healthmedicinet

We report the detection rate of selected viral and bacterial pathogens among children
5 years of age hospitalized with SARI in Niger. We detected respiratory viruses in
78 % of our study sample. The high detection rate of viruses found in our study is
consistent with results from similar studies conducted in Burkina Faso (73 %) 23], Kenya (68 %) 24] and Brazil (85 %) 12]. However, lower rates of viral detection were reported from other studies from countries
such as Ghana (26 %) 25], China (56 %) 26] and Egypt (60 %) 4]. These differences can be attributed to different climatic conditions, enrollment
criteria, case definitions and testing platforms.

In our study, RSV was the predominant virus detected and was most commonly found in
children 1 year of age. RSV has been reported to be an important pathogen in children
and especially in young infants in several studies 12], 25]–29]. In addition, RSV detection has been reported to be strongly associated with illness
from studies comparing symptomatic cases to controls 30]. Rhinovirus was the second most commonly detected virus (29 %) with similar rates
among infants 1 year of age and children aged 1–4 years, which has been reported
in previous studies 31], 32]. However, other studies reported RV as the most prevalent virus among children 5 years
of age 16], 23], 28], 33]. In addition RV has been commonly detected among asymptomatic persons in several
studies indicating that RV can act as both pathogen and by-stander, consequently hindering
the ability to infer an association between detection and illness 34]–36]. Among the PIV and CV detected in this study, PIV type 3 and CV type OC43 were the
most common virus types, which has been reported in other studies 12], 16].

We also found a high detection rate of bacterial pathogens. S. pneumoniae (56 %) and Hib (12 %) were the most common bacteria detected in nasopharyngeal specimens.
Elevated colonization rates of these bacteria have been reported in children, but
only a proportion of colonizations result in invasive disease 9], 11], 37]. The high detection rate of S. pneumoniae in our study is likely due to the fact that S. pneumoniae is a commensal of the nasopharynx 38]. It has been shown that the prevalence of S. pneumoniae carriage in healthy children 5 years of age ranges from 20 % to 93 % in low income
countries 11]. The detection of S. pneumoniae from sterile sites like blood or cerebrospinal fluid, reflecting invasive pneumococcal
disease, has been shown to be lower (5–9 %) 8], 39]. Nonetheless, S. pneumoniae has been reported to be responsible for 12 % of meningitis cases in Niger based on
cerebrospinal fluid testing; 26 different serotypes were detected among cases of meningitis
prior to the introduction of the pneumococcal conjugate vaccine in 2014 40]. Hib and S. aureus, the 2
^d
and 3
^rd
most prevalent bacterial pathogens in our study, have also been shown to be commensal
organisms with high nasopharyngeal carriage rates especially in young children 11]. The substantial Hib nasopharyngeal colonization density found in this study should
be investigated further as Hib vaccine has been available in the Niger expanded immunization
program since 2008.

Nasopharyngeal specimens may be used to aid in the diagnosis of certain bacterial
respiratory pathogens that do not tend to colonize the nasopharynx, such as M. pneumoniae and C. pneumoniae38], 41]. C. pneumoniae was detected at low rates (2.5 %), and M. pneumoniae was not detected in our study. Using serological methods, prevalence rates as high
as 30 % have been reported for C. pneumoniae9]; in contrast, other studies report significant detection of M. pneumoniae (10 %) and low detection of C. pneumoniae (1 %) 12], 26], 42].

In our study we found an elevated prevalence (78 %) of viral–bacterial co-detections,
which has been reported in other studies 12], 42]. It has been shown that viral infections may predispose to bacterial super-infection
by favoring bacterial attachment sites on nasopharyngeal epithelial cells and through
increased mucous production that promotes bacterial growth 38], 42].

Our study has limitations that warrant discussion. First, the small sample size of
our study hindered our ability to accurately assess the seasonality of the pathogens
included in our study. Nonetheless, our results suggest that RSV, PIV and HMPV are
more commonly detected during the hot season (October to December), while RV and HBV
are detected more frequently during the rainy season (June to September). No difference
in the detection rate of the other viruses and bacteria was noted across seasons in
our study. The small sample size of our study also hindered our ability to detect
patterns of co-detection and the association between specific viral and bacterial
co-detections. Second, we did not keep formal records of the proportion of patients
consenting to participate in the SARI surveillance. However, a review of the performance
of the surveillance system implemented through hospital record review at sentinel
sites revealed that only a few patients that met the study case definition were missed
by the surveillance program. Third, the lack of controls in our study limited our
ability to assess the association of pathogen detection with disease. While most of
the viral and bacterial pathogens identified in this study have been described by
previous studies as causative agents of ARI, the assignation of causality remains
challenging 39], 43]. Fourth, influenza-positive samples were excluded from our study. Co-detection of
other viral and bacterial pathogens with influenza is expected and this may have
resulted in an underestimation of the prevalence of the pathogens included in this
study, especially during the cold season when the majority of influenza-positive cases
were detected. Last, we did not systematically collect information on progression
of illness (including in-hospital outcome) or risk factors for severe disease, which
hindered our ability to evaluate pathogen contribution to the more severe spectrum
of illness or to identify groups at high risk for severe disease.