Pathology Associates Of Lexington, P.A.
Pathology Associates Of Lexington, P.A.
Pathology Associates Of Lexington, P.A.
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        Germs With Us!

Our Body's ECOSYSTEM2: The human body has a microbiome of commensal (friendly) bacteria (about 1000 different strains), fungi, and parasites that vary somewhat from person to person and within which microbiome one finds various pathogenic (bad) organisms held in check by uncertain forces and balances of nature...a sort of personal ecosystem.

Our microbiome resides on all skin, within the intestinal tract, within the vagina, within the mouth, and in the outer airways & nose. A healthy person's microbiome may account for as much as 3% of their body mass! And, said another way, we have 10 organism cells for every human cell. We are (1) a person plus (2) our personal microbial zoo3! We may even be missing the benefits of a mutually balanced abnormal infestation of gut hookworms and/or pinworms; our immune systems may be the worse off for (1) a lack of impact from such organisms as well as (2) our fastidious cleanliness of homes & bodies (and attempts to nearly sterilize our bodies)3! Modern dietary & nondietary (even medicinal) intake may serve to unbalance the beneficially balanced population of our non-human intimate colleagues & partners (our microbiome "zoo"). For example, the unbalancing & inadvertant induction of antibiotic-induced C. difficile colitis leads to deaths in the USA in 2007 amounting to 17,000 deaths that year by such routes as acute toxic megacolon [L14-5689]!

SKIN: There is a normal and healthy flora of microbes that coat the skin surface. The same is true of the vagina & gut. But, here are some odd, non-dramatic skin infections (this is just a small sample) or populations (some dramatic stuff HERE) of various organism types:

  • bacterial:
    • erythrasma: brownish patches in intertriginous areas (armpits, under breasts, groin); it is due to Wood's-light fluorescing (because the bacteria contain porphyrins) Corynebacterium minutissimum (Wood's exam can be neg if patient bathed vigorously prior to office exam...therefore, could histology be false neg in same situation?. [clinical photo]1 Histology is of Gram negative rods & filamentous shapes in the cornified layer [S07-7665]. Treat with topical gel of 2% erythromycin.
    • post-injury skin infections: scratches, scrapes, stings, bites, punctures, and this includes surgical & other diagnostic and/or treatment-related & produced defects. These can become infected with bacteria that can cause kidney disease, bad MRSA skin infections and even "flesh eating bacteria".
    • vaginosis or vaginitis: overgrowth of non-lactobacilli, HERE.
  • mycobacterial:
    • histologically obvious granulomatous reaction: infectious vs. sarcoid ( surrounding lymphocytes...& non caseous granulomata which tend to be separate & negative for polys, eos, or plasma cells).
    • non-granulomatous reaction:
      • when severely immunocompromised patient (AIDS, etc.).
      • some of the atypical AFBs [S-02-6281].
  • viral: HSV vesicles (fever blister); dermatomal hypesthesia with & without vesicles...VZV; HPV warts; small pox (variola virus).
  • parasitic:
    • Demodex: extremely common in USA; a mite living in hair follicles...may cause demodecosis of eyelid margins and nose [HERE]...folliculitis & erythema. We frequently see these in follicles in skin biopsies (apparently NOT causing any disease).
    • malaria: mosquito transmitted, we diagnose a couple of cases per year at LMC.
    • babesia: carried mostly in the USA by the white tail deer tick (Xodes), maybe a case a year or less is diagnosed at LMC; a group of tick-borne protozoan parasites possibly visible in a blood smear within RBCs & causing hemolysis (elevated serum LDH) & always "bad". Other parasites in the tick could be Borrelia, Ehrlichia, and Anaplasma; and the spirochete of Lyme disease comes through ticks9.
    • sparganosis (tapeworm)6: Rare in the USA; it is an unusual complication of having (or having had) tapeworms; Skin lesions, LMC= S-84-71, LMC-89-590, S09-9949. At MUSC when EBS was there= S69-15382, S74-11406, S74-22621, & S74-23414.
    • Gnathostomiasis: rare in USA; from eating undercooked or raw infected foods, including freshwater fish, crustaceans (shrimp, crab, crayfish), frog meat, pork and chicken.
    • Paragonimiasis: rare in USA; liver or lung flukes from under-cooked crayfish and crabs.
    • Naegleria ameba infection: only 32 cases detected in USA 2001-2010; from swimming in stagnant, fresh water; Naegleria fowleri species infects humans, and does so by entering the body through the nose, where the amoeba then causes an infection called primary amebic meningoencephalitis (PAM).
    • Trichomonas vaginalis infection: this organism is a "protist" and simpler than an ameba & is one cause of vaginal discharge & is very common in the USA. Another far less common protist is Trichomonas tenax in the oral cavities of some dogs, cats, and humans.
  • fungal: follicles & hairs [S-04-4151], skin, nails:
    • Malassezia yeast/fungal ("tinea versicolor"...caused by the various M. & Pityrosporum species): pustular follicultitis, skin-multi-discolored & faintly scaling dermatosis, Gougerot-Carteau disease (confluent and reticulated papillomatosis), a pigmented eruption occurring mainly on the chest, back and neck of adolescent girls, & seborrheic dermatitis...excellent patient photos, etc., HERE. The fungal stains may show the yeasts in all cases (very scant in seb. derm.) and a mix of yeasts & hyphae in tinea versicolor (in a "spaghetti and meatballs" pattern...the skin lesions colored under Wood's light fluorescent light exam). Treatment
    • dermatophytic: dermatophytosis (skin infected); onychomycosis (nails infected).
    • uncertain consequences: Pityrosporum yeasts often are seen in skin follicles and between the keratotic layers in skin keratoses.
  • spirochetal:
    • large pox: the syphilis spirochete (Treponema pallidum).
    • erythema chronicum migrans (erythema migrans): skin lesion of early Lyme disease & caused by tick-borne Borrelia burgdorferi (any single tick-borne illness has a reasonable likelihood that that tick or another tick from that tick infested environment might have also passed on an additional agent such as babesia). The skin problem of late lyme disease is acrodermatitis chronicum atrophicans. Other Borrelia cause this lesion (at least one other in S. C. in 2010) and respond to the same treatment; but our Lyme serology test is burgdorferi specific. Lyme disease can go to a late stage with some serious consequences. Early stage Lyme disease serial serology testing is variably reported as 50% sensitive (that is, 50% with acute Lyme disease will have a negative serology) and can be blunted by deliberate or co-incidental antibiotic therapy. My (EBS's) daughter developed Bell's Palsy in 1989 at age 18 just as she began antibiotic treatment of acne. The serological test series showed a distinct rise and fall for Lyme disease that was blunted. Testing decision tree, HERE. Late stage disease serology is variably reported as 29-78% positive . So, it is very important to question about prior skin lesions even years prior and prior tick bites.
    • leptospirosis: skin jaundice when severe hepatitis.

