Lists of Bacterial Pathogens Associated with Intrinsic Antibiotic Resistance

Last updated on February 1st, 2020

Generally, when people (either general public or a physician or laboratory personnel) listen/read the term “antibiotic resistance” they may think, ‘a bacterium which was previously sensitive to a particular antibacterial agent has now developed resistance against it (either through acquisition of gene via horizontal gene transfer or by mutation)’ but in this universe there are innumerable species of bacteria which are innately resistant to a particular drugs.

According to CLSI, “Intrinsic resistance is so common that susceptibility testing is unnecessary. For example, Citrobacter species are intrinsically resistant to ampicillin”.

Intrinsic antibiotic resistance is a naturally occurring phenomenon which is independent of previous antibiotic exposure and is not caused by a horizontal gene transfer. Remember the famous example of intrinsic resistance, penicillin not working against Mycoplasma. Penicillin kills bacteria by interfering with their cell wall synthesis.

Will it be able to kill those that do not have cell wall?

Intrinsic antibiotic resistance is mainly mediated by impermeability of cellular envelopes, the activity of multidrug efflux pumps or lack of drug targets. Enzymes (such as transferases) which are involved in basic bacterial metabolic processes also confer intrinsic resistance in some bacterial species such as Pseudomonas aeruginosa, and Staphylococcus aureus.

According to the published findings such natural insensitivity can be due to:

  • lack of affinity of the drug for the bacterial target
  • inaccessibility of the drug into the bacterial cell
  • extrusion of the drug by chromosomally encoded active exporters
  • innate production of enzymes that inactivate the drug

Intrinsic Antibiotic Resistance in Gram Negative Bacteria

Bacterial pathogen that are Intrinsically resistance to Ampicillin

  1. Acinetobacter baumanni complex
  2. Citrobacter freundii
  3. Citrobacter koseri
  4. Klebsiella (formerly Enterobacter) aerogenes
  5. Enterobacter cloacae complex
  6. Klebsiella pneumoniae
  7. Morganella morganii
  8. Proteus vulgaris
  9. Pseudomonas aeruginosa
  10. Serratia marcescens
  11. Yersinia enterocolitica

Bacterial pathogens that are Intrinsically Resistant to Amoxicillin-Clavulanate combination

  1. Citrobacter freundii
  2. Klebsiella (formerly Enterobacter) aerogenes
  3. Enterobacter cloacae complex
  4. Morganella morganii
  5. Pseudomonas aeruginosa
  6. Serratia marcescens
  7. Yersinia enterocolitica

Bacterial pathogens that are Intrinsically Resistant to Ampicillin-sulbactam combination

  1. Acinetobacter baumanni complex
  2. Citrobacter freundii
  3. Citrobacter koseri
  4. Klebsiella (formerly Enterobacter) aerogenes
  5. Enterobacter cloacae complex
  6. Proteus vulgaris
  7. Pseudomonas aeruginosa
  8. Serratia marcescens

Citrobacter koseri is intrinsically resistant to piperacillin whereas Proteus spp is intrinsically resistant to tetracycline/tigecycline, nitrofurantoin and polymyxin B and colistin

Acinetobacter baumanni complex is notorious pathogen which is resistant to most of the available antibiotics. It is intrinsically resistant to

  1. Ampicillin, Amoxicillin
  2. Ampicillin-sulbactam
  3. Aztreonam
  4. Ertapenem
  5. Trimethoprim
  6. Chloramphenicol

Similarly Pseudomonas aeruginosa is intrinsically resistant to

  1. Ampicillin, Amoxicillin
  2. Ampicillin-sulbactam
  3. Amoxicillin-Clavulanate
  4. Cefotaxime
  5. Ceftriaxone
  6. Ertapenem
  7. Tetracyclines/Tigecyclines
  8. Trimethoprim
  9. Trimethoprim-sulfamethoxazole
  10. Chloramphenicol

Both Acinetobacter and Pseudomonas are also intrinsically resistant to penicillin (ie, benzylpenicillin), cephalosporin I (cephalothin,cefazolin), cephalosporin II (cefuroxime), cephamycins (cefoxitin, cefotetan), clindamycin, daptomycin, fusidic acid, glycopeptides(vancomycin, teicoplanin), linezolid, macrolides (erythromycin, azithromycin, clarithromycin), quinupristin-dalfopristin, and rifampin.

Bacteroides spp. which is one of the most frequently isolated anaerobic Gram negative bacilli is intrinsically resistant to

  • Aminoglycosides
  • Penicillin and
  • Ampcillin

Intrinsic Antibiotic Resistance in Gram Positive Bacteria

Among gram positive bacteria, S. saprophyticus is intrinscially resistance to novobiocin which is  the basis for Novobiocin sensitivity test done in urine isolate (if CONS is isolated).

Enterococcus faecalis/faecium are intrinsically resistant to

  • Cephalosporin*
  • Aminoglycosides*
  • Clindamycin*
  • Trimethoprim
  • Trimethoprim-sulfamethoxazole*
  • Fusidic acid
    *may appear active in vitro but are not effective clinically and should not be reported as susceptible.

Both Enterococci and Staphylococci are also intrinsically resistant to aztreonam, polymyxin B/colistin, and nalidixic acid.

Anaerobic Gram-positive bacilli, Clostridium spp. is resistant to aminoglycosides.

References and further reading 

  1. CLSI: M100S: Performance Standards for Antimicrobial Susceptibility Testing 
About Acharya Tankeshwar 466 Articles
Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. I am working as an Asst. Professor and Microbiologist at Department of Microbiology and Immunology, Patan Academy of Health Sciences, Nepal. If you want me to write about any posts that you found confusing/difficult, please mention in the comments below.


  1. Hello Sir,
    I am very intersting with that communication. I am now working and Learning microbiology at the University of Kinshasa. I would be happy if you can send me supplies in mediums and usuals techniques.
    I really read your article and want to say that in Kinshasa also we have resistance due to bad use of antibiotic. And also,many patients don’t do antibiogram because it cost a lot and many lab can’t do it.

    Dr EKILA IFINJI Richard
    Junior Assistant
    Cliniques Universitaires de Kinshasa

    [email protected]

    • Dear Dr. Eklia Ifinji Richard
      Thank you so much for your compliment and sharing your knowledge. Increase in antimicrobial resistance is now a global problem, we are also going through similar problems here. I have listed commonly used tests in this title: // Please go through it and leave me comments. Keep in touch.

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