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. 2024 Aug 2;13(8):655.
doi: 10.3390/pathogens13080655.

Prevalence of Respiratory Pathogens in Nasopharyngeal Swabs of Febrile Patients with or without Respiratory Symptoms in the Niakhar Area of Rural Senegal

Dame Ndiaye  1   2   3 , Georges Diatta  3 , Hubert Bassene  3 , Sébastien Cortaredona  1   2   4 , Masse Sambou  3 , Anna Julienne Selbe Ndiaye  1   2 , Marielle Bedotto-Buffet  5 , Sophie Edouard  1   2 , Oleg Mediannikov  2   6   7 , Cheikh Sokhna  1   2   3 , Florence Fenollar  1   2
Affiliations

Prevalence of Respiratory Pathogens in Nasopharyngeal Swabs of Febrile Patients with or without Respiratory Symptoms in the Niakhar Area of Rural Senegal

Dame Ndiaye et al. Pathogens. .

Abstract

Acute respiratory tract infections are one of the leading causes of morbidity and mortality worldwide. More data are needed on circulating respiratory microorganisms in different geographical areas and ecosystems. We analyzed nasopharyngeal swabs from 500 febrile patients living in the Niakhar area (Senegal), using FTDTM multiplex qPCR and simplex qPCR to target a panel of 25 microorganisms. We detected at least one microorganism for 366/500 patients (73.2%), at least one virus for 193/500 (38.6%), and at least one bacterium for 324/500 (64.8%). The most frequently detected microorganisms were Streptococcus pneumoniae (36.8%), Haemophilus influenzae (35.8%), adenovirus (11.8%), influenza viruses (6.4%), rhinovirus (5.0%), SARS-CoV-2 (4.0%), and RSV (4.0%). The main microorganisms significantly associated with respiratory symptoms, with a p-value ≤ 0.05, were influenza virus (11.9% in patients with respiratory symptoms versus 2.9% in patients without), RSV (6.5% versus 2.6%), metapneumovirus (5.4% versus 1.3%), HPIVs (7.6% versus 1.0%), S. pneumoniae (51.9% versus 28.0%), and H. influenzae (54.6% versus 24.5%). Co-infections were significantly associated with respiratory symptoms (65.4% versus 32.9%). All the epidemiological data show a high level of circulation of respiratory pathogens among febrile patients, including those preventable by vaccination such as S. pneumoniae, raising the question of the serotypes currently circulating. Furthermore, the availability of affordable real-time etiological diagnostic tools would enable management to be adapted as effectively as possible.

Keywords: Haemophilus influenzae; RSV; SARS-CoV-2; Senegal; Streptococcus pneumoniae; acute respiratory tract infections; adenovirus; human coronaviruses; influenza; sub-Saharan Africa.

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Conflict of interest statement

The authors have no conflicts of interest to declare. Funding sources played no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript.

Figures

Figure 1
Figure 1
Location of the Niakhar area in rural Senegal (West Africa).
Figure 2
Figure 2
Seasonal prevalence of a first series of respiratory viruses (SARS-CoV-2, Flu A, Flu B, HRV, HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43) from nasopharyngeal swabs in 500 febrile patients from the Niakhar area in rural Senegal (number of samples tested in brackets).
Figure 3
Figure 3
Seasonal prevalence of a second series of respiratory viruses (HPIV-3, HPIV-2, HPIV-1, hMPV, hBoV, RSV, PEC, EV, and AdV) from nasopharyngeal swabs in 500 febrile patients from the Niakhar area in rural Senegal (number of samples tested in brackets).
Figure 4
Figure 4
Seasonal prevalence of bacteria from nasopharyngeal swabs in 500 febrile patients from the Niakhar area in rural Senegal (number of samples tested in brackets).
See this image and copyright information in PMC

References

    1. Hijazi Z., Pacsa A., Eisa S., El Shazli A., Abd El-Salam R.A. Laboratory diagnosis of acute lower respiratory tract viral infections in children. J. Trop. Pediatr. 1996;42:276–280. doi: 10.1093/tropej/42.5.276. - DOI - PubMed
    1. Kaplan N.M., Dove W., Abu-Zeid A.F., Shamoon H.E., Abd-Eldayem S.A., Hart C.A. Human bocavirus infection among children, Jordan. Emerg. Infect. Dis. 2006;12:1418–1420. doi: 10.3201/eid1209.060417. - DOI - PMC - PubMed
    1. van Rijn A.L., Nijhuis R.H.T., Bekker V., Groeneveld G.H., Wessels E., Feltkamp M.C.W., Claas E.C.J. Clinical implications of rapid ePlex® respiratory pathogen panel testing compared to laboratory-developed real-time PCR. Eur. J. Clin. Microbiol. Infect. Dis. 2018;37:571–577. doi: 10.1007/s10096-017-3151-0. - DOI - PMC - PubMed
    1. Lu X., Chittaganpitch M., Olsen S.J., Mackay I.M., Sloots T.P., Fry A.M., Erdman D.D. Real-time PCR assays for detection of bocavirus in human specimens. J. Clin. Microbiol. 2006;44:3231–3235. doi: 10.1128/JCM.00889-06. - DOI - PMC - PubMed
    1. Dare R., Sanghavi S., Bullotta A., Keightley M.-C., George K.S., Wadowsky R.M., Paterson D.L., McCurry K.R., Reinhart T.A., Husain S., et al. Diagnosis of human metapneumovirus infection in immunosuppressed lung transplant recipients and children evaluated for pertussis. J. Clin. Microbiol. 2007;45:548–552. doi: 10.1128/JCM.01621-06. - DOI - PMC - PubMed

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