reflected light is used to visualize bacteria too thin to be seen by bright field (e.g. Treponema pallidum) (diagnoses syphillis well)

stains extracellular medium, not cells (e.g. india ink stain for visualizing capsules)

Procedure = (1) crystal violet - primary stain (purple); (2) iodine - mordant (fixative); (3) alcohol - decolorizer; (4) Saffarnin - counterstain (red)

Gram-positive cell wall (extensive peptidoglycan layer) retains crystal violet-iodine complex; Gram-negative wall does not

round (shape)

clusters (arrangement)

chain (arrangement)

rod (shape)

Bacillus are Gram(+)positive

Two Bacillus species are considered medically significant: B. anthracis, which causes anthrax, and B. cereus, which causes a foodborne illness similar to that of Staphylococcus.A third species, B. thuringiensis, is an important insect pathogen, and is sometimes used to control insect pests. The type speciesis B. subtilis, an important model organism. It is also a notable food spoiler, causing ropiness in bread and related food.  

curved rod (shape) e.g. Vibrio

spirochetal (shape) e.g. Treponema

a bacterial flagellar antigen; important in serological identification of bacteria

a bacterial capsular antigen, external to the cell wall; important for serological identification

an aggregate of microorganisms in which cells adhere to each other in a self-producing matrix; a protected structure of bacterial cells/microcolonies enmeshed in mucoid (hydrated) exopolysaccharide adhering to a wet surface (inert or living) ... biofilms may form on living or non-living surfaces, and may be prevalent in industrial/hospital settings

bacteria with cell walls consisting of thick layers of peptidoglycan will retain the violet inkstain of the Gram stain procedure

bacteria with thinner cell walls with less peptidoglycan will lose the violet inkstain during the decolorization stage of Gram staining procedure

fabric shell encasing the cell; network of polymers, containing N-acetylmuramic acid and N-acetylglucosamine; N-acetylmuramic acid subunits on different strands are cross-linked via their peptide stems (aka amino acid sidechains), which provides mechanical strength and prevents the cell from bursting via osmotic pressure

lipopolysaccharide (aka endotoxin)

antigen occurring in the lipopolysaccharide layer of the wall of Gram-negative bacteria

the peptidoglycan layer … major function is osmotic protection; also function in nutrient uptake, sensory (chemotaxis) mechanism, degradative enzymes

composed of disaccharides, phosphate groups, and fatty acids … the toxicity of LPS lipopolysaccharide is primarily associated with Lipid A

part of LPS lipopolysaccharide; may contain sugars, aminosugar, sugar acids, sugar alcohols; often contains the uniqe sugar ketodeoxyoctulonate (KDO)

ketodeoxyoctulonate; unique sugar found in core polysaccharide of LPS

consists of a unit (sugars, aminosugars, sugar acids, sugar alcohols) repeated N-number of times … highly specific region, e.g. Salmonella

certain bacteria lack O-antigenic (LPS) chain, only contain Lipid A and extended core - e.g. Neisseria meningitidis, N. gonorrhoeae, Haemophilus influenzae, Haemophilus ducreyi

LOS is a potent endotoxin that can cause petichae, purpura, septic shock 

systemic inflammatory response syndrome … similar to acute inflammation (acute phase response), but on a systemic scale with macrophages, PMNs, endothelial cells serving as effector cells

disseminated intravascular coagulation; pathological activation of blood clotting

the presence of both (a) proven infection - e.g. pneumonia, UTI, bacteremia, as well as (b) SIRS

the presence of both (a) sepsis [= infection + SIRS] as well as (b) organ failure

the bresence of both (a) severe sepsis, as well as (b) refractory hypotension

caused by loss of fluid from the vascular system; blood pressure drops … not vascular obstructive, not cardiogenic

also known as autoprothrombin IIA and blood coagulation factor XIV ... protein C inhibits clotting (anticoagulant), activates fibrinolysis, inhibits inflammation ... does this by inactivating Factor Va and Factor VIIIa

pt's with deficiency or resistance to protein C will be at a significantly increased risk of forming dangerous blood clots (thrombosis)

