Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens | CDC EID

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Volume 16, Number 12–December 2010
Dispatch
Co-detection of Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens

Kassi Koon, Catherine M. Sanders, Comments to Author Jessica Green, Leslie Malone, Holly White, Delineliz Zayas, Rebecca Miller, Stanley Lu, and Jian Han

Author affiliations: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA (K. Koon, C.M. Sanders, J. Han); and Diatherix Laboratories, Huntsville (J. Green, L. Malone, H. White, D. Zayas, R. Miller, S. Lu)

Suggested citation for this article

Abstract
From May through October 2009, a total of 10,624 clinical samples from 23 US states were screened for multiple respiratory pathogen gene targets. Of 3,110 (29.3%) samples positive for pandemic (H1N1) 2009 virus, 28% contained >1 other pathogen, most commonly Staphylococcus aureus (14.7%), Streptococcus pneumoniae (10.2%), and Haemophilus influenzae (3.5%).

For previous and current influenza A pandemics, postmortem studies have established a strong link between secondary bacterial infections and increased deaths (1,2). Numerous respiratory pathogens can be detected from a single sample by using a multiplex molecular method called target-enriched multiplex PCR (3–6). During the 2006 influenza season, this method was used at Vancouver Children and Women's Hospital to study 1,742 patients with acute respiratory infections; >2 pathogens were detected for ≈27% of patients studied (7). We used this method to learn more about infections occurring concurrently with pandemic (H1N1) 2009.

The Study

From May through October 2009, a total of 10,624 clinical samples from 23 states throughout the United States were submitted to Diatherix Laboratories (www.diatherix.com; Huntsville, AL, USA) and screened for multiple respiratory pathogen gene targets. Diatherix, a reference laboratory certified by the Clinical Laboratory Improvement Amendments, provides molecular differential detection services based on target-enriched multiplex PCR technology. The respiratory infections panel detects bacterial and viral pathogens associated with respiratory infections and includes targets for the following: adenovirus (types 3, 4, 7, 21), coxsackievirus, echovirus, human metapneumovirus (types A and B), influenza virus (types A and B), parainfluenza virus (types 1–4), respiratory syncytial virus (types A and B), rhinovirus, Acinetobacter baumannii, Chlamydophila pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Mycoplasma pneumoniae, Neisseria meningitidis, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes (group A). Additionally, targets specific for pandemic (H1N1) 2009 virus were developed, validated, and approved by the US Food and Drug Administration under Emergency Use Authorization provisions for patient testing.

Of the respiratory specimens shipped by overnight mail from the 23 states, >95% were nasopharyngeal swabs in transfer buffer. High-throughput nucleic acid extraction was performed automatically by using KingFisher 96 instrumentation (Thermo Scientific, Hudson, NH, USA) and MagnetX chemistry (Scigenix, Marietta, GA, USA) according to manufacturers' specifications. Multiplex PCR amplification and Luminex (Austin, TX, USA) liquid suspension detection methods were based on internally validated protocols. Reactions were amplified by using ABI 9700 thermocyclers (Applied BioSystems, Singapore), and the resulting PCR products were detected by using the LiquiChip 200 Workstation (Luminex) according to previously described protocols (3,6).

Of the 10,624 samples studied, 4,690 (44.1%) were negative for all pathogens detectable with the assay. Among the 7,514 (70.73%) samples negative for pandemic (H1N1) 2009 virus, 3 bacterial pathogens predominated: S. aureus (875; 11.65%), S. pneumoniae (573; 7.63%), and H. influenzae (411; 5.47%) (Table 1). The most common viral pathogens in the pandemic (H1N1) 2009–negative samples were from the family Picornaviridae: coxsackie/echovirus (650; