The demographics are described in Table 1. The median age of CLH was 4.8 years and 3.5 for HUC. CLH were malnourished and stunted as compared to HUC [WAZ for CLH -2.456 vs. -1.33 for HUC, p=<0.001]; [HAZ for CLH-1.89 vs. -.92 for HUC, p=<0.001]. 98% of mothers of CLH were HIV-infected. Mothers contributed 92% of all parental swabs.
Nearly 36% (18/49) of CLH were on antiretroviral treatment (ART) and 51% were on Trimethoprim/Sulfomethoxazole prophylaxis (Table 2). 53% of parents of CLH were on ART. The majority of CLH had immune classification of severe [15/49, (30%)] or moderate [22/49, (45%)] disease. The median CD4 count was 650 cells/mm3.
We noted the clinical history of children prior to NP specimen collection, and found 28% of CLH, and 21% of HUC, were sick in the past week. The major symptoms included fever, cough, rhinitis or diarrhea; however, during swab collection all children were afebrile (<100.4 °F). Over 23% of CLH had a history of ear infection within one month prior to study, compared to 4% in HUC (p=0.06).
Nasopharyngeal bacteria and viruses in children versus parents
A total of 169 NP swabs (92 from children; 77 from parents) were tested for viruses and 147 (83 from children, 64 from parents) for bacteria (Table 3). Bacteria were identified in 67% of the children, and 54% of parents. Staphylococcus aureus was the most common bacterium identified in children [53%, 44/83], followed by Streptococcus pneumoniae [37.3%, 31/83], and Chlamydia pneumoniae [2%, 2/83]. Similar trends were seen in their parents, [S. aureus (53%); pneumococcus (20%)]. Higher rates of pneumococcus were found in children compared to parents (p=0.02).
Pneumococcus with S. aureus were the most frequent bacteria co-detected (24%) in children. Viruses were detected in higher numbers (44%) in children than their parents (30%) (p=0.049), particularly rhinovirus (p=0.02). Viruses with bacteria were more frequently co-detected in children (26%), than virus alone (3%). For example, 13 out of 15 times rhinovirus was detected with bacteria, and adenovirus was found with bacteria 8 out of 9 times.
Nasopharyngeal microbes and viruses in children with and without HIV
Bacterial pathogens were tested in specimens from 43 CLH, 40 HUC, and viruses in 49 CLH, 43 HUC (Table 4). Samples for bacterial testing were lower due to the loss of reactions in bacterial standards.
Bacteria were identified in 70% of CLH and 65% of HUC. S. aureus was identified in an increasing fashion in CLH, as compared to HUC (63% vs. 42%; p=0.06). Similar pneumococcus and C. pneumoniae rates were found in CLH and HUC (37%; 2% each). Co-occurrence of pneumococcus with S. aureus was found more often in CLH (30%), than in HUC (17%), although not significant (p=0.17).
Respiratory virus detection
In the 92 samples tested, viruses were detected in 41% of CLH and 49% of HUC. Rhinovirus and adenovirus were most frequently detected in CLH (14% each), followed by bocavirus 4%, RSV 2%, coronavirus-229 2%, human metapneumovirus 2% and human parainfluenza-3 virus (2%). Of interest, viruses were identified mainly in children with stage 2 and 3 HIV disease (13/14), than stage 1 (1/14) (p=<0.001). 57% of CLH with viral positivity were not on ART. Rhinovirus was also most frequent in HUC (18%). Influenza B was identified only in HUC (9%). Being on an antibiotic in the past week, increased the risk of virus by 3.85 times, (95% CI 1.05-14, p=0.04).
The co-occurrence of ≥1 bacteria with ≥1 viruses was found in 28% of CLH, and 25% of HUC. The co-occurrence was mainly found in children with stage 2 and stage 3 HIV disease (11/12), as compared to stage 1 (1/12) (p<0.001). Interestingly, wood used for cooking within households, increased the risk of virus (OR 3.09, 1.0-9.21, p=0.042) and virus-bacteria detection (OR 4.75, 1.2-17, p=0.019) among children, suggesting indoor air pollution may increase the risk for viruses.
Nasopharyngeal bacteria and viruses identified in parents with and without HIV
Bacteria were tested in 33 PCLH and 31 PHUC specimens, and viruses in 44 PCLH and 33 PHUC. Bacteria were detected in 51% of PCLH and 58% of PHUC. S. aureus was most frequent in both PCLH (51%) and PHUC (58%). Similar rates of pneumococcus (20-21%) were detected in both parents, and their children. Viruses were detected in 34% of PCLH and 27% of PHUC. Adenovirus was most common in PCLH (11%), and RSV in PHUC (12%). Virus-bacteria co-detection was found in 16% of PHUC and 12% of PCLH.
Co-detection of nasopharyngeal bacteria with viruses
Virus-bacteria co-detections were found in 12 CLH and 10 HUC. Of the 12 CLH, 7 had co-occurrence of S. pneumoniae + S. aureus with viruses. The remaining 5 CLH had co-occurrence of viruses with pneumococcus (2), or S. aureus (3). Among the HUC, viruses were co-detected with pneumococcus (3), S. aureus (3), S. pneumoniae + S. aureus (3), or, C. pneumoniae (1). Among parents, viruses were co-detected only with S. aureus (8/64).
Nasopharyngeal carriage in children with and without history of symptoms
A history of respiratory symptoms in the past week was associated with more than 4 times increased risk of virus detection in children (OR 4.2; 1.5-11.7; p=0.005), and 3.65 times virus-bacteria co-detection (OR 3.65; 1.3-10; p=0.01). CLH with symptoms in the past week, had 6 times increased risk of virus detection (6.44; 1.62-25; p=0.008), as compared to 2 fold in HUC (2.6; .56-12; p=0.22). Bocavirus and RSV were identified only with symptom history, while rhinovirus and adenovirus were detected regardless of history.
Association of viruses with S. pneumoniae and its nasopharyngeal density in children
s. pneumoniae was associated with co-occurrence of viral species in children (OR 3.9) (Table 5). Particularly adenovirus, co-detection increased the likelihood of pneumococcal detection six fold (p=0.036).
In CLH, positive associations were found between pneumococcus with rhinovirus (OR 15), and between pneumococcus, S. aureus, and rhinovirus (OR 8.7). Increased pneumococcal density was seen with co-detection of viruses (Coeff 3.6), multiple viruses (Coeff 5), and rhinovirus specifically (Coeff 4.5).