additional polymer of glycerol or ribitol phosphate, found in Gram-positive cell wall stain … functions in adherence, antiphagocytic

additional polymers of glycerol or ribitol phosphate, found in Gram-positive cell wall stain … function to produce endotoxin-like shock, interacts with C-reactive protein, activates alternative complement pathway

pathogen-associated molecular patterns; include peptidoglycan, teichoic acids, CpG nucleotides, and of course LPS

the complete viral particle

protein subunits of the capsid; repetetive polypeptide subunits arranged in symmetric patterns = capsid

the protein shell (or coat) that encloses the core of the NA nucleic acid genome of a virus + any associated proteins

protein associated with the NA nucleic acid genome; the capsid together with the NA genome plus any associated proteins

the viral membrane; the "skullcap" or "scalp"; viral envelope is composed of virus-specific proteins plus host-derived lipids and carbohydrates (from nuclear, ER, Golgi, or cytoplasmic membranes) that the virus "wears" on its outer membrane; useful for identification

spikes … viral glycoproteins that form spike-like projections on the surface of the envelope and play a role in attachment

amorphous layer b/w nucleocapsid and envelope that mediates the interaction b/w capsid and envelope

infectious protein (misfolded) which causes disease in the CNS … NOT a virus

type of capsid symmetry found in animal viruses; capsomeres are arranged in triangles that form a symmetric figure

type of capsid symmetry found in animal viruses; capsomeres are arranged in a hollow core that appears helix-shaped

positive sense RNA resembles mRNA and thus can be immediately translated by the host cell ... the viral nucleic acid serves as mRNA, but they must encode for an RNA-dependent RNA polymerase to make the antisense RNA to produce the viral genome

have a reverse transcriptase (RNA dependent-DNA polymerase) which transcribes the (+)ssRNA to DNA, then the mRNA is transcribed from the viral specific DNA … this is the target for many anti-HIV drugs, e.g. AZT

RNA viruses can be classified according to the sense or polarity of their RNA. Positive sense viral RNA is similar to mRNA (can be immediately translated); whiel negative-sense RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation

These virions must contain functional proteins (an RNA-dependent-RNA polymerase) to make the mRNA as well as possess the gene that codes for the protein

involves lethal or non-lethal damage/alteration to cells and their functions, as a result of infection

involves periods of incubation or persistence, where there is an absence of disease symptoms during infection

ability of fungus to grow as a mycelial (mold) form at room temperature and a yeast form at 37*C

growth occurs by elongation of hyphae to form a mycelium … sexual and asexual spores produced

a long, branching filamentous structure of a fungus, or also the unrelated Actinobacteria (hypha of penicillum, above) ... cells are branching cylindrical tubules +/- septa or crosswalls; collectively called mycelium

mass of intertwined hyphae

eukaryotic microorganisms classified under the kingdom fugi ... yeasts are unicellular; asexual reproduction by budding

aka yeast

large (macro) spores (conidia), which are not enclosed in any sort of special structure, naked spores … macroconidia are infectious form for fungi that infect skin (Dermatophytes)

small (micro) spores (conidia), which are not enclosed in any sort of special structure, naked spores … microconidia are small enough to get to alveoli when inhaled and are the infectious form for certin fungi

protozoa; microscopic; single cells … motile by means of cytoplasmic extensions (pseudopodia)

protozoa; microscopic; single cells … motile by means of flagella

protozoa; microscopic; single cells … motile by means of cilia

protozoa; microscopic; single cells … complex life cycles with asexual and sexual stages

the worms. Adults mostly macroscopic, eggs microscopic. Mostly monoecious w/ male and female sex organs in the same individual

flatworms

tapeworms

round worms, nematodes

have complex growth requirements (specific nutrient, atmospheric, or temperature demands); this makes them difficult to cultivate in the laboratory

have less complex growth requirements, and are easier to cultivate in the laboratory

"salt lovers", e.g. Vibrio chlorae, V. parahaemolyticus

can grow in the presence of O2 because they produce enzymes which detoxify superoxide radicals and hydrogen peroxide

can grow in the presence of O2 because they produce enzymes which detoxify superoxide radicals and hydrogen peroxide

