New PCR-based GI panel for stool diagnostics and C. difficile testing update

The GLA microbiology lab is now performing a new PCR-based method for testing for gastrointestinal pathogenic microorganisms. This replaces routine stool bacterial cultures and also detects C. difficile, norovirus, and common parasites, including Entamoeba histolytica, Giardia lamblia, and Cryptosporidium.

A full list of the pathogens targeted with this test is available at:

This test is orderable as “GI Panel” in CPRS and is available from the Microbiology Test Order Screen that can be reached from many inpatient and outpatient order sets. Stool O&Ps and specific testing for Microsporidia now require ID approval.

Please note that for patients with new-onset diarrhea who are on or have recently received antibiotics, C. difficile PCR testing should be ordered, not the full GI Panel. C. difficile testing has also recently been updated, as all positive PCR tests (either from the GI Panel or the specific C. difficile PCR) will be reflexed for toxin immunoassay testing. Samples that are PCR positive and toxin negative are likely to represent colonization with C. difficile and not active infection.

Also remember that stool microbiology testing should be done on frankly liquid bowel movements (Bristol stool chart 7). Also do not test in the setting of recent laxatives, stool softener, or tube feed initiation.

Please contact the Infectious Diseases service (fellow pager UCLA 89321; antibiotic approval pager VA 73022) with any questions.

New GLA antibiogram from 2018

Our 2018 antibiogram, which compiles antimicrobial resistance data from GLA isolates from the calendar year 2018 is now available here.  Overall resistance patterns are largely stable compared to 2017 with a few caveats (see below). 

For Gram-negative rods in the hospital setting:

  • Amikacin resistance remains very low and so is still the most active agent vs. multi-drug resistant Gram-negative rod infections at GLA.

  • Carbapenem-resistant Enterobacteriaceae remain somewhat uncommon at GLA.

  • There is not much overall difference between piperacillin-tazobactam, cefepime, and meropenem for most Enterobacteriaceae and Pseudomonas (all are better than fluoroquinolones), though there has been a slight decrease in susceptibility to cefepime among all nosocomial non-urine isolates.  Please note that >30% nosocomial Pseudomonas isolates are resistant to meropenem.

  • Ceftriaxone resistance is increasing among all nosocomial E. coli isolates (non-urine: 47% vs. 19% from 2017; urine: 36% vs. 26% from 2017)

  • Pseudomonas is less frequently encountered in the urine as compared to other sites.

For Gram-negative rods in the outpatient setting:

  • While cephalexin and cefadroxil remain first-line options for outpatient UTI treatment at GLA, our outpatient E. coli urinary isolate cefazolin susceptibility has decreased to 77% according to breakpoints established for serum (was 92% in 2017).  We are in the process of determining susceptibility according to breakpoints established for urine (which are much higher).

  • Fluoroquinolones and TMP-SMX susceptibilities remain similar (~75-80%).

Key trends among Gram-positive isolates:

  • MRSA remains quite common (~60% of nosocomial non-blood isolates, ~30% of nosocomial blood isolates, and ~40% of outpatient isolates).

  • Doxycycline resistance decreased among non-blood nosocomial S. aureus isolates (19% vs. 30%) from 2017.