title: Identification of viral and bacterial pathogens from hospitalized children with severe acute respiratory illness in Lusaka, Zambia, 2011-2012: a cross-sectional study.
abstract: BACKGROUND
  Morbidity and mortality from respiratory infections are higher in resource-limited countries than developed countries, but limited studies have been conducted in resource-limited settings to examine pathogens from patients with acute respiratory infections. Influenza surveillance has been conducted in Zambia since 2008; however, only 4.3% of patients enrolled in 2011-2012 were positive for influenza. Therefore, we examined non-influenza respiratory pathogens in children with severe acute respiratory illness (SARI) in Zambia, to estimate the scope of disease burden and determine commonly-identified respiratory pathogens.
  
  
  METHODS
  Two reverse transcriptase polymerase chain reaction (rRT-PCR) methods (single and multiplex) were used to analyze nasopharyngeal and throat swabs collected from SARI cases under five years of age from January 2011 through December 2012. All specimens were negative for influenza by rRT-PCR. The panel of singleplex reactions targeted seven viruses, while the multiplex assay targeted thirty-three bacteria, fungi, and viruses.
  
  
  RESULTS
  A set of 297 specimens were tested by singleplex rRT-PCR, and a different set of 199 were tested by multiplex rRT-PCR. Using the singleplex assay, 184/297 (61.9%) specimens were positive for one or more viruses. The most prevalent viruses were human rhinovirus (57/297; 19.2%), human adenovirus (50/297; 16.8%), and respiratory syncytial virus (RSV) (45/297; 15.2%). Using multiplex PCR, at least one virus was detected from 167/199 (83.9%) specimens, and at least one bacteria was detected from 197/199 (99.0%) specimens. Cytomegalovirus (415/199; 208.5%) and RSV (67/199; 33.7%) were the most commonly detected viruses, while Streptococcus pneumonie (109/199; 54.8%) and Moraxella catarrhalis (92/199; 46.2%) were the most commonly detected bacteria.
  
  
  CONCLUSIONS
  Single infections and co-infections of many viruses and bacteria were identified in children with SARI. These results provide an estimate of the prevalence of infection and show which respiratory pathogens are commonly identified in patients. Further studies should investigate causal associations between individual pathogens and SARI.
authors.affiliation: Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. psimusika@yahoo.co.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Simusika
authors.affiliation: Centre for Infectious Disease Research in Zambia, 34681, Lusaka, Zambia. bateman.allen@gmail.com.
authors.forename: Allen C
authors.initials: AC
authors.lastname: Bateman
authors.affiliation: Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. masoziuk@gmail.com.
authors.forename: Andros
authors.initials: A
authors.lastname: Theo
authors.affiliation: Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia. jaffekwenda@gmail.com.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Kwenda
authors.affiliation: Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia. christine.mfula@gmail.com.
authors.forename: Christine
authors.initials: C
authors.lastname: Mfula
authors.affiliation: Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. edwardchents@yahoo.com.
authors.forename: Edward
authors.initials: E
authors.lastname: Chentulo
authors.affiliation: Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. mmonze@uthlabs.org.zm.
authors.forename: Mwaka
authors.initials: M
authors.lastname: Monze
mesh_terms: D000208:Acute Disease; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D002648:Child; D002675:Child, Preschool; D003430:Cross-Sectional Studies; D005260:Female; D006760:Hospitalization / Q000706:statistics & numerical data; D006801:Humans; D007223:Infant; D008297:Male; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods; D009305:Nasopharynx / Q000821:virology; D015995:Prevalence; D012141:Respiratory Tract Infections / Q000453:epidemiology / Q000382:microbiology* / Q000628:therapy / Q000821:virology*; D012720:Severity of Illness Index; D014780:Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D015024:Zambia / Q000453:epidemiology