Infection and Disease I

The Normal Microflora of the The Normal Microflora of the Human BodyHuman Body

Humans as Habitats

Bodies are great places to be!Bodies are great places to be! Warm, stable, lots of nutrients available, constant pH and osmotic pressure, etc.Warm, stable, lots of nutrients available, constant pH and osmotic pressure, etc.

Our bodies are not uniform environments, thoughOur bodies are not uniform environments, thoughEach region or organ differs: skin, GI tract, respiratory tract, etc. provide Each region or organ differs: skin, GI tract, respiratory tract, etc. provide

different conditionsdifferent conditions

Animals possess great defense mechanismsAnimals possess great defense mechanismsThe successful colonizers (and the successful pathogens -- more on this next The successful colonizers (and the successful pathogens -- more on this next

lecture) are those that can get around these defenseslecture) are those that can get around these defenses

““Normal” doesn’t mean non-pathogenic; we sometimes have Normal” doesn’t mean non-pathogenic; we sometimes have pathogens (pathogens (S. pyogenes, S. aureus, S. pyogenes, S. aureus, etc.) in low numbers in and etc.) in low numbers in and on uson us

Humans as Habitats (cont.)Colonization (and infection) frequently begin at Colonization (and infection) frequently begin at

mucous membranesmucous membranesThese are found throughout the body. Consist of single or multiple These are found throughout the body. Consist of single or multiple layers of layers of epithelial cellsepithelial cells, tightly packed cells in direct contact with the , tightly packed cells in direct contact with the external environment.external environment.

Bacteria may Bacteria may associate loosely associate loosely or firmlyor firmly

Breaches in the Breaches in the mucosal barrier mucosal barrier can result in can result in infection infection (pathogenesis)by (pathogenesis)by opportunistic opportunistic pathogenspathogens

How we get our indigenous microflora?

• Normally, a human fetus has Normally, a human fetus has nono resident resident microorganismsmicroorganisms

• Initial colonization comes during breaking of fetal Initial colonization comes during breaking of fetal membranes and, especially, birth itself.membranes and, especially, birth itself.

• Environment in general is colonization source: Environment in general is colonization source: mother, father, doctor, etc. Can vary by wards.mother, father, doctor, etc. Can vary by wards.

• Initial microflora depends on whether infant is Initial microflora depends on whether infant is breastfed or not. breastfed or not. BifidobacteriumBifidobacterium vs. others. vs. others.

Effects of breastfeeding vs. bottle-feeding on indigenous microflora

• Large effect seen -- breastfed infants develop primarily Large effect seen -- breastfed infants develop primarily BifidobacteriumBifidobacterium populations, bottle-fed get a mixture of populations, bottle-fed get a mixture of various species of coliforms, various species of coliforms, ClostridiumClostridium, , StaphylococcusStaphylococcus, , StreptococcusStreptococcus, , LactobacillusLactobacillus, etc., etc.

• Breastfed infants have Breastfed infants have lower pHlower pH and and less buffering less buffering capacitycapacity in large intestine. This disfavors enterobacteria in large intestine. This disfavors enterobacteria and favors and favors Bifidobacteria. Bifidobacteria.

• BifidobacteriumBifidobacterium seem to seem to compete with potential pathogenscompete with potential pathogens like like ClostridiumClostridium difficiledifficile and some enterobacteria and some enterobacteriaOne study demonstrated that bottle-fed infants were 4X as likely as One study demonstrated that bottle-fed infants were 4X as likely as

breastfed ones to harbor breastfed ones to harbor C. difficileC. difficile..

Normal flora of specific regions• SkinSkin• Oral cavityOral cavity• Gastrointestinal tractGastrointestinal tract• Other areasOther areas

Upper respiratory tractUpper respiratory tract Lower respiratory tractLower respiratory tract Urogenital tractUrogenital tract

Microorganisms are normally Microorganisms are normally notnot found in the found in the organs, blood, or lymph. (if they are, you’re in organs, blood, or lymph. (if they are, you’re in trouble!)trouble!)

