Respiratory viruses detected in Mexican children younger than 5 years old with community-acquired pneumonia: a national multicenter study

Background: Acute respiratory infections are the leading cause of mortality in children worldwide, especially in developing countries. Pneumonia accounts for 16% of all deaths of children under 5 years of age and was the cause of death of 935 000 children in 2015. Despite its frequency and severity, information regarding its etiology is limited. The aim of this study was to identify respiratory viruses associated with community-acquired pneumonia (CAP) in children younger than 5 years old. Methods: One thousand four hundred and four children younger than 5 years of age with a clinical and/or radiological diagnosis of CAP in 11 hospitals in Mexico were included. Nasal washes were collected, placed in viral medium, and frozen at �70 C until processing. The first 832 samples were processed using the multiplex Bio-Plex/Luminex system and the remaining 572 samples using the Anyplex multiplex RT-PCR. Clinical data regarding diagnosis, clinical signs and symptoms, radiographic pattern, and risk factors were obtained and recorded. Results: Of the samples tested, 81.6% were positive for viruses. Respiratory syncytial virus (types A and B) was found in 23.7%, human enterovirus/rhinovirus in 16.6%, metapneumovirus in 5.7%, parainfluenza virus (types 1–4) in 5.5%, influenza virus (types A and B) in 3.6%, adenovirus in 2.2%, coronavirus (NL63, OC43, 229E, and HKU1) in 2.2%, and bocavirus in 0.4%. Co-infection with two or more viruses was present in 22.1%; 18.4% of the samples were negative. Using biomass for cooking, daycare attendance, absence of breastfeeding, and co-infections were found to be statistically significant risk factors for the presence of severe pneumonia. Conclusions: Respiratory syncytial virus (types A and B), human enterovirus/rhinovirus, and metapneumovirus were the respiratory viruses identified most frequently in children younger than 5 years old with CAP. Co-infection was present in an important proportion of the children

Effect of Malnutrition on the Expression of Cytokines Involved in Th1 Cell Differentiation

Malnutrition is a common cause of secondary immune deficiency and has been linked to an increased susceptibility to infection in humans. Malnutrition specifically affects T-cell-mediated immune responses. The aim of this study was to assess in lymphocytes from malnourished children the expression levels of IL-12, IL-18 and IL-21, molecules that induce the differentiation of T cells related to the immunological cellular response (Th1 response) and the production of cytokines related to the immunological cellular response (Th1 cytokines). We found that the expression levels of IL-12, IL-18 and IL-21 were significantly diminished in malnourished children compared to well-nourished children and were coincident with lower plasmatic levels of IL-2 and IFN-γ (Th1 cytokines). In this study, we show for the first time that the gene expression and intracellular production of cytokines responsible for Th1 cell differentiation (IL-12, IL-18 and IL-21) are diminished in malnourished children. As expected, this finding was related to lower plasmatic levels of IL-2 and IFN-γ. The decreased expression of Th1 cytokines observed in this study may contribute to the deterioration of the immunological Type 1 (cellular) response. We hypothesize that the decreased production of IL-12, IL-18 and IL-21 in malnourished children contributes to their inability to eradicate infections

DNA reads obtained after NGS sequencing of LRTI samples.

a<p>Valid DNA reads after discarding those that did not pass the quality filter, and removing repeated reads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113570#s2" target="_blank">Methods</a>).</p><p>DNA reads obtained after NGS sequencing of LRTI samples.</p

DNA reads obtained after NGS sequencing of URTI samples.

a<p>The samples that were pooled for sequencing are indicated.</p>b<p>Valid DNA reads after discarding those that did not pass the quality filter, and removing repeated reads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113570#s2" target="_blank">Methods</a>).</p><p>DNA reads obtained after NGS sequencing of URTI samples.</p

Genome coverage for viruses present in URTI samples.

a<p>RSV, respiratory syncytial virus; RV-A, rhinovirus species A; RV-B; rhinovirus species B; RV-C; rhinovirus species C; HBoV, human bocavirus, HCoV, human coronavirus OC43; TTV, torque teno virus; TTMV, torque teno mini virus; TTMDV, torque teno midi virus; BKV, bovine kobuvirus; BVDV, bovine viral diarrhea virus; BatPV, bat picornavirus; HPV, human papillomavirus; PVY, potato virus Y, ToMV, tomato mosaic virus; CMV, cucumber mosaic virus; HHV, human herpes virus; HVE-A, human enterovirus A; SAFV, Saffold virus; WSSV, white spot syndrome virus; HASTV, human astrovirus.</p><p>Genome coverage for viruses present in URTI samples.</p

Frequency of viral pathogens in children with URTI and LRTI.

a<p>The number of viruses include those present in single and mixed infections. The percentage refers to the total number of viruses detected.</p><p>Frequency of viral pathogens in children with URTI and LRTI.</p

Taxonomic classification of the generated DNA sequencing reads.

<p>Valid DNA reads obtained by NGS of LRTI and URTI clinical samples were split into human, bacterial, fungal, and viral origin. Those reads not present in the four previous categories were classified as "undefined". Average values for all LRTI and URTI samples are shown.</p

Pathogens identified by NGS in children with upper respiratory tract infections.

a<p>When more than one sample were pooled for sequencing, the code for the various samples is mentioned.</p>b<p>Number of valids DNA reads in the sample por the corresponding pathogen.</p><p>Pathogens identified by NGS in children with upper respiratory tract infections.</p

Pathogens identified by NGS in children with lower respiratory tract infections.

a<p>Number of valids DNA reads in the sample por the corresponding pathogen.</p><p>Pathogens identified by NGS in children with lower respiratory tract infections.</p