adenoviridae Epidemic keratoconjuctivitis, Respiratory illness of childhood

Poxviridae Small pox, vaccinia virus

Parvoviridae Erythema infectiosum, Transient aplastic anaemia crisis

Papillomaviridae Human papilloma viruses

Polyomaviridae BK polyoma virus, JC polyoma virus

RNA Reoviridae Rotavirus

Picornaviridae Poliovirus

Caliciviridae Noroviruses

Togaviridae Alphaviruses, Rubella(rubivirus)

Flaviviridae Yellow fever virus, Dengue virus

Coronaviridae Common cold, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-

CoV

Retroviridae HIV-1, HIV-2

Bunyaviridae Hanta virus, Rift valley fever virus

Orthomyxoviridae Influenza viruses

Paramyxoviridae Parainfluenza virus, measles virus, mumps virus

Rhabdoviridae Rabiesvirus

Arenaviridae Lassa fever virus

Filoviridae Ebolavirus, Marburg virus

▪ The word helminth is derived from the Greek word for worm

▪ Helminths are multicellular organisms, they worms and range in size from microscopic to large enough to be seen by the naked eye.

▪ Those of medical importance can be classified based on their morphology into –

▪ Platyhelminths (flatworms) – these include:

▪ Trematodes (flukes)

▪ Cestodes (tapeworms)

▪ Nematodes (roundworms)

Trematode(fluke)

Cestode(Tapeworm)

Nematode(roundworm)

▪ Either

▪ The adult forms of these worms may reside in the gastrointestinal tract, blood, lymphatic system or subcutaneous tissues.

▪ Or

▪ The immature forms or larva may infect or invade various body tissues to cause disease.

▪ Thus we can also classify the helminths based on where in the body they reside

▪Intestinal helminthic infections

▪Nematodes▪ Enterobius vermicularis (pinworm)

▪ Trichuris trichiura (whipworm)

▪ Ascaris lumbricoides (human roundworm)

▪ Ancylostoma duodenale and Necator americanus (human hookworms)

▪ Strongyloides stercoralis (human threadworm)

▪ Trichinella spiralis

▪Trematodes▪ Fasciolopsis buski (giant intestinal fluke)

▪Cestodes▪ Taenia saginata (beef tapeworm)

▪ Taenia solium (pork tapeworm)

▪ Diphyllobothrium latum (broad fish tapeworm)

▪ Hymenolepis nana (dwarf tapeworm)

▪ Dipylidium caninum (dog tapeworm)

▪Blood and tissue helminthic infections

▪ Nematodes

▪ Wuchereria bancrofti (lymphatic filariasis)

▪ Brugia malayi (lymphatic filariasis)

▪ Onchocerca volvulus (river blindness)

▪ Dracunculus medinensis (Guinea worm)

▪ Ancylostoma duodenale and Necator americanus (hookworm)

▪ Strongyloides stercoralis (larva currens—see intestinal helminthic infections)

▪ Trichinella spiralis (trichinellosis from larvae—see intestinal helminthic infections)

▪ Trematodes

▪ Fasciola hepatica (sheep liver fluke)

▪ Clonorchis sinensis (Chinese liver fluke)

▪ Paragonimus westermani (lung fluke)

▪ Schistosoma mansoni, Schistosoma japonicum, Schistosoma haematobium (blood flukes)

▪ Cestodes (infections caused by the larval stages)

▪ Taenia solium (cysticercosis/neurocysticercosis—see intestinal helminthic infections)

▪ Echinococcus granulosus (hydatid cyst)

▪ Protozoa are microscopic, one-celled organisms

▪ The protozoa that infect humans can be classified into four groups based on their mode of movement:

▪ Sarcodina –(the amoeba) move with pseudopodia e.g. Entamoeba

▪ Mastigophora – (the flagellates) move with flagella e.g. Giardia, Leishmania

▪ Ciliophora – (the ciliates) move with cilia e.g. Balantidium

▪ Apicomplexa (Sporozoa) – organisms that have an apical complex and do not have flagella, cilia or pseudopods e.g. Plasmodium, Cryptosporidium

▪ They may also be classified based on where in the body they infect

Sarcodina(amoe

ba)

Mastigophora(flagellat

es)

Ciliophora(ciliat

es)

Apicomplexa(Sporoz

oa)

▪ Intestinal protozoa▪ G. lamblia (flagellate)

▪ Entamoeba histolytica (ameba)

▪ Balantidium coli (ciliate)

▪ Cryptosporidium hominis (sporozoa)

▪ Cyclospora cayetanensis (sporozoa)

▪ Sexually transmitted protozoan infection▪ Trichomonas vaginalis (flagellate)

▪ Blood and tissue protozoan infections

▪ Flagellates▪ T. brucei rhodesiense and T. brucei gambiense

▪ T. cruzi

▪ Leishmania donovani, Leishmania tropica, Leishmania mexicana

▪ Amebae▪ Entamoeba histolytica (see intestinal protozoa)

▪ Naegleria fowleri and Acanthamoeba castellanii

▪ Sporozoa▪ Plasmodium vivax, Plasmodium falciparum, Plasmodium ovale, and Plasmodium malariae

▪ Babesia microti

▪ Toxoplasma gondii

▪ Microsporidia

▪ Mandel, Douglas and Bennetts’ principles and practice of infectious diseases. 9th

ed.Philadelphia. Churchhill Livingstone Elsevier

▪ Jawetz, Melnink and Adelberg’s medical microbiology. 28th edition

▪ Clinical Microbiology Made Ridiculously Simple. Mark Gladwin Bill Trattler. Edition 3