Skin surface is unfavorable habitat. Skin surface is unfavorable habitat. Usually only populated by Usually only populated by transienttransient microbes microbes Exceptions are moister areas: scalp, face, ears, Exceptions are moister areas: scalp, face, ears,

underarms, genitourinary, palms, toes.underarms, genitourinary, palms, toes.

Most Most residentresident skin microorganisms inhabit deeper skin microorganisms inhabit deeper layers of the epidermis, sweat glands, and layers of the epidermis, sweat glands, and follicles.follicles.

Most of the residents are Gram-positives, especially Most of the residents are Gram-positives, especially Staphylococcus Staphylococcus and and PropionibacteriumPropionibacterium

Normal flora of the skin

Normal flora of the skin (cont.)

The dermis and subcutaneous tissue are normally sterileThe dermis and subcutaneous tissue are normally sterile

Microorganisms are primarily associated with glands:Microorganisms are primarily associated with glands:1) 1) Eccrine glandsEccrine glands

Widely distributedWidely distributed Main glands for perspiration; secrete a hypotonic saline solution with a Main glands for perspiration; secrete a hypotonic saline solution with a

variety of organic and inorganic substancesvariety of organic and inorganic substances Relatively devoid of microorganisms, probably due to salinity and low pHRelatively devoid of microorganisms, probably due to salinity and low pH

2) 2) Apocrine glandsApocrine glands Restricted to underarms, genitals, etc.Restricted to underarms, genitals, etc. Don’t develop before pubertyDon’t develop before puberty Apocrine sweat has higher pH than eccrine sweatApocrine sweat has higher pH than eccrine sweat Population numbers can be highPopulation numbers can be high

3) 3) Sebacious glandsSebacious glands -- associated with hair follicles -- associated with hair follicles Produce Produce sebumsebum, chief component of skin lipids, chief component of skin lipids These lipids have antibacterial activity, esp. against Gram-positive cocciThese lipids have antibacterial activity, esp. against Gram-positive cocci..

Normal flora of the skin (cont.)

Common Skin Bacterium May Be New Opportunistic Common Skin Bacterium May Be New Opportunistic PathogenPathogen

(A.H. Chagla, A.A. Borczyk, R.R. Facklam, and M. Lovgren. 1998. Breast abscess (A.H. Chagla, A.A. Borczyk, R.R. Facklam, and M. Lovgren. 1998. Breast abscess associated with associated with Helocococcus kunziiHelocococcus kunzii. Journal of Clinical Microbiology. 36:2377-2379.). Journal of Clinical Microbiology. 36:2377-2379.)

A usually harmless bacterium, commonly found on human skin, may be A usually harmless bacterium, commonly found on human skin, may be an emerging opportunistic pathogen, say researchers from the London Public an emerging opportunistic pathogen, say researchers from the London Public Health Laboratory; the Central Public Health Laboratory of Toronto; the National Health Laboratory; the Central Public Health Laboratory of Toronto; the National Center for Streptococcus in Edmonton, Alberta, Canada; and the U.S. Centers for Center for Streptococcus in Edmonton, Alberta, Canada; and the U.S. Centers for Disease Control and Prevention. They report a case of infection by this organism Disease Control and Prevention. They report a case of infection by this organism the August 1998 issue of the the August 1998 issue of the Journal of Clinical MicrobiologyJournal of Clinical Microbiology..

Helococcus kunziiHelococcus kunzii is a recently identified bacterium that is thought to be is a recently identified bacterium that is thought to be a nonpathogenic member of normal human skin flora and is rarely associated with a nonpathogenic member of normal human skin flora and is rarely associated with skin infections. In the study though, the researchers report the isolation of the skin infections. In the study though, the researchers report the isolation of the organism from an infected cyst on the breast of a 57-year-old organism from an infected cyst on the breast of a 57-year-old immunocompromised woman.immunocompromised woman.

