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May '26 Infectious Diseases Update

Posted by Doug Black, PharmD., Ann Lloyd, PharmD. on May 12th 2026

Article of the Month (Editors' Choice) 

Disruption of the Microbiome by Antibiotics

By Douglas J Black, Pharm.D.

  • Available evidence links the gut microbiome to human health. Antibiotics are known disruptors of the gut microbiome.
  • Baldanzi et al. (Nat Med 2026;32:1351) studied the association between oral antibiotic use in the past 8 years and the composition of the gut microbiome by combining individual-level data from the Swedish National Prescribed Drug Register (NPDR) with fecal metagenomic data of 14,979 adults collected as part of three population-based cohorts in Sweden.
  • The NPDR captures all antibiotics and other prescription medications dispensed to outpatients in Sweden. The investigators divided the antibiotics into 11 groups: tetracyclines, extended-spectrum penicillins (only amoxicillin and pivmecillinam in Sweden), β-lactamase-sensitive penicillins (only penicillin V), β-lactamase-resistant penicillins (only flucloxacillin), penicillins combined with β-lactamase inhibitors (only amoxicillin-clavulanate), cephalosporins, TMP-SMX, macrolides, lincosamides (only clindamycin), fluoroquinolones, and nitrofurantoin. Prescriptions were divided into three periods: <1 year, 1 to <4 years, and 4 to <8 years before fecal sampling.
  • Three study findings are noteworthy:
    • Antibiotic use <1 year before fecal sampling was most strongly associated with lower diversity and differences in the abundance of species, but similar associations were also observed with antibiotic use 1-4 years and 4-8 years before fecal sampling.
    • The associations were mainly related to three antibiotic classes: lincosamides (i.e., clindamycin), β-lactamase-resistant penicillins (i.e., flucloxacillin), and fluoroquinolones. Use of these antibiotic classes 4-8 years before fecal sampling was associated with altered abundance of 10-15% of the species studied. Penicillin V, amoxicillin, pivmecillinam, and nitrofurantoin were associated with only a few species.
    • A single course of tetracyclines, flucloxacillin, fluoroquinolones, clindamycin, TMP-SMX, cephalosporins, or macrolides <4 or 4-8 years before fecal sampling was associated with lower gut microbiome diversity.
  • Differences in gut microbiome associations across antibiotic classes may relate to differences in spectrum of antibacterial activity and pharmacokinetics.
  • In summary, the effect of antibiotics of the gut microbiome may persist for multiple years. Clindamycin, fluoroquinolones, and flucloxacillin have a particularly large impact.

Antimicrobial Stewardship

PEN-FAST in Pharmacist-led Medication Reconciliation

  • A new retrospective study conducted at 2 community hospitals describes the use of the PEN-FAST tool to identify low-risk penicillin allergy during pharmacist-led medication reconciliation in adult patients regardless of indication for antibiotics.
  • PEN-FAST is a validated tool used to identify low-risk penicillin allergies that do not require formal allergy testing. A score of 0-2 indicates a very low-low risk of a positive penicillin allergy test and allows for direct oral challenge and delabeling. Pharmacists at site 1 used PEN-FAST scoring in both the emergency department (ED) and inpatient units during medication reconciliation for patients with a documented penicillin allergy. At site 2, the tool was used only in the ED. 
  • Of the 95 patients where the pharmacist conducted medication reconciliation using PEN-FAST, 74% had a score <3 and were classified as having low-risk allergy, and 56 patients had a score of 0. However, only 10% of the low-risk patients had the allergy label removed from the medical record.The findings of this study demonstrate the feasibility of using PEN-FAST to identify patients with low-risk penicillin allergy and also highlight obstacles that prevent allergy delabeling and direct oral penicillin challenge. Antimicrobial stewardship teams could consider incorporating pharmacist-led use of the PEN-FAST tool to identify patients at low risk of allergy. Am J Health Syst Pharm. 2026 Apr 25:zxag129. doi: 10.1093/ajhp/zxag129. Epub ahead of print. PMID: 42033754.

New Combination Drug for HIV-1 Treatment

  • Doravirine-Islatravir (Idvynso)* is a complete two-drug regimen for the treatment of HIV-1 in adults. It is FDA-approved to replace the current ARV regimen in those who are virologically-suppressed (HIV-1 RNA <50 copies/mL) on a stable regimen with no history of virologic treatment failure and no known substitutions associated with resistance to doravirine. Doravirine is an NNRTI that inhibits HIV-1 replication by non-competitive inhibition of reverse transcriptase (RT). Islatravir, a deoxyadenosine analog, is the first nucleoside reverse transcriptase translocation inhibitor (NRTTI). It inhibits RT via multiple mechanisms. The usual dosage is one tablet once daily, with or without food. Each tablet contains 100 mg of doravirine and 0.25 mg of islatravir. Drug interactions are a concern: doravirine is a CYP3A substrate, and islatravir depends on deoxycytidine kinase (dCK) for phosphorylation and activation and is primarily metabolized by adenosine deaminase (ADA) to form an inactive deoxyinosine metabolite.