Some examples of facultative anaerobic bacteria are Staphylococcus (Gram positive), Escherichia coli and Shewanella oneidensis (Gram negative), andListeria (Gram positive). Certain eukaryote phyla are also facultative anaerobes, including fungi such as yeasts and many aquatic invertebrates such asNereid (worm) polychaetes, for example. There are also circulating white blood cells that are classified as facultative anaerobes. These include neutrophils,monocytes and tissue macrophages.  

enzyme of aerobes that detoxifies superoxide anion (O2*-)

enzyme of aerobes that detoxifies H2O2

require the presence of atmospheric O2 for growth, e.g. Mycobacterium tuberculosis

require the presence of some O2 but NOT at atmospheric levels (reduced O2), e.g. Campylobacter

can grow in the presence or absence of O2 … many pathogens are facultative anaerobes, e.g. enteric bacteria

can survive in the presence of O2, e.g. Lactobacillus spp.

are killed by the presence of O2, they are lacking in the enzymes superoxide dismutase and catalase, e.g. Clostridium, Bacteroides, and others

O2 is the terminal electron acceptor, which is reduced to water by the electron transport system … common among pathogenic microorganisms and humans

inorganic compounds (nitrate, sulfate, etc.) serve as terminal electron acceptors … this is significant especially for pregnant females, high levels of nitrites can cause methemoglobinemia (MetHb) especially in the fetus

kidney stones … the more alkaline pH in the urinary tract, the more the Ca2+ and NH4+ ions in the urine can form salts which may precipitate out, accumulating in stones

phase in the growth cycle, in which there is no change in cell number

follows lag phase in the growth cycle … growth occurs at an exponential/logarithmic rate during this phase

the time required for a parent to divide into two daughter cells … also known as the doubling time

phase in the growth cycle which follows log phase and where no net increase in cell numbers occurs

defined as the phase which follows the stationary phase of the growth cycle, and where cell death begins to occur at a logarithmic rate

a DNA or RNA molecule that controls its own replication and is capable of self-duplication

plasmids are DNA molecules that are separate from, and capable of replicating independently of, the chromosomal DNA; they are considered replicons, capable of autonomous replication, although they use the bacteria's replication machinery ... plasmids are double stranded covalently closed circular DNA molecules which reside in the bacterial cytoplasm. So they are extra-chromosomal elements.

encode for a mechanism of plasmid transfer (sex pilus)

encode for drug resistance

viruses (either DNA or RNA) which infect bacteria. Some bacteriophages can exist in a latent state in the bacterial cells. The viral DNA (prophage) either integrates into the host cell's chromosome or functions as a plasmid in the bacterial cytoplasm.

ability of bacteria to detect the size of their own population; a system of stimulus and response correlated to population density; can be used to coordinate gene expression

Some of the best-known examples of quorum sensing come from studies of bacteria. Bacteria use quorum sensing to coordinate certain behaviors based on the local density of the bacterial population. Quorum sensing can occur within a single bacterial species as well as between diverse species, and can regulate a host of different processes, in essence, serving as a simple communication network. A variety of different molecules can be used as signals. Common classes of signaling molecules are oligopeptides in Gram-positive bacteria, N-Acyl Homoserine Lactones (AHL) in Gram-negative bacteria, and a family of autoinducers known as autoinducer-2 (AI-2) in both Gram-negative and Gram-positive bacteria. 

process of acquiring new genetic information that involves acquisition of a gene from EXTERNAL sources

mechanism of horizontal gene transfer … occurs when there is replacement of a portion of the recipient's genome are replaced by homologous chromosomal genes from another (donor) bacteria; recipient must be "competent," so it can incorporates free donor DNA into its genome, e.g. recombination

mechanism of horizontal gene transfer … when the source of external genetic information is a conjugative (transmissable) plasmid carrying new or altered genes (from donor cell)

bacterial virus; any number of viruses that infect bacteria ... they do this by injecting genetic material (ssRNA, dsRNA, ssDNA, dsDNA) that was stored in their capsid into the bacteria ... phages are one of the most common and diverse entities in the biosphere