"Our finding provides further support for the opportunistic role of "Our finding provides further support for the opportunistic role of H. H. kunziikunzii in causing infection in both immunosuppressed and immunocompetent in causing infection in both immunosuppressed and immunocompetent patients," say the researchers.patients," say the researchers.

Aromabacter malodorens is the bacterium that colonizes healthy human skin. This organism grows on sweat and produces butyrate and other organic acids which smell bad in high concentrations.

This past year, scientists affiliated with the International Society for Microbial Ecology created a genetically engineered strain of this microorganism that can help banish unpleasant underarm odor.

Scientists removed the butyrate synthase gene that causes one of the unpleasant odors. Scientists then inserted the DNA from an Asian Musk Deer that encodes muskolic acid. Muskolic acid is the compound that gives musk oil its characteristic smell.

In preliminary studies, this new strain of Aromabacter malodorens survives well on the human skin. Scientists are now working on ways for the genetically engineered bacteria to out compete native populations of foul-smelling bacteria.

The ISME plans to market an underarm deodorant containing these new bacteria and license this technology to other deodorant manufacturers. Because the deodorant is self-replicating, it requires only monthly application.

If this microorganism sells well, the ISME plans to genetically engineer a mint-flavored bacterium for the mouth.

If you would like more information or would like to participate in a deodorant trial, please email Dr. Gutensmell. Enjoy April Foolery.

Normal flora of the mouth

A great place to live! (in contrast to the skin)A great place to live! (in contrast to the skin)The only negatives: salivary enzymes (The only negatives: salivary enzymes (lysozymelysozyme and and

lactoperoxidaselactoperoxidase), and constant need to re-attach), and constant need to re-attach

InitiallyInitially (i.e. at birth) (i.e. at birth), there are only a limited number , there are only a limited number of bacterial types (aerotolerant anaerobes like of bacterial types (aerotolerant anaerobes like LactobacillusLactobacillus and and StreptococcusStreptococcus), then ), then as teeth eruptas teeth erupt there are more anaerobes and bacteria adapted to there are more anaerobes and bacteria adapted to living in crevices and on smooth surfaces.living in crevices and on smooth surfaces.

Biofilm (plaque) formation

Begins as thin film of glycoproteins Begins as thin film of glycoproteins in salivain saliva

This is colonized (quickly) by This is colonized (quickly) by individual individual StreptococcusStreptococcus ( (S. S. mutansmutans, etc.) cells, which grow to , etc.) cells, which grow to microcoloniesmicrocolonies

Extensive growth of these results in Extensive growth of these results in formation of a thick biofilm. formation of a thick biofilm. Further colonization can include Further colonization can include filamentous forms, spirochetes, filamentous forms, spirochetes, and various anaerobes.and various anaerobes.

Scanning electron micrograph of dental plaque. The many different kinds of Scanning electron micrograph of dental plaque. The many different kinds of bacteria composing the plaque exhibit specific attachments to the tooth bacteria composing the plaque exhibit specific attachments to the tooth

and to each otherand to each other

Plaque accumulates calcium salts to form tartarPlaque accumulates calcium salts to form tartar

http://www.buckman.com/eng/biofilm3.htmhttp://www.buckman.com/eng/biofilm3.htm

CaCa33(PO(PO44) ) 22 scale (tartar) from human scale (tartar) from human toothtooth

Scale magnified 7,000x to show imbedded Scale magnified 7,000x to show imbedded bacterial biofilmbacterial biofilm

http://www.buckman.com/eng/biofilm3.htmhttp://www.buckman.com/eng/biofilm3.htm

Normal flora of the GI tract

The body is like a The body is like a donut, with the donut, with the alimentary canal alimentary canal the ‘inside’ of the the ‘inside’ of the donut. Things donut. Things inside the inside the alimentary canal alimentary canal are not truly are not truly ‘inside’ the body‘inside’ the body

Normal flora of the GI tract (cont.)

