tetano
Editor, Senior Moderator
Int J Infect Dis
. 2022 Jun 11;S1201-9712(22)00346-0.
doi: 10.1016/j.ijid.2022.06.011. Online ahead of print.
Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017
Malefu Moleleki[SUP] 1 [/SUP], Mignon du Plessis[SUP] 2 [/SUP], Kedibone Ndlangisa[SUP] 2 [/SUP], Cayla Reddy[SUP] 2 [/SUP], Orienka Hellferscee[SUP] 3 [/SUP], Omphe Mekgoe[SUP] 4 [/SUP], Meredith McMorrow[SUP] 5 [/SUP], Sibongile Walaza[SUP] 6 [/SUP], Cheryl Cohen[SUP] 6 [/SUP], Stefano Tempia[SUP] 7 [/SUP], Anne von Gottberg[SUP] 2 [/SUP], Nicole Wolter[SUP] 2 [/SUP]
Affiliations
Abstract
Objectives: We describe the use of a multi-pathogen platform, TaqMan array card (TAC) real-time PCR, 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-squared 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 H. influenzae (225/637; 35%), S. pneumoniae (224/637; 35%), rhinovirus (144/637; 23%), S. aureus (129/637; 20%), K. pneumoniae (85/637; 13%), M. tuberculosis (75/637; 12%), and respiratory syncytial virus (57/637; 9%). Multiple pathogens (≥2) were co-detected in 57% (364/637) of patients.
Conclusion: While 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: Taqman array card; community-acquired pneumonia; real-time PCR; severe respiratory illness.
. 2022 Jun 11;S1201-9712(22)00346-0.
doi: 10.1016/j.ijid.2022.06.011. Online ahead of print.
Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017
Malefu Moleleki[SUP] 1 [/SUP], Mignon du Plessis[SUP] 2 [/SUP], Kedibone Ndlangisa[SUP] 2 [/SUP], Cayla Reddy[SUP] 2 [/SUP], Orienka Hellferscee[SUP] 3 [/SUP], Omphe Mekgoe[SUP] 4 [/SUP], Meredith McMorrow[SUP] 5 [/SUP], Sibongile Walaza[SUP] 6 [/SUP], Cheryl Cohen[SUP] 6 [/SUP], Stefano Tempia[SUP] 7 [/SUP], Anne von Gottberg[SUP] 2 [/SUP], Nicole Wolter[SUP] 2 [/SUP]
Affiliations
- PMID: 35700877
- DOI: 10.1016/j.ijid.2022.06.011
Abstract
Objectives: We describe the use of a multi-pathogen platform, TaqMan array card (TAC) real-time PCR, 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-squared 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 H. influenzae (225/637; 35%), S. pneumoniae (224/637; 35%), rhinovirus (144/637; 23%), S. aureus (129/637; 20%), K. pneumoniae (85/637; 13%), M. tuberculosis (75/637; 12%), and respiratory syncytial virus (57/637; 9%). Multiple pathogens (≥2) were co-detected in 57% (364/637) of patients.
Conclusion: While 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: Taqman array card; community-acquired pneumonia; real-time PCR; severe respiratory illness.