Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017

Malefu Moleleki; Mignon du Plessis; Kedibone Ndlangisa; Cayla Reddy; Orienka Hellferscee; Omphe Mekgoe; Meredith McMorrow; Sibongile Walaza; Cheryl Cohen; Stefano Tempia; Anne von Gottberg; Nicole Wolter

doi:10.1016/j.ijid.2022.06.011

Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017

Int J Infect Dis. 2022 Sep:122:389-397. doi: 10.1016/j.ijid.2022.06.011. Epub 2022 Jun 11.

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: malefum@sun.ac.za.
² Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
³ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Department of Medical Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁵ Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
⁶ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁷ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, United States of America; Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; MassGenics, Duluth, GA, United States of America.

PMID: 35700877
DOI: 10.1016/j.ijid.2022.06.011

Abstract

Objectives: We describe the use of a multipathogen platform, TaqMan array card (TAC) real-time polymerase chain reaction, for the detection of pathogens in patients hospitalized with severe respiratory illness (SRI).

Methods: Prospective hospital-based syndromic surveillance for acute and chronic SRI was carried out at two sentinel sites in South Africa between January and December 2017. We tested respiratory specimens for 21 respiratory pathogens and blood samples for nine bacteria using TAC. Pathogen detection was compared by age group and HIV status using the chi-square test.

Results: During 2017, 956 patients of all ages were enrolled in the SRI surveillance, and of these, 637 (67%) patients were included in this study (637 blood, 487 naso- and oro-pharyngeal swabs, and 411 sputum specimens tested). At least one pathogen was detected in 83% (527/637) of patients. Common pathogens detected included Haemophilus influenzae (225/637; 35%), Streptococcus pneumoniae (224/637; 35%), rhinovirus (144/637; 23%), Staphylococcus aureus (129/637; 20%), Klebseilla pneumoniae (85/637; 13%), Mycobacterium tuberculosis (75/637; 12%), and respiratory syncytial virus (57/637; 9%). Multiple pathogens (≥2) were codetected in 57% (364/637) of patients.

Conclusion: Although the use of a multi-pathogen platform improved pathogen yield, pathogen co-detections were common and would need clinical assessment for usefulness in individual-level treatment and management decisions.

Keywords: Community-acquired pneumonia; Real-time PCR; Severe respiratory illness; Taqman array card.

MeSH terms

Hospitalization
Humans
Pathology, Molecular
Pneumonia* / diagnosis
Prospective Studies
Respiratory Tract Infections* / diagnosis
Respiratory Tract Infections* / epidemiology
Respiratory Tract Infections* / microbiology
South Africa / epidemiology