New or Updated Guidelines

  • Asian Pediatric Nephrology Association (AsPNA) clinical practice guidelines for the management of infection-related glomerulonephritis (Pediatr Nephrol 2026;41:1867). Specific subtypes, including Staphylococcus-associated glomerulonephritis (GN), endocarditis-associated nephritis and shunt nephritis are discussed. Other etiologies of acute GN are not addressed.
  • British Association for Sexual Health and HIV (BASHH) national guideline for the management of infection with Mycoplasma genitalium*, 2025 (Int J STD AIDS 2026;37:576). This guideline updates the previous guideline published in 2018. PDF available.

Immunizations

  • CDC ACIP Master Immunization Schedules dated 2025 that reflect full evidence-based GRADE published by ACIP remain in effect (see cdc.gov). For other schedules, see our Master Immunizations Schedules* page. 

Antimicrobial Shortages (US)

  • New shortages:
    • None
  • Resolved shortages:
    • Penicillin VK, all oral formulations (8 May 2026)
  • Antimicrobial drugs recently discontinued: 
    • None
  • Antimicrobial drugs or vaccines in continued reduced supply or unavailable due to increased demand, manufacturing delays, product discontinuation by a specific manufacturer, or unspecified reasons: 
    • Antibacterial drugs:
      • Aminoglycosides:
        • Gentamicin injection (22 Feb 2021)
      • Cephalosporins:
        • Cefazolin injection (4 Jun 2018)
        • Cefotaxime injection (10 Jun 2015)
          • FDA is allowing temporary importation of product from SteriMax in Canada, in conjunction with Provepharm Life Solutions and its distributor Direct Success.
      • Fluoroquinolones:
        • Levofloxacin injection in D5W (29 May 2024)
        • Levofloxacin oral solution, 25 mg/mL (15 Sep 2023)
        • Moxifloxacin injection (13 Jan 2026)
        • Moxifloxacin 400 mg tablets (6 Dec 2023)
      • Glycopeptides, glycolipopeptides, lipopeptides:
        • Vancomycin injection (1 Jun 2015)
      • Lincosamides:
        • Clindamycin phosphate injection (25 Jun 2015)
      • Macrolides, azalides:
        • Azithromycin injection (6 Jan 2026)
        • Azithromycin oral suspension, 1 gm packets (20 Nov 2024)
        • Erythromycin lactobionate injection (21 Apr 2025)
      • Miscellaneous
        • Bacitracin ophthalmic ointment 500 units/gm (12 Sep 2024)
        • Benzylpenicilloyl polylysine [Pre-pen] (19 Mar 2026)
        • Chloramphenicol injection (9 Oct 2023)
        • Neomycin and Polymyxin B sulfates GU irrigant (25 Jun 2023)
        • Nitrofurantoin oral suspension (5 Jun 2018)
        • Rifaximin 200 mg tablets (11 Apr 2024)
      • Oxazolidinones:
        • Linezolid injection (16 Oct 2024)
      • Penicillins:
        • Amoxicillin, all oral formulations (18 Oct 2022)
        • Amoxicillin-clavulanate, all oral formulations (17 Nov 2022)
        • Dicloxacillin 250 mg, 500 mg capsules (18 Aug 2021)
        • Oxacillin injection (4 Nov 2025)
        • Penicillin G benzathine injection (1 Feb 2023) Availability update
        • Penicillin G benzathine/Penicillin G procaine (31 Mar 2023) Availability update
    • Antifungal drugs: 
      • Amphotericin B Lipid Complex (5 Aug 2022)
      • Ibrexafungerp 150 mg tablets (3 Dec 2024)
    • Antimycobacterial drugs: 
      • No current shortages
    • Antiparasitic drugs:
      • Nitazoxanide oral susp 100 mg/5 mL (15 Feb 2024)
    • Antiviral drugs: 
      • Acyclovir injection (16 Dec 2025)
      • Oseltamivir, all formulations (1 Nov 2022)
      • Peginterferon alfa-2a (Pegasys) (8 Jan 2025)
      • Ribavirin for inhalation solution (23 May 2023)
  • For more information including estimated resupply dates, see ASHP Drug Shortages website.
  • Data shown are current as of 9 May 2026.
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