Stomach

• pH of stomach is low, around 2pH of stomach is low, around 2

• Acts as a microbiological barrierActs as a microbiological barrier

• Bacterial count of stomach contents is low, Bacterial count of stomach contents is low, but walls can be heavily colonized.but walls can be heavily colonized.Primarily Primarily LactobacillusLactobacillus and and StreptococcusStreptococcus

Gram-stained preparation of the stomach wall of a 14-day old Gram-stained preparation of the stomach wall of a 14-day old mouse, showing extensive development of lactic acid mouse, showing extensive development of lactic acid

bacteria in association with the epithelial layerbacteria in association with the epithelial layer

Helicobacter pylori, cause of stomach ulcers

Infection with Helicobacter pylori, the bacteria responsible for peptic ulcers, may be transmitted via

the hands In the study, researchers analyzed In the study, researchers analyzed H. pyloriH. pylori infections in a small, infections in a small,

rural population in Guatemala, testing blood samples, oral rural population in Guatemala, testing blood samples, oral samples and samples from underneath the fingernails. They samples and samples from underneath the fingernails. They found that over half of the subjects tested positive via blood test, found that over half of the subjects tested positive via blood test, nearly 90 percent tested positive for oral carriage of the nearly 90 percent tested positive for oral carriage of the infection and over half tested positive for fingernail carriage.infection and over half tested positive for fingernail carriage.

"Helicobacter pylori infection remains one of the most common in "Helicobacter pylori infection remains one of the most common in humans, but the route of transmission of the bacterium is still humans, but the route of transmission of the bacterium is still uncertain," say the researchers. "The results of this study uncertain," say the researchers. "The results of this study suggest that oral carriage of H. pylori may play a role in the suggest that oral carriage of H. pylori may play a role in the transmission of infection and that the hand may be instrumental transmission of infection and that the hand may be instrumental in transmission.”in transmission.”

(S.A. Dowsett, L. Archila, V.A. Segreto, C.R. Gonzalez, A. Silva, K.A. Vastola, R.D. Bartizek and M.J. Kowolik. 1999.Journal of Clinical Microbiology. 37: 2456-2460.)

Normal flora of the GI tract (cont.)

The upper portions of the The upper portions of the small intestinesmall intestine are are acidic and resemble the stomach. The lower acidic and resemble the stomach. The lower portions have increasing numbers of portions have increasing numbers of bacteria, from 10bacteria, from 1055 to 10 to 1077 per gram. per gram.

The The large intestinelarge intestine has enormous numbers of has enormous numbers of bacteria, 10bacteria, 101010 to 10 to 101111 cells/gram! Is cells/gram! Is essentially a fermentation vessel.essentially a fermentation vessel.

Why don’t all these commensal bacteria produce a constant and massive inflammation

of the GI tract epithelial cells?

A recent study published in the journal A recent study published in the journal ScienceScience indicates that the normal flora indicates that the normal flora apparently apparently shuts offshuts off the inflammation the inflammation

response in host epithelial cellsresponse in host epithelial cells

See See http://www.http://www.sciencemagsciencemag.org/.org/cgicgi/content/full/289/5484/1483/content/full/289/5484/1483

Normal flora of other places

Urogenital tractUrogenital tract -- bladder usually sterile but -- bladder usually sterile but urethra epithelium colonized by facultative urethra epithelium colonized by facultative Gram-neg. rods like Gram-neg. rods like E. coliE. coli. These can . These can become opportunistic pathogens. become opportunistic pathogens.

Upper respiratory tractUpper respiratory tract -- -- Staphylococcus, Streptococcus, Staphylococcus, Streptococcus, diphtheroid bacilli, Gram-neg. diphtheroid bacilli, Gram-neg. cocci. Also some pathogenscocci. Also some pathogens

Lower respiratory Lower respiratory tracttract -- essentially -- essentially sterilesterile