Case Based Pediatrics For Medical Students and Residents
Department of Pediatrics, University of Hawaii John A. Burns School of Medicine
Chapter VI.2. Basic Bacteriology
Loren G. Yamamoto, MD, MPH, MBA
February 2003

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You arrive at your clinic in the morning and a nurse tells you that the lab has called with three positive culture reports. The nurse hands you the lab reports and the patients' charts.

The first culture is a beta strep, not group A. This is a throat culture from a 10 year old boy seen in the clinic yesterday for a sore throat. He was treated with penicillin pending the outcome of the culture. You know that group A strep should be treated for 10 days, but you ask your associate what to do about non-group A beta hemolytic strep. He tells you that non-group A strep in the throat is non-pathogenic.

The second culture is a blood culture with gram positive rods. This is from a 14 month old male who was seen in the clinic 3 days ago with fever. A CBC was normal at the time. He was treated with fever medications and no antibiotics. You call his home and his mother says that he has not had any fever for the past two days. He is now well and he seems back to his usual self. He comes to the clinic for a follow-up exam and you determine that he is no longer ill. You conclude that this organism must be a non-pathogen (i.e., a contaminant of the blood culture bottle).

The third culture is a urine culture with 100,000 colony forming units (cfu) per ml of gram negative rods. This is an 18 month old female who presented with fever and vomiting. Her UA showed 25-50 wbc's per high powered field (hpf). She was treated with IM ceftriaxone and oral cephalexin. She is seen in follow-up later today and she is doing well. Her antibiotics are continued. Her urine culture the next day identifies the organism as E.coli which is sensitive to cephalosporins.

Basic microbiology knowledge can be very useful clinically if one focuses on the clinically important aspects of bacteriology. It can greatly help in the preliminary management of patients before definitive identification of the organisms and antibiotic sensitivities are determined.

Gram stain morphology results are the first step in identification. Gram positive cocci and gram positive rods greatly narrow the possibilities. Gram negative organisms are more difficult to narrow down.

Gram positive cocci are either staphylococci or streptococci. One could distinguish these morphologically since staph are usually arranged in clusters, while strep are usually arranged in pairs and/or chains. The catalase assay is more reliable since staph are catalase positive and strep are catalase negative. There are only two types of clinically important staph species, Staph epi and Staph aureus. These two are distinguished by the coagulase test. Staph epi is coag negative, while Staph aureus is coag positive. Aureus means "gold", because most Staph aureus colonies (growing on a Petri plate) have a gold color, while most Staph epi colonies have a white color. Staph aureus is methicillin and cephalosporin resistant about 25% of the time. MRSA (methicillin resistant Staph aureus) are similarly resistant to oxacillin, cloxacillin, nafcillin, dicloxacillin and cephalosporins. Staph epi is methicillin and cephalosporin resistant over 90% of the time. Vancomycin can be used for resistant Staph epi and Staph aureus.

Staph epi is usually not a clinical pathogen and it is frequently a contaminant in blood cultures. If Staph epi grows from a blood culture, it is more likely to be a contaminant if the patient is healthy and doing well by the time the culture comes back. Staph epi growing from a blood culture is more likely to be a true pathogen if the patient has any type of indwelling plastic or prosthetic materials, such as a ventriculoperitoneal shunt, a central venous catheter, etc., since Staph epi has a propensity to adhere to indwelling plastic devices forming slime layers of bacterial colonization onto the device which often requires removal of the device since antibiotic treatment alone is often insufficient to eradicate the colonization.

Staph aureus frequently causes skin and soft tissue infections, such as cellulitis, impetigo and abscesses. Staph aureus is a common cause of more serious infections such as septic arthritis, osteomyelitis, discitis, severe pneumonia, etc. Staph aureus can produce an exotoxin which can result in septic shock but additionally, these toxins can cause several clinical entities depending on the type of toxin produced. Toxic shock syndrome (TSS) is due to a staph aureus toxin which causes an erythroderma (commonly mistaken for scarlet fever), high fever and shock. Staphylococcal scalded skin syndrome (SSSS) toxin causes a generalized exfoliative desquamation and severe infection. Bullous impetigo causes localized blistering due to a less virulent exfoliative toxin. Staph aureus food poisoning is a heat stable toxin that results in vomiting and diarrhea very soon after the ingestion of contaminated food containing pre-formed toxin.

