Cross-sectional health centre and community-based evaluation of the impact of pneumococcal and malaria vaccination on antibiotic prescription and usage, febrile illness and antimicrobial resistance in young children in Malawi: the IVAR study protocol

Introduction Vaccination is a potentially critical component of efforts to arrest development and dissemination of antimicrobial resistance (AMR), though little is known about vaccination impact within low-income and middle-income countries. This study will evaluate the impact of vaccination on reducing carriage prevalence of resistant Streptococcus pneumoniae and extended spectrum beta-lactamase-producing Escherichia coli and Klebsiella species. We will leverage two large ongoing cluster-randomised vaccine evaluations in Malawi assessing; first, adding a booster dose to the 13-valent pneumococcal conjugate vaccine (PCV13) schedule, and second, introduction of the RTS, S/AS01 malaria vaccine. Methods and analysis Six cross-sectional surveys will be implemented within primary healthcare centres (n=3000 users of outpatient facilities per survey) and their local communities (n=700 healthy children per survey): three surveys in Blantyre district (PCV13 component) and three surveys in Mangochi district (RTS, S/AS01 component). We will evaluate antibiotic prescription practices and AMR carriage in children ≤3 years. For the PCV13 component, surveys will be conducted 9, 18 and 33 months following a 3+0 to 2+1 schedule change. For the RTS, S/AS01 component, surveys will be conducted 32, 44 and 56 months post-RTS, S/AS01 introduction. Six health centres in each study component will be randomly selected for study inclusion. Between intervention arms, the primary outcome will be the difference in penicillin non-susceptibility prevalence among S. pneumoniae nasopharyngeal carriage isolates in healthy children. The study is powered to detect an absolute change of 13 percentage points (ie, 35% vs 22% penicillin non-susceptibility). Ethics and dissemination This study has been approved by the Kamuzu University of Health Sciences (Ref: P01-21-3249), University College London (Ref: 18331/002) and University of Liverpool (Ref: 9908) Research Ethics Committees. Parental/caregiver verbal or written informed consent will be obtained prior to inclusion or recruitment in the health centre-based and community-based activities, respectively. Results will be disseminated via the Malawi Ministry of Health, WHO, peer-reviewed publications and conference presentations.


GENERAL COMMENTS
Thank you for the opportunity to review this interesting protocol with valid design utilizing randomized studies with supplemental data collection. In general, this protocol deals with an important and relevant topic and I look forward to reading the eventual results of the study. The language is clear and well written. However, there is some room for better clarity in the text and figures.

DETAILED REVIEWER COMMENTS
The BMJ Open instructions for the protocol articles do not require a section of "Discussion" which is a disadvantage for an interested reader. Therefore, the strengths and weaknesses are only shortly reported in the "Article Summary". This should be improved by more clearly describing the rationale for the decisions on the protocol and mentioning the strengths and weaknesses of the protocol elsewhere in the text as the topic is described.
Examples on this are missing details like -estimated frequency of over-the-counter antibiotic use outside health care setting -coverage of the full malaria vaccination schedule in the study population -methods for blinding the study assessments -adjustment between the rural vs urban HCs for the malaria study The 2nd bullet point in the "Article Summary" is too general and not understandable for a reader. The chapter "Study site selection" should follow immediately the study setting for clarity. Further, 3+3 HCs are selected but the Figure  2 includes 4+3 HCs. Similarly, the text says "For IVAR, RTS,S/AS01-exposed (n=5 HCs) and non-exposed (n=3 HCs) clusters have been selected," but the Figure 3 shows 3+3 HCs. row 218: b) Inclusion and exclusion criteria. It remains unclear whether repeated visits of the children previously enrolled are allowed.

REVIEWER
Hasso-Agopsowicz, Mateusz World Health Organization Department of Immunization Vaccines and Biologicals, Immunization Vaccines and Biologicals REVIEW RETURNED 02-Mar-2023

GENERAL COMMENTS
The protocol describes a study that aims to measure the impact of two interventions on various AMR indicators: 1) switching from a 3+0 to a 2+1 schedule for a pneumococcal conjugate vaccine, and 2) introducing the malaria RTS,S vaccine. The protocol is well written and adequately describes the rationale and methodology for the study. However, I suggest that the protocol could be further strengthened by: 1) In the introduction, the authors should explain the scientific rationale behind the switch to the 2+1 schedule and how it would impact AMR.
2) The authors should explain why they chose the incidence of febrile illness as the endpoint instead of the incidence of malaria.
3) To measure the impact of the RTS,S vaccine, the authors could consider endpoints that would indicate resistance of the malaria parasite, such as the length of treatment or incidence of re-infection. 4) The authors propose measuring antibiotic prescription incidence as a proportion of outpatient department visits. However, it is possible that the vaccine could significantly improve a child's health and reduce the total number of visits, resulting in only more severe cases being seen at the clinic. In such cases, the proposed indicator would increase despite the vaccine's positive impact. The authors could consider other denominators, such as the number of children in the catchment area.

VERSION 1 -AUTHOR RESPONSE
Reviewer: 1 Dr. Maria Khan, Rehman Medical Institute Comments to the Author: Very good effort by the authors.
Reviewer: 2 Dr. Arto A. Palmu, Natl Inst Hlth Comments to the Author: Thank you for the opportunity to review this interesting protocol with valid design utilizing randomized studies with supplemental data collection. In general, this protocol deals with an important and relevant topic and I look forward to reading the eventual results of the study. The language is clear and well written. However, there is some room for better clarity in the text and figures.

DETAILED REVIEWER COMMENTS
The BMJ Open instructions for the protocol articles do not require a section of "Discussion" which is a disadvantage for an interested reader. Therefore, the strengths and weaknesses are only shortly reported in the "Article Summary". This should be improved by more clearly describing the rationale for the decisions on the protocol and mentioning the strengths and weaknesses of the protocol elsewhere in the text as the topic is described.
Examples on this are missing details like -estimated frequency of over-the-counter antibiotic use outside health care setting -coverage of the full malaria vaccination schedule in the study population -methods for blinding the study assessments -adjustment between the rural vs urban HCs for the malaria study Thank you for this excellent suggestion. We have included a discussion reflecting on the points you have highlighted above (lines 490-548). Please note that to our knowledge there are no estimates of over-the-counter antibiotic use in Malawi to datewe have noted this in the discussion. Similarly, although vaccine coverage is something that we are collecting as part of this study, vaccine coverage rates for the malaria vaccine (RTS,S/AS01) in the general study population have not yet been publicly reported.
The 2nd bullet point in the "Article Summary" is too general and not understandable for a reader.
We have made this point a bit more specific (lines 41-43).
The chapter "Study site selection" should follow immediately the study setting for clarity. Further, 3+3 HCs are selected but the Figure 2 includes 4+3 HCs. Similarly, the text says "For IVAR, RTS,S/AS01exposed (n=5 HCs) and non-exposed (n=3 HCs) clusters have been selected," but the Figure 3 shows 3+3 HCs. row 218: b) Inclusion and exclusion criteria. It remains unclear whether repeated visits of the children previously enrolled are allowed.
We have moved the study site selection section earlier in the manuscript. Many thanks for spotting the omission on the RTS,S/AS01 evaluation, this was intended to refer to the 8 HCs already selected for the existing evaluation of which IVAR has selected 6. We have improved clarity in lines 158-160. Regarding repeated visits, we have clarified this in lines 235-236 and 338-339.
Reviewer: 3 Dr. Mateusz Hasso-Agopsowicz, World Health Organization Department of Immunization Vaccines and Biologicals Comments to the Author: The protocol describes a study that aims to measure the impact of two interventions on various AMR indicators: 1) switching from a 3+0 to a 2+1 schedule for a pneumococcal conjugate vaccine, and 2) introducing the malaria RTS,S vaccine. The protocol is well written and adequately describes the rationale and methodology for the study. However, I suggest that the protocol could be further strengthened by: 1) In the introduction, the authors should explain the scientific rationale behind the switch to the 2+1 schedule and how it would impact AMR.
We have included a brief rationale on lines 100-103.
2) The authors should explain why they chose the incidence of febrile illness as the endpoint instead of the incidence of malaria.
We have included a discussion of this in lines 527-532. We have also added lines 409-411 indicating that we will consider mRDTs as secondary outcomes.
3) To measure the impact of the RTS,S vaccine, the authors could consider endpoints that would indicate resistance of the malaria parasite, such as the length of treatment or incidence of re-infection.
From the data we are collecting we would indeed be able to consider these as additional outcomes and have included a note to this effect on lines 409-411. Due to issues with case follow-up, defining re-infection in this population may prove challenging. As such, we have opted to consider multiple positive mRDT results instead as a proxy. Length of prescribed antibiotic treatment has also been added as an outcome (line 404).
4) The authors propose measuring antibiotic prescription incidence as a proportion of outpatient department visits. However, it is possible that the vaccine could significantly improve a child's health and reduce the total number of visits, resulting in only more severe cases being seen at the clinic. In such cases, the proposed indicator would increase despite the vaccine's positive impact. The authors could consider other denominators, such as the number of children in the catchment area.
The Reviewer raises a difficult and important area. Unfortunately, there is an inconsistent availability of census data throughout much of Malawi, and as such in many cases other denominators are simply not available. This remains a limitation of this study. As suggested by Reviewer 2, we have now included a discussion which addresses this point (lines 539-542). However, we have also included the possibility of taking the approach suggested by yourself as an additional outcome (lines 247-249).

GENERAL COMMENTS
The authors' responses are satisfactory. No further comments on the revised version.

Hasso-Agopsowicz, Mateusz
World Health Organization Department of Immunization Vaccines and Biologicals, Immunization Vaccines and Biologicals REVIEW RETURNED 25-Apr-2023

GENERAL COMMENTS
I would like to thank the authors for incorporating the suggested changes. The paper is well-written and I recommend it for publication.