Wise Use of Antibiotics: Trust the Timeline, Not the Temptation to Treat
WISE use of antibiotics in pertussis: when they help—and when they don’t. Balancing antibiotic stewardship with controlling public health outbreaks.
Children tend to cough for various reasons, including normal viral patterns in infancy and toddlerhood, bronchiolitis, pneumonia, asthma, gastroesophageal reflux, allergies, and habit coughs, to name a few. Amid surging pertussis cases, likely driven by waning vaccine immunity and increased vaccine hesitancy, it is important to know when to have pertussis on your differential, when to test, and when to treat.
What is pertussis?
Pertussis, or whooping cough, is a highly communicable respiratory illness caused by the bacterium Bordetella pertussis. The illness occurs year-round. It is characterized by three phases after an incubation period that generally lasts seven to 10 days (but can range from five to 21 days).
- Catarrhal Stage: Symptoms consist of mild upper respiratory symptoms similar to the common cold and last one to two weeks. Treatment during this phase can shorten the illness course, but the illness is difficult to diagnose early without a known exposure given its similarities to viral infections.
- Paroxysmal Stage: Symptoms advance to repetitive coughing, often associated with inspiratory whoop/gasp and post-tussive emesis. Infant symptoms can present differently, which is highlighted later in the article. This phase commonly lasts one to six weeks. Fever is absent to mild. Treatment during this phase can prevent spread of illness, but does not affect length of symptoms.
- Convalescent Stage: Consists of a gradually waning cough over weeks to months that lives up to its nickname of the 100-day cough. Treatment at this stage does not affect symptoms or spread of illness.1
Infants under 6-12 months of age are at greatest risk of severe disease, complications and hospitalization, especially with risk factors such as prematurity or under-immunized status. For infants younger than 6 months, the catarrhal phase can be atypical or shorter, the paroxysmal stage may not include the typical “whoop,” and the convalescent phase can take longer. Severe symptoms for infants can include gasping, bradycardia and apnea. Other complications can include pneumonia, pulmonary hypertension, conjunctival hemorrhages, hernias, hypoxia, seizures, encephalopathy and death.1
Vaccines
Our biggest defense against pertussis is vaccination. Pregnant women are recommended to receive Tdap vaccine during pregnancy (between 27 and 36 weeks of gestation). Adults in close proximity to newborns are also recommended to receive the vaccine. Children receive DTaP at age 2 months, 4 months, 6 months, 15-18 months, 4-6 years, and a Tdap booster at 11-12 years. A booster is recommended every 10 years thereafter.3
When to consider testing
The new Children’s Mercy Pertussis Clinical Pathway7 helps guide testing and treatment recommendations. Testing should be considered in symptomatic patients who are in the appropriate time frame regardless of immunization or exposure status. Currently, there are several tests available, including culture, PCR and serology. In general, PCR is preferred based on a more rapid turnaround time, which affects treatment decisions.
Source: Centers for Disease Control and Prevention.4
When to treat
Treatment should be based on where patients are in the timeline of symptoms. As mentioned above, the catarrhal phase is the only phase where treatment can shorten the length of symptoms. Since this phase is characterized by common upper respiratory symptoms, it is often difficult to start treatment in time. Treatment should be given in the paroxysmal phase to prevent the spread of disease, but does not affect symptoms. Treatment is not beneficial once the convalescent phase is reached. Macrolides are the drug class of choice, with sulfamethoxazole/trimethoprim as an alternative.1 Azithromycin is typically the preferred treatment due to availability, tolerability, drug interactions and side effect profile. It is important that individuals being treated for pertussis isolate at home for five full days from the start of the first dose of antibiotics to avoid spread of infection.7
What to do with contacts
Contacts who are under immunized should receive age-appropriate pertussis vaccine.
Asymptomatic close contacts should be treated with post-exposure prophylaxis (PEP). PEP is recommended for household contacts, individuals who are high risk, those who will have contact with high-risk individuals, or those working in high-risk areas (such as the NICU, day care, or maternity ward), if exposure has occurred within the past 21 days. The same antibiotics used for treatment can be used for PEP. Asymptomatic contacts do not need to isolate unless they become symptomatic, in which case they should contact their primary care clinician or local health department for additional guidance.5 Pertussis is a nationally notifiable disease, and local health departments should be contacted for additional questions, guidance on returning to school or work, and management of large outbreaks.
Preventing antibiotic resistance
While macrolide-resistant Bordetella pertussis (MRBP) has not been highly prevalent in the United States, rates have been increasing in other parts of the world. It is important to use antibiotics wisely to help keep resistance to a minimum. Testing and treatment should be guided by exposure and onset of symptom timetables.6
Resources:
- Committee on Infectious Diseases, American Academy of Pediatrics. Pertussis. In: Kimberlin DW, Banerjee R, Barnett ED, Lynfield R, Sawyer MH, eds. Red Book: 2024–2027 Report of the Committee on Infectious Diseases 33rd ed. American Academy of Pediatrics; 2024:656-667.
- Clinical features of pertussis. Centers for Disease Control and Prevention. December 1, 2025. Accessed April 23, 2026. https://www.cdc.gov/pertussis/hcp/clinical-signs/index.html
- Whooping cough vaccination. Centers for Disease Control and Prevention. December 2, 2025. Accessed April 23, 2026. https://www.cdc.gov/pertussis/vaccines/index.html
- Laboratory testing for pertussis. Centers for Disease Control and Prevention. December 2, 2025. Accessed April 23, 2026. https://www.cdc.gov/pertussis/php/laboratories/index.html
- Postexposure antimicrobial prophylaxis. Centers for Disease Control and Prevention. April 2, 2024. Accessed April 23, 2026. https://www.cdc.gov/pertussis/php/postexposure-prophylaxis/index.html
- Antibiotic-resistant Bordetella pertussis. Centers for Disease Control and Prevention. December 4, 2025. Accessed April 23, 2026. https://www.cdc.gov/pertussis/hcp/antibiotic-resistance/index.html
- Pertussis clinical pathway. Children’s Mercy. Last updated May 6, 2026. https://www.childrensmercy.org/siteassets/media-documents-for-depts-section/documents-for-health-care-providers/block-clinical-practice-guidelines/mobileview/pertussis-algorithm.pdf