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PERCH Study Details

About PERCH: Pneumonia Etiology Research for Child Health

The PERCH (Pneumonia Etiology Research for Child Health) project is a multi-country, case-control study to determine the etiology of and risk factors for severe and very severe pneumonia in children 1-59 months of age. 

Program Overview


Primary Objectives

  • Determine the association between pneumonia and infection with known and putative viral, bacterial, mycobacterial, and fungal pathogens.
  • Estimate the fraction of pneumonia attributable to pathogens for which vaccines are currently under development (including S. pneumoniae common protein vaccines, respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza and Staphylococcus aureus) as well as other known, but poorly quantified causes of pneumonia in children including, but not limited to, non-typeable H. influenzae, non-typhoidal Salmonellae, human metapneumovirus, M. tuberculosis, Pneumocystis jiroveci, and potentially fastidious bacteria.
  • Assess putative factors for infection and/or disease due to novel or under-recognized pneumonia pathogens.

Secondary Objectives

  • Determine the association between disease severity and etiology.
  • Develop a set of specimens for novel pathogen discovery among episodes with no known etiology (completely negative with comprehensive testing).
  • Determine patterns of antimicrobial resistance among invasive isolates including, but not limited to, M. tuberculosis, S. aureus, and S. pneumoniae.
  • Develop a set of isolates of key pathogens associated with pneumonia including, but not limited to, influenza, S. pneumonia, non-typhoidal Salmonellae, and S. aureus for molecular epidemiologic analyses.
  • Develop a robust clinical severity index based on analyses of PERCH putative criteria and outcomes.
  • Provide a robust platform for ancillary studies of pneumonia epidemiology including, but not limited to, the utility of digital auscultation, chest radiograph, viral quantification and other diagnostics.


Nine sites in seven countries have been selected for PERCH:
  • Johannesburg, South Africa
  • Lusaka, Zambia
  • Kilifi, Kenya
  • Basse, the Gambia
  • Bamako, Mali
  • Sa Kaeo and Nakhon Phanom, Thailand
  • Dhaka and Matlab, Bangladesh

PERCH Study Sites



PI Name




<5 Mortality Rate



Anthony Scott

Kilifi-KEMRI Wellcome Trust




Dhaka, Matlab


Abdullah Brooks







Stephen Howie






South Africa

Shabir Madhi

University of Witswatersrand;

Very High





Karen Kotloff

University of Maryland




Sa Kaeo,
Nakhon Phanom


Henry Baggett/Susan Maloney

CDC - Thailand






Donald Thea

Boston University






Collaborating institutions include the University of Witswatersrand in Johannesburg, South Africa, KEMRI Wellcome Trust Research Programme in Kilifi, Kenya, the University of Maryland’s Center for Vaccine Development in Bamako, Mali, the Thailand Ministry of Public Health – United States Centers for Disease Control and Prevention Collaboration’s at two sites in rural Thailand, Boston University at the University Teaching Hospital of Lusaka, Zambia, the Medical Research Council Unit in Basse, The Gambia and theInternational Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B) at two sites in Bangladesh.  Laboratory methods design and standardization as well as testing oversight was led by the University of Otago and Canterbury Health Laboratories in Christchurch, New Zealand with clinical field sites conducting the majority of lab testing on site.


PERCH Organogram

Core Team

The PERCH Project is led by a Principal Investigator located at Johns Hopkins Bloomberg School of Public Health.  Dr. Kate O’Brien serves as the PERCH PI having assumed these responsibilities following Dr. Orin Levine who served as the PERCH PI from its inception until September 2012. The role of the PERCH PI includes oversight of the entire project, providing strategic direction, management of personnel and budgets, and assuring scientific conduct of high quality and integrity. The PERCH PI (Levine and O’Brien) has been supported by two co-PIs (Drs. Anthony Scott and Maria Knoll).  The PERCH Study is governed by the PERCH Executive Committee, which consists of three representatives of the Core Team (O’Brien, Murdoch, Feikin), and the seven Site Principal Investigators.  The PERCH Executive Committee is responsible for all strategic, management, and study conduct decisions. The PERCH PI is also responsible for leading the Core Team whose members are located at JHSPH and at University of Otago; members of the Core Team include pediatricians, epidemiologists, laboratory scientists, and statisticians.

During the conduct of the study, several working groups (see organogram), consisting of  a Team Leader, a PERCH Core Team coordinator, and members from each of the site teams, were active.  The responsibility of the team leader was to direct that section of the study in keeping with the scientific objectives while accounting for inherent variations in site capacity and resources.  The Team Leader and the PERCH coordinators assigned to the Working Group convened regular meetings to identify challenges in study design and conduct and to propose and implement solutions. The Team Leaders reported to the PERCH PI and co-PIs.

Core Team members participated in working groups according to their experience and knowledge. Dr. O'Brien participated in all Working Groups, assuring there was cohesion and integration across working groups. The Team Leaders reported to the PERCH Core Team on a weekly basis thereby assuring that working group decisions, needs, and approaches were kept on track from a strategic, budget, and scientific perspective. 

Study Design


Multiple body specimens were obtained from each case and control:

  • Acute blood
  • Convalescent blood (cases only)
  • Nasopharyngeal and oropharyngeal swabs
  • Induced sputum or gastric aspirate if sputum is not obtained (cases only)
  • Pleural fluid (cases only, when clinically indicated)
  • Lung aspirates (cases only, in select sites)
  • Urine
  • Post mortem lung needle biopsy (fatal cases only, in select sites)

Sample size

The PERCH study enrolled cases and controls over a 24 month period at each study site.  Enrollment took place between August 2011 and January 2014. A total of 4,232 patients hospitalized with severe or very severe pneumonia and 5,325 community based controls were enrolled using a standardized methodology. As such, the study is expected to offer improved precision and accuracy on existing estimates of pneumonia etiology and to determine associations with risk factors that may not have been detectable previously.