Measuring the change in genetic markers of antibiotic resistance carried in the nasopharynx of children with pneumonia in Blantyre, Malawi, and assessing whether this is associated with poor health outcomes

Nasopharyngeal resistome evolution under selective pressure and association with adverse health outcomes in a paediatric population in Blantyre, Malawi

Status

Recruiting

Phases

Unknown

Study type

Observational

Source

ISRCTN

Registry ID

ISRCTN64027792

Enrollment

350

Registered

2025-08-13

Start date

2025-08-13

Completion date

Unknown

Last updated

2025-09-08

For informational purposes only — not medical advice. Sourced from public registries and may not reflect the latest updates. Terms

Conditions

Pneumonia Respiratory

Interventions

This observational study will recruit 350 children aged 12-24 months in four groups: healthy children in the community, children with pneumonia being treated with oral antibiotics in the community, ch

Eligibility

Sex/Gender

All

Inclusion criteria

Inclusion criteria: Inclusion criteria for healthy children in the community: 1. Child aged between 12-24 months living in Ndirande community, in Blantyre, Malawi. Inclusion criteria for children with pneumonia in the community: 1. Child aged between 12-24 months presenting to Ndirande community healthcare centre, Blantyre, Malawi. 2. Presence of ALL of the following symptoms: fever, cough, difficulty in breathing and fast breathing. 3. Participant has been prescribed antibiotics for treatment of a lower respiratory tract infection on this presentation. Inclusion criteria for children hospitalised with pneumonia: 1. Child aged between 12-24 months admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. 2. Presence of ALL of the following symptoms: fever, cough, difficulty in breathing and fast breathing. 3. Participant has been prescribed antibiotics for treatment of a lower respiratory tract infection on this presentation. Inclusion criteria for children re-hospitalised with pneumonia: 1. Child aged between 12-24 months admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. 2. Presence of all of the following symptoms: fever, cough, difficulty in breathing and fast breathing. 3. Participant has been prescribed antibiotics for treatment of a lower respiratory tract infection on this admission. 4. Hospital admission to ANY hospital with a lower respiratory tract infection within the past 3 months.

Exclusion criteria

Exclusion criteria: Exclusion criteria for healthy children in the community: 1. Presence of any of the following symptoms: fever, cough, difficulty in breathing or fast breathing. 2. Currently taking long-term antibiotic prophylaxis, TB treatment or immunosuppressive medications. 3. Diagnosis of an immunosuppressive illness, including HIV infection. 4. Hospital admission within the past six months. Exclusion criteria for children with pneumonia in the community and children hospitalised with pneumonia: 1. Severe anaemia, with a recorded haemoglobin level < 70 grams per Litre. 2. Currently taking long-term antibiotic prophylaxis, TB treatment or immunosuppressive medications. 3. Diagnosis of an immunosuppressive illness, including HIV infection. 4. Hospital admission within the past six months. Exclusion criteria for children re-hospitalised with pneumonia: 1. Severe anaemia, with a recorded haemoglobin level < 70 grams per Litre. 2. Currently taking long-term antibiotic prophylaxis, TB treatment or immunosuppressive medications. 3. Diagnosis of an immunosuppressive illness, including HIV infection.

Design outcomes

Primary

Measure	Time frame
1.Diversity of antibiotic resistance genes (ARGs) in the nasopharyngeal resistome (NPR) of healthy children in Blantyre, children with pneumonia in the community and children hospitalised with pneumonia when measured using metagenomic sequencing of nasopharyngeal swabs (NPS), to assess whether there is a significant difference. The NPS will be taken at recruitment for healthy community participants, and 3-month follow up for participants with pneumonia. 2.Relative abundance of ARGs in the NPR of healthy children in Blantyre, children with pneumonia in the community and children hospitalised with pneumonia, as above. 3.Diversity of ARGs in the NPR of children hospitalised with pneumonia and children re-hospitalised with pneumonia at the point of hospitalisation. 4.Diversity of ARGs in the NPR of children hospitalised with pneumonia and children re-hospitalised with pneumonia at the point of hospitalisation.	—

Measure

Time frame

1.Diversity of antibiotic resistance genes (ARGs) in the nasopharyngeal resistome (NPR) of healthy children in Blantyre, children with pneumonia in the community and children hospitalised with pneumonia when measured using metagenomic sequencing of nasopharyngeal swabs (NPS), to assess whether there is a significant difference. The NPS will be taken at recruitment for healthy community participants, and 3-month follow up for participants with pneumonia. 2.Relative abundance of ARGs in the NPR of healthy children in Blantyre, children with pneumonia in the community and children hospitalised with pneumonia, as above. 3.Diversity of ARGs in the NPR of children hospitalised with pneumonia and children re-hospitalised with pneumonia at the point of hospitalisation. 4.Diversity of ARGs in the NPR of children hospitalised with pneumonia and children re-hospitalised with pneumonia at the point of hospitalisation.

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Secondary

Measure	Time frame
1. Diversity of antibiotic resistance genes (ARGs) in the nasopharyngeal resistome (NPR) of children hospitalised with pneumonia when measured at admission, discharge and 3-month follow up using metagenomic sequencing of nasopharyngeal swabs (NPS), to assess whether there is a significant difference between these time-points. 2. Relative abundance of ARGs in the NPR of children hospitalised with pneumonia when measured at admission, discharge and 3-month follow (as above). 3. Diversity of ARGs in the NPR of children with pneumonia in the community at presentation to a healthcare centre and 3-month follow up. 4. Relative abundance of ARGs in the NPR of children with pneumonia in the community at presentation to a healthcare centre and 3-month follow up. 5. Diversity of ARGs in the NPR of healthy children in Blantyre and children with pneumonia in the community at presentation to a healthcare centre. 6. Relative abundance of ARGs in the NPR of healthy children in Blantyre and children with pneumonia in the community at presentation to a healthcare centre. 7. Repeat antibiotic exposure is measured using caregiver report and health passport records at 3-month follow-up in children discharged from hospital 8. Re-hospitalisation for pneumonia is measured using caregiver report and health passport records at 3-month follow-up in children discharged from hospital	—

Measure

Time frame

1. Diversity of antibiotic resistance genes (ARGs) in the nasopharyngeal resistome (NPR) of children hospitalised with pneumonia when measured at admission, discharge and 3-month follow up using metagenomic sequencing of nasopharyngeal swabs (NPS), to assess whether there is a significant difference between these time-points. 2. Relative abundance of ARGs in the NPR of children hospitalised with pneumonia when measured at admission, discharge and 3-month follow (as above). 3. Diversity of ARGs in the NPR of children with pneumonia in the community at presentation to a healthcare centre and 3-month follow up. 4. Relative abundance of ARGs in the NPR of children with pneumonia in the community at presentation to a healthcare centre and 3-month follow up. 5. Diversity of ARGs in the NPR of healthy children in Blantyre and children with pneumonia in the community at presentation to a healthcare centre. 6. Relative abundance of ARGs in the NPR of healthy children in Blantyre and children with pneumonia in the community at presentation to a healthcare centre. 7. Repeat antibiotic exposure is measured using caregiver report and health passport records at 3-month follow-up in children discharged from hospital 8. Re-hospitalisation for pneumonia is measured using caregiver report and health passport records at 3-month follow-up in children discharged from hospital

—

Countries

Malawi

Contacts

Public ContactLucy O'Connor

lucy.oconnor@lstmed.ac.uk+44(0)151 705 3100

Outcome results

None listed

Source: ISRCTN (via WHO ICTRP) · Data processed: Feb 4, 2026