RB is a 46-year-old female who presented to the ED two days ago with dysuria, flank pain, temperature of 101F, and WBC count of 18,000/mm³. Her urinalysis was suggestive of urinary tract infection (UTI), so she was started on ceftriaxone 1 g IV Q24hr for suspected pyelonephritis.  Today her urine culture and both blood cultures revealed growth of Gram-positive cocci. The gram stain of this organism from the blood culture initially demonstrated Gram-positive cocci in chains and pairs. Which of the following pathogens is the most likely cause of RB’s pyelonephritis?

A. Chlamydia pneumoniae

B. Enterococcus faecalis

C. Escherichia coli

D. Staphylococcus aureus

Answer with rationale:

The correct answer is B.

UTI is one of the most common infections that pharmacists will encounter in both the inpatient and outpatient settings. UTI can clinically present as simple cystitis (bladder infection), complicated UTI (e.g. catheter-related), and/or pyelonephritis (involvement of kidney).  The vast majority of UTIs are caused by Gram-negative rods, but in this case the Gram stain of the patient's blood culture appears to indicate a Gram-positive infection. 

Although a Gram stain cannot definitively identify the bacterial species causing an infection, it can provide clues that narrow down the suspects. A Gram stain can also be performed far quicker than the time it takes to determine the exact identity and susceptibilities of the pathogen. The bacteria growing in a culture are first stained with a violet dye that binds to peptidoglycans in the bacterial cell wall. A wash is then performed that removes the violet dye from the Gram-negative bacteria, which have only a thin peptidoglycan layer making up their cell wall. Gram-positive bacteria, which have a thicker peptidoglycan layer, retain the violet dye during the wash and appear purple when viewed under a microscope. The bacteria are stained with a second dye that allows Gram-negative bacteria to appear pink under a microscope. The shape of the bacteria can also be seen through the microscope.

Although Escherichia coli is the most common cause of UTI, it is a Gram-negative rod, so answer C is incorrect. Chlamydia pneumoniae is an atypical organism. It is also Gram-negative morphologically (stains poorly by the Gram stain method), so answer A is incorrect. Furthermore, Chlamydia pneumoniae usually causes pneumonia, not UTI. It is not the same as Chlamydia trachomatis, a Gram-negative organism that causes the sexually transmitted infection (STI). Of interest, Mycoplasma species, such as Mycoplasma pneumoniae, lack cell walls and thus will not stain on gram stain. This also explains pharmacologically why this organism will not respond to beta-lactam therapy as these therapies inhibit cell wall formation. The drugs of choicee for Mycoplasma species are often macrolides, tetracyclines, or fluroquinolones. 

When viewed under a microscope, Gram-positive cocci will be organized in either chains or clusters. Staphylococcus species will appear in clusters and pairs, which makes answer D incorrect. Streptococcus species and Enterococcus species will appear in chains and pairs. Therefore, answer B is correct. Enterococcus faecalis is a common Gram-positive cause of UTI, along with Staphylococcus saprophyticus.

As an important aside, no cephalosporin has activity against Enterococcus species, so the empiric antibiotic regimen in this case would need to be adjusted in light of the organism detected. Rapid diagnostic technology, such as multiplex PCR, would detect this much earlier than required for physical growth in microbiology lab on culture plate, allowing for antimicrobial stewardship intervention of optimizing the antibiotic regimen.