CSVS 2024 Antibiogram Report

Author

Oguchi Nkwocha, MD., MS.

Goal:

Choosing the best single antibiotic, based on evidence, for empiric treatment of infections pending availability of definitive culture-sensitivity results.

History:

Each year, starting in 2022, we construct a yearly antibiogram from urine samples sent to Foundation Laboratory for culture and sensitivity testing when UTI is suspected among our patients. Based on the antibiogram, we select and promote the best antibiotic for immediate initiation of the treatment of presumed UTI while awaiting formal confirmation which takes up to 3 to 5 days. Confirmation leads to either continuation to completion of the erstwhile empiric treatment for the recommended duration of treatment, or a change in regimen to reflect actual findings. This is the report and analysis for 2024, which will inform treatment in 2025.

In 2022 (analyzed early 2023), the best antibiotic was Trimethoprim-Sulfa (TMP/SMZ); in 2023 (applied in 2024), it was Nitrofurantoin. The following procedure identifies the best antibiotic for empiric treatment of UTI for the year, 2024; the information will be applied the rest of 2025 until we will construct another antibiogram in 2026.

Raw Data Source:

We obtained culture orders report from Foundation Lab for CSVS patients for the year 2024 for the purpose of constructing an ANTIBIOGRAM.

EXPLORATORY DATA ANALYSIS

In 2024, CSVS had 6335 unique specimen culture orders, out of which 4801 were urine sourced (75.8%). 38.6% (1854) were acceptable for complete analysis. Here’s the breakdown:

Focusing on the urine cultures, by convention, only the first isolate of a multi-isolate specimen result was counted and used for susceptibility / resistance testing; this subset totalled 1494, yielding 31.1% of all cultured urine specimen – a little under a third . Here’s the flowsheet for the rest of the process:

Regarding organisms, the chart below shows that gram neg E coli and gram pos Enterococcus spp dominated the isolates list:

Of 1494 total isolates,

  • 865 or 58% were Escherichia coli
  • 281 or 18.8% were Enterococcus sp.,

together adding up to 77% of all organisms isolated.

Antibiogram

Using the global application tool, WHONET and it’s companion program, BacLink, the dataset from above was mapped and standardized to produce the universal antibiogram-related reports. From the reports, the following output was created…

2024 Antibiogram CSVS
Urine Isolate - Antibiotic Percent Susceptibility Table
Organism Gram Type nbr of isolates Nitro-furantoin TMP/SMX Cipro Levo-Floxacin Cepha-zolin Ceftri-oxone Amp
Escherichia coli Gram Negative 865 100 99.8 100 0.2 100 100 0
Enterococcus sp. Gram Positive 281 100 100 100 100 100 100
Klebsiella pneumoniae ss. pneumoniae Gram Negative 82 0 100 100 100 100 100 0
Proteus mirabilis Gram Negative 62 0 100 100 100 100 100 0
Streptococcus agalactiae Gram Positive 44 100 100 100 100 100
Morganella morganii ss. morganii Gram Negative 26 0 7.7 23.1 23.1 0 100 0
Klebsiella oxytoca Gram Negative 20 100 0 100 100 0 0 0
Citrobacter koseri Gram Negative 15 100 100 100 100 100 100
Klebsiella aerogenes Gram Negative 14 100 100 100 100 0 100
Staphylococcus aureus ss. aureus Gram Positive 14 100 85.7 85.7
Serratia marcescens Gram Negative 10 0 100 100 100 0 100
Enterobacter cloacae Gram Negative 9 11.1 100 100 100 0 88.9
Pseudomonas aeruginosa Gram Negative 8 100 100 100
Raoultella ornithinolytica Gram Negative 7 100 100 100 100 0 100 0
Citrobacter freundii Gram Negative 6 100 100 100 100 0 100
Staphylococcus epidermidis Gram Positive 4 100 100 100
Raoultella planticola Gram Negative 2 100 100 100 100 100 100 0
Enterococcus faecium Gram Positive 2 100 100 0
Streptococcus gallolyticus ss. gallolyticus Gram Positive 2 100 100
Staphylococcus haemolyticus Gram Positive 2 100 100 100
Streptococcus sp. Gram Positive 2 100 100
Streptococcus viridans, alpha-hem. Gram Positive 2 100 100
Rhizobium radiobacter Gram Negative 1 0 0 100 100
Pantoea sp. Gram Negative 1 100 100 100 100 100
Stenotrophomonas maltophilia Gram Negative 1 100 100
Proteus vulgaris Gram Negative 1 0 100 100 100 0 100 0
Serratia liquefaciens Gram Negative 1 0 100 100 100 0 100
Serratia odorifera Gram Negative 1 0 100 100 100 0 100
Serratia plymuthica Gram Negative 1 0 100 100 100 0 100
Enterococcus faecalis Gram Positive 1 100 100 100
Streptococcus anginosus Gram Positive 1 100 100
Staphylococcus, coagulase negative Gram Positive 1 100 100 0
Staphylococcus lentus Gram Positive 1 100 100
Staphylococcus simulans Gram Positive 1 100 100 100
Staphylococcus sp. Gram Positive 1 100 100 0 100 100 100

Interpretation

  • E coli (58%), Enteroccoccus sp. (19%), Klebsiella pn. (6%), Proteus m. (4%) and Strep ag. (3%) make up almost 90% of UTI organisms;

  • Cipro provides the best coverage for those organisms and is oral.

    • Cipro provides the best coverage for all the organisms tested.

  • Ceftrioxone is just as good, but it is parenterally administered (available on CSVS Formulary for IM injection). Effectiveness does not carry over to oral cephalosporins

  • Nitrofurantoin is the next best antibiotic, missing Klebsiella and Proteus; followed by

  • SMX/TMP, which has no effect on Enterococcus and other gram positive organisms

  • Ampicillin covers only gram positive organisms (24% of isolates), and Gram negative Pseudomonas, an insignificant (by numbers) cause of UTI. This would constitute an inadequate choice for empiric antibiotic UTI treatment

Summary

“All things being equal…”, for empiric UTI treatment pending culture results:

  • First choice:
    • Cipro
  • Second choice:
    • Nitrofurantoin (comes as MacroBID for BID dosing)
  • Third choice:
    • TMP/SMX
    • Levaquin
  • Not Recommended:
    • Ampicillin

BTW: Fosfomycin (for UTI, a single dose regimen) was not tested; efficacy and safety profile favors its use in pregnancy

Caveat:

  • Always obtain UA if thinking of, or ruling out UTI / Cystitis;
  • Obtain culture / sensitivity
    • if any abnormality in Nitrites, Heme or Leuko; or
    • if planning to treat.
  • Susceptibility patterns do not necessarily carry over to other members of an antibiotic class
    • The profile in the table above is specific to the named antibiotic, and is not an antibiotic class property
  • Fosfomycin (single dose for UTI) [Culture-Sensitivity not run, as above] is guideline-acceptable treatment in all pregnancy trimesters