infects the bacterial host cell, replicates, then kills (lyses) the bacterium releasing the new progeny to injfect other cells … involved in transduction, form of horizontal gene transfer

infects the host bacterial cell, after which the phage has two options - either undergo the normal lytic cycle (infect, replicate, then lyse) or can become latent thus "lysogenizing" the bacterium (either by reamaining as plasmid in cytoplasm or by integrating/inserting into host cell DNA)

can remain latent inside bacterial host cell either by remaining as a plasmid in the cytoplasm or by integrating/inserting into the host cell DNA

when the recipient bacterial host cell is infected by a temperate virus … a bacterium exhibits a new phenotype due to the acquisition of a prophage (latent bacteriophage) which encodes for the new phenotype

PCR is the in vitro amplification of target DNA or RNA from an organism; the purpose is to amplify nucleic acid sequences which cannot be detected directly … i.e. standard for diagnosis of specific agents detection of Herpes simplex virus JC virus, enteroviruses, rabiesvirus in CNS

Microorganisms that are expected to be present, and that under normal circumstances do not cause disease, but instead participate in maintaining health, are deemed members of the normal flora. 

Normal flora bacteria can act as opportunistic pathogens at times of lowered immunity.  

indicators of fecal contamination and food; Gram-negative rods, facultative anaerobes

produced by Gram-negative organisms, is pyrogenic (fever-causing), is heat stable (survives autoclaving), does not form toxoids, broad spectrum of activity (affects a wide variety of animal species)

essentially always cause infection and/or disease in a specific host

microbial life form that essentially never cause disease, even if the host is severely compromised (e.g. lactobacillus)

determinants of virulence; any of a pathogens genetic, biochemical or structural features that enable it to produce disease in a host

virulence factors allow pathogens to colonize a host, evade immune responses, and obtain nutrition

Some virulence factors are intrinsic (capsule, endotoxin) while others are obtained from external (plasmids). LPS is the prototypical endotoxin; exotoxins include the tetanus toxin and the botulinum toxin 

similar to colonization; refer to someone who is actually infected or has been previously infected with a pathogen, carries that pathogen with them as part of their normal flora (transmission potential), but does not exhibit disease manifestations referable to the pathogen (i.e. inapparent carriage; or in salmonella carriage)

pathogen is present; but not active or manifest

clinically apparent invasion and multiplication of microbes in body tissues, causing local tissue injury

rapid onset (hours or days) and brief duration (days or weeks)

disease comes from a unique combination of events involving a (harmful) agent, a (susceptible) host, all in the same (proper) environment … disease can be blocked at any three of these "sides" of the "triangle"

zoonoses

herd immunity

the time between exposure to a pathogen and the appearance of the first symptoms of disease

administration of antimicrobials prior to onset of symptoms

antibiotics, for example, can be administered to patients with disorders of immune system dysfunction, to prevent opportunistic infection 

a significant (and usually sudden) increase above the endemic and sporadic rate of a disease … could be hours, days, months

a global epidemic (above the normal global endemic rate)

 e.g. herpes simplex virus 

w/ periods of dormancy

 e.g. measles virus (SSPE); human immunodeficiency virus (HIV)

A toxoid is a bacterial toxin (usually an exotoxin) whose toxicity has been weakened or suppressed either by chemical (formalin) or heat treatment, while other properties, typically immunogenicity, are maintained.

Toxoids are used as vaccines because they induce an immune response to the original toxin or increase the response to another antigen. For example, the tetanus toxoidis derived from thetetanospasmin produced by Clostridium tetani. The latter causes tetanus. Botulin is produced by Clostridium botulinum and it causes the deadly disease botulism.  

Septum is a small fissure formed during bacterial cell division ... Bacteria reproduce by an asexual process called binary fission. First, the DNA replicates and the cell elongates. In the middle of the elongated cell, a septum forms and this develops in to a cell wall that divides two seperate cells.

Inhibition of peptidoglycan synthesis inside an actively-dividing cell results in osmotic lysis; so if an organism is dividing more frequently, it will be lysed more frequently by the antibiotic

many antimicrobials utilize this - e.g. the penicillins, the cephalosporins, the carbapenems