When a blood culture grows Staph aureus, it should always be considered to be a serious pathogen. Empiric coverage with IV vancomycin should be started for potentially serious Staph aureus infections until culture and sensitivities are known, since the resistance rate to methicillin and cephalosporins is too high (at least 25%). However, if the Staph aureus infection is deemed less serious, such as impetigo or a small abscess, treatment with a cephalosporin (75% sensitive) or clindamycin (95% sensitive) may be satisfactory.

Streptococci are first classified using their hemolytic pattern on sheep blood agar. Clear colonies are called beta hemolytic. Green colonies are called alpha hemolytic. Streptococcal colonies which do not result in any hemolysis are called non-hemolytic or gamma hemolytic. For the most part, non-hemolytic strep are not clinically important since they don't cause much clinical disease. Alpha hemolytic strep include Strep pneumoniae (pneumococcus), Strep viridans, and other miscellaneous non-pathogenic alpha strep (often found in mouth and nasal flora). Strep pneumoniae and Strep viridans can be distinguished by several lab sensitivity tests to bile and Optochin.

Pneumococci cause many human infections including pneumonia, meningitis, sinusitis, otitis media, occult bacteremia, primary peritonitis, sepsis, osteomyelitis and septic arthritis. Some pneumococci contain polysaccharide capsules which add virulence to the organism. Non-encapsulated pneumococci are less virulent and are often implicated in otitis media or other minor infections. Severe pneumococcal infections are usually due to encapsulated pneumococci. The immune system forms antibodies against the polysaccharide antigens. Pneumococcal vaccines are developed against these polysaccharide serotypes. Several multivalent pneumococcal vaccines are currently available. Pneumococcus is usually sensitive to penicillin, but resistance is emerging requiring treatment with higher penicillin doses, cephalosporins or for high level resistance, vancomycin is required. Strep viridans (not a species, but rather a group of organism species) is a less common human pathogen, sometimes causing bacterial endocarditis.

Beta hemolytic strep are further classified using the Lancefield classification, which utilizes letters. Group A strep (also known as Strep pyogenes) causes strep pharyngitis, tonsillitis, impetigo, scarlet fever and cellulitis. It occasionally causes pneumonia, endocarditis and necrotizing fasciitis (commonly called the flesh eating bacteria syndrome). Group A strep are still penicillin sensitive. Post-infectious complications include acute rheumatic fever and acute glomerulonephritis.

Group B strep (also known as Strep agalactiae) commonly colonizes the maternal gyn tract. Newborns are exposed to this, so group B strep is a common cause of neonatal pneumonia, meningitis and sepsis. Maternal infections with group B strep include chorioamnionitis and endometritis. Since this organism is common and potentially highly virulent, mothers are currently screened for group B strep routinely and if found, they are given ampicillin prophylaxis to reduce the risk of neonatal sepsis. Group B strep are still penicillin sensitive. They are sensitive to cephalosporins, but less so, such that treatment with penicillin or ampicillin is still recommended even in neonates treated with cephalosporins.

Terminology such as "beta strep" or "group A strep" may be considered incomplete. Technically, beta strep is not the name of an organism since there are many different types of beta hemolytic strep (group A, B, C, D, etc.). However, "group A strep" is unambiguous, since by definition, only beta hemolytic strep can be group A. Thus, it is not necessary to say "group A beta hemolytic strep", since "group A strep" will suffice. It is only sufficient to say "beta hemolytic strep" or "beta strep" if your intention is to refer to all beta hemolytic strep, but this does NOT refer to a single specific organism.

Group C strep are less pathogenic. They are sometimes found in the pharynx. While group C strep may cause pharyngitis, such infections are almost always self limited without suppurative or post-infectious complications. Thus, antibiotic treatment with penicillin may be used to treat non-group A beta hemolytic strep pharyngitis (such as group C strep) if the patient is symptomatic with a sore throat or fever, but it is not absolutely necessary since such infections are generally self limited.

Group D strep is a confusing group, because this is the only group which does not name a single organism. There are two important group D strep organisms; Strep faecalis and Strep bovis. The term "enterococcus" is often used to refer to Strep faecalis; however "enterococcus" can be Enterococcus faecalis (new name for Strep faecalis), Enterococcus faecium or others. Additionally, group D strep are not always beta hemolytic. Thus, group D strep are identified on a separate plate (other than sheep blood agar) for identification. Group D strep are difficult to treat, often requiring two drug therapy such as ampicillin and an aminoglycoside. You may see the abbreviation "VRE" which stands for vancomycin resistant enterococci.

Gram positive rods are uncommon causes of human infection. Lactobacilli may be found in urine. Diphtheroids are frequent contaminators of blood cultures. Clostridium, corynebacteria, bacillus and listeria are all capable of causing severe disease, but these are all uncommon infections. They are generally penicillin sensitive (with the exception of Clostridium difficile). Clostridium and bacillus species are spore formers. These dormant spores are highly resistant to environmental stress such as dehydration and heat, making it difficult to eradicate the infectious particles from the environment.

Clostridium are anaerobes which produce disease through exotoxin production. C. tetani and C. botulinum produce potent neurotoxins. Children are routinely immunized with tetanus toxoid. Botulism is prevented by strict regulation of canned goods (heat and/or pressure cooking requirements), but infant botulism may still occur from exposure to spores (usually from soil or foods). C. difficile (penicillin resistant) produces a toxin which causes pseudomembranous colitis, which results from gastrointestinal C. difficile overgrowth with prolonged broad spectrum antibiotic treatment. C. perfringens causes cellulitis and tissue gas gangrene (tissue necrosis results from exotoxin production).

Corynebacterium diphtheria causes a severe throat infection, but its exotoxin is cardiotoxic and neurotoxic. Immunization with diphtheria toxoid prevents the toxin effects and severe infection. Listeria monocytogenes is an uncommon infection which may be transmitted in foods (commonly deli meats and cheese). It produces mild gastroenteritis in most individuals, but it may cause sepsis in pregnant women, neonatal sepsis, and severe infections in immunocompromised patients.

Bacillus species, are aerobic gram positive rods. The major pathogen is bacillus anthracis which is an uncommon organism except when used for biological warfare. It can cause cutaneous anthrax (localized necrotic infection) or anthrax pneumonia (high mortality).

Gram negative organism species are more numerous. They generally produce endotoxins, as opposed to the exotoxins produced by many gram positive organisms. Their laboratory identification methods are more complex and beyond the scope of this chapter.

The most common gram negative rods are those found in the GI tract, commonly called the Enterobacteriaceae. Human disease from these organisms most commonly originates from the GI tract. Urinary tract infection (UTI), neonatal sepsis and peritonitis most commonly result from exposure to stool organisms. The most common organism involved is Escherichia coli. E. coli is the most common cause of UTI and a common cause of neonatal sepsis (along with group B strep). Normal flora gram negative rods include E. coli, klebsiella, proteus, serratia, etc. These can sometimes causes disease, but usually because they have entered the wrong part of the body (such as UTI, neonatal sepsis and aspiration pneumonia). Most E. coli are normal flora, but some E. coli subtypes are pathogenic such as E. coli 0157 (causes dysentery and hemolytic uremic syndrome), enterotoxigenic E. coli (causes traveler's diarrhea) and enteropathogenic E. coli (causes pediatric diarrhea). Pathologic gram negative rods include salmonella, shigella, yersinia, pseudomonas, etc. Most gram negative rods are covered by aminoglycosides, cephalosporins, broad spectrum penicillins, sulfonamides and quinolones. Pseudomonas is particularly resistant so it commonly emerges in patients treated with prolonged courses of antibiotics.

Gram negative cocci are basically Neisseria and Moraxella species. Moraxella catarrhalis is part of the upper respiratory tract normal flora. It is commonly found in otitis media and sinusitis. It is usually treated with a broad spectrum penicillin such as amoxicillin, but some M. catarrhalis are resistant.

Neisseria meningitidis (also called meningococcus) is highly virulent causing meningitis and meningococcal sepsis (known as meningococcemia). Meningococcus contains a polysaccharide capsule adding to its virulence. A meningococcal vaccine directed against the polysaccharide capsule is available. Neisseria gonorrhoeae (also called gonococcus or GC) is sexually transmitted causing urethritis, epididymitis cervicitis, pelvic inflammatory disease and pharyngitis. Disseminated GC causes polyarticular and monoarticular septic arthritis. Infants exposed to GC may develop ophthalmia neonatorum. All newborns receive routine eye prophylaxis with ophthalmic silver nitrate or antibiotics. Meningococcus is still penicillin sensitive. GC used to be penicillin sensitive, but most GC today are penicillinase producing (known as penicillinase producing Neisseria gonorrhoeae, or PPNG for short). PPNG can still be treated with ceftriaxone, doxycycline or azithromycin.

Haemophilus species used to be a major pediatric pathogen. They are gram negative organisms commonly called coccobacilli, or pleomorphic (variable forms) rods. Haemophilus influenzae (H.flu) is either capsulated (only one major polysaccharide serotype called type B) or non-encapsulated. Haemophilus influenzae type B (known as HiB for short) was a major cause of sepsis, meningitis, septic arthritis, pneumonia, epiglottitis and cellulitis in young children. These serious and life threatening infections from HiB have largely been eliminated from our community through widespread HiB immunization (a major public health and pediatric accomplishment). This is a polysaccharide vaccine which does not provide immunity against non-encapsulated (also called non-typable H.flu). Since non-typable H.flu does not have a polysaccharide capsule, it is less virulent, so it is associated with only minor infections such as otitis media and sinusitis. H.flu (non-typable and type B) is 30% resistant to amoxicillin, due to beta-lactamase production. Anti-beta-lactamase drugs (clavulinic acid, sulbactam, etc.) overcome this resistance. Thus, amoxicillin-clavulinic acid and high generation cephalosporins cover 100% of H.flu.

Gram negative anaerobes typically cause polymicrobial infection. Most anaerobes are sensitive to penicillin with one major exception and that is Bacteroides fragilis (B.frag), which is commonly found in bowel (stool). Anaerobes cause a putrid (foul decay) odor (e.g., feces). Esophageal and mouth anaerobes typically do not contain B.frag., which is why most texts refer to anaerobe infections above the diaphragm (B.frag unlikely) versus anaerobe infections below the diaphragm (B.frag is likely). Thus, classically, the anaerobe component of aspiration pneumonia may be treated with penicillin as opposed to peritonitis due to a ruptured appendix which is likely to involve B.frag. Bacteroides fragilis is classically treated with clindamycin, metronidazole or chloramphenicol. Some cephalosporins such a cefoxitin and cefotetan have better coverage against B.frag, but they are not 100%. If an anaerobic infection is suspected, culture samples must be sent to the lab in special anaerobic culture/transport media (e.g., thioglycolate).

Other gram negative organisms that deserve mention include Legionella, Bordetella, Brucella, Francisella, Campylobacter, Helicobacter, Vibrio and Pasteurella. Spirochetes include Treponema (syphilis, yaws, etc.), Borrelia (Lyme disease) and Leptospira (leptospirosis).

Mycobacterium species do not stain well with the gram stain. They stain best with the acid-fast stain. Mycobacterium tuberculosis causes tuberculosis. M. leprae causes leprosy (Hansen's disease). M. avium-intracellulare causes pulmonary infections in immunocompromised patients. M. marinum is a marine organisms which causes "fish tank" granulomas in those who are frequently exposed to aquarium and marine environments.

Mycoplasma and Chlamydia are similar to viruses in that they are obligate intracellular organisms. They cannot be grown on Petri plates because they require cells to grow. Mycoplasma and Chlamydia must be grown in cell media (similar to viruses) in labs, thus, they are difficult to culture. Despite their obligate intracellular requirements, they utilize bacterial DNA ribosomes and are thus, susceptible to erythromycins, tetracyclines and some quinolones. The epidemiology of infections with Mycoplasma and Chlamydia is unclear since these organisms are difficult to identify definitively. It was once thought that Mycoplasma pneumonia only occurred in young adults, but it is now known to occur in all age groups, although its frequencies in each age group are unclear. It was once thought that Chlamydia infections were largely limited to an eye infection called trachoma. However, it is now known that Chlamydia causes respiratory infections and pelvic inflammatory disease. The true epidemiology of these organisms is still unclear. They may play a role in many other infections that we have yet to discover. Other obligate intracellular organisms include Rickettsia (Rocky Mountain Spotted Fever, typhus), Coxiella, Ehrlichia, and Bartonella (not intracellular).

Summary Table:

Gram Positive Cocci:
. . . . Catalase (+) Staph:
. . . . . . . . . Coagulase (+) Staph aureus
. . . . . . . . . Coagulase (-) Staph epidermidis
. . . . Catalase (-) Strep:
. . . . . . . . . Alpha hemolysis on sheep blood agar (green colonies):
. . . . . . . . . . . . . . Bacitracin sensitive: Strep pneumoniae (pneumococcus)
. . . . . . . . . . . . . . Bacitracin resistant: Strep viridans
. . . . . . . . . Beta hemolysis on sheep blood agar (clear colonies):
. . . . . . . . . . . . . . Group A (Strep pyogenes)
. . . . . . . . . . . . . . Group B (Strep agalactiae)
. . . . . . . . . . . . . . Group C (not very pathogenic)
. . . . . . . . . . . . . . Group D (not always beta hemolytic)
. . . . . . . . . . . . . . . . . . . Strep faecalis (enterococcus)
. . . . . . . . . . . . . . . . . . . Strep bovis

Gram positive rods:
. . . . Clostridium (tetanus, botulism, perfringens, difficile)
. . . . Corynebacterium (diphtheria)
. . . . Listeria monocytogenes
. . . . Bacillus (anthracis)
. . . . Lactobacillus
. . . . Diphtheroids (flora)

Gram negative cocci:
. . . . Neisseria (gonorrhoeae, meningitidis)
. . . . Moraxella

Gram negative rods:
. . . . Enteric gram negative rods (E. coli, Proteus, Klebsiella, Serratia, etc.)
. . . . Pathologic gram negative rods (Salmonella, Shigella, Yersinia, Pseudomonas, etc.)

Gram negative coccobacilli:
. . . . Haemophilus influenzae

Gram negative anaerobes:
. . . . Bacteroides fragilis (penicillin resistant)
. . . . Most others (penicillin sensitive)

. . . . Treponema, Borrelia, Leptospira

Acid-fast bacilli:
. . . . Mycobacterium (TB, leprae, avium-intracellulare, marinum)

Non-viral obligate intracellular organisms:
. . . . Mycoplasma
. . . . Chlamydia
. . . . Rickettsia
. . . . Other: Coxiella, Ehrlichia, Bartonella (not intracellular)


1. A lab slip returns which says "coag negative staph". What does this mean and what is the likelihood that this organism is sensitive to methicillin and cephalosporins?

2. At laparotomy, a patient is found to have a ruptured appendix and peritonitis. A swab from the peritoneal fluid is expected to grow what types of organisms? Is there any special swab or sample that must be sent to properly culture this fluid?

3. Name two characteristics of anaerobic infections?

4. Name 5 disease conditions which result largely from toxin production?

5. Group A streptococcal pharyngitis is usually a self limited infection even without antibiotic treatment. What is the reason for treating "strep throat"?

6. A lab tech identifies beta hemolytic colonies on a sheep blood agar plate. What is the next step to identify the organism?

7. Two days after a blood culture is drawn, the lab reports gram positive cocci. This patient is a 10 month old with fever and no other identifiable clinical infection. The child is now afebrile and looks good. What organism possibilities could be growing in this blood culture?

8. A lumbar puncture is done on a very ill 8 month old infant. The fluid is cloudy and the gram stain shows many WBCs and gram positive cocci. What organism is likely causing the meningitis? What organism would be likely if the gram stain showed gram negative cocci instead?

9. A new resident on the pediatric service orders a gram stain on a stool sample. What is the result likely to be?

10. If staph epi grows from a blood culture, how can one determine whether this is a contaminant or a staph epi bacteremia?


1. Hawley LB. High-Yield Microbiology and Infectious Diseases. 2000, Philadelphia: Lippincott Williams & Wilkins.

2. Chapter 24: The Gram-Positive Pyogenic Cocci. In: Volk WA, Gebhardt BM, Harmmarskjold ML, Kadner RJ (eds). Essentials of Medical Microbiology, fifth edition. 1996, Philadelphia: Lippincott-Raven, pp. 329-347.

Answers to questions

1. This is Staph epi which is almost always resistant to methicillin and cephalosporins.

2. The peritoneal fluid is likely to grow multiple stool organisms. E. coli will predominate. A polymicrobial anaerobic infection is also likely. To properly culture anaerobes, an anaerobic culture swab sent in special anaerobic media (e.g., thioglycolate) must be sent.

3. They are usually polymicrobial and they have a foul odor.

4. Tetanus, botulism, diphtheria, toxic shock, staphylococcal scalded skin syndrome, scarlet fever, etc.

5. Early antibiotic treatment results in a slightly shorter course of symptoms, but the main reason to treat is to prevent suppurative complications and rheumatic fever.

6. Lancefield classification to determine if this organism is group A, group B, etc.

7. Pneumococcus or Staph epi (contaminant).

8. Most likely gram positive cocci is pneumococcal meningitis. Most likely gram negative cocci is meningococcal meningitis.

9. This is an inappropriate order. The stool will be full of enterobacteriacae, anaerobes, and enterococcus. The gram stain will show mostly gram negative rods and perhaps a few gram positive cocci.

10. It is not possible to determine this with certainty in most instances. However, healthy patients who are no longer ill by the time the culture comes back are unlikely to have had Staph epi bacteremia. Thus, in these patients, the Staph epi is most likely a contaminant. In patients with indwelling plastic (central catheters, ventriculoperitoneal shunts), it should be assumed that the Staph epi is a clinically important infection, probably colonizing the plastic tubing.

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