GASTRO-INTESTINAL TRACT: The out-of balance gut microbiome has become a fscinating study. During the American Civil War, two people died of infectious diseases for every soldier death primarily by trauma. And most of those deaths were dysentery and pneumonia7. In 19008, the leading cause of cancer deaths in the USA is said to have been gastric cancer. But, it would be in the 1980-1990s before the gastric-infesting Helicobacter organism would be associated as an onco-pathogen8.

But, the normal intestinal ecosystem is now being recognized as ancient, the mix of bacteria not random, and the population selection mix having been selected over eons of time. Currently, the mix of flora is changing...with health consequences. The two biggest change causers are C-section births and the promiscuous use of antibiotics8. Dietary changes may have influenced the mix: formula vs. breast milk


  1. Miller SD, NEJMed 351(16):1666, 14 October 2004, HERE.
  2. Nature, 20 June 2012 issue, HERE.
  3. Matt Ridley, MIND & MATTER (column): Bug Me, Our Bodies Need Microbes and Worms, Wall Street Journal, 29 June 2012, HERE.
  4. Wikipedia, Human Microbiome.
  5. Rob Dunn, The Wild Life of Our Bodies: Predators, Parasites, and Partners That Shape Who We Are Today, 2011. HERE.
  6. Norman, S. H.; Kreutner, A., Jr. (cases EBS collected while a resident at MUSC) "Sparganosis - clinical and pathologic observations in 10 cases", Southern Medical Journal 73(3):297-300, March 1980.
  7. History Channel video, April 2015.
  8. Medscape Video (15 minutes): Eric Topol, M. D. interviews Martin J. Blaser, M. D. (Human Microbiome Center at New York University, and has been a leader in infectious diseases for decades), 13 April 2015
  9. Kirkland E, et. al., "Thinking Outside of the Lines: Diagnosing Babesiosis in the Lowcountry [coastal South Carolina], J. of the S. C. Med. Assoc., March/April 2015, issue 1, page 21-23.

(posted 2 February 2004; latest addition 24 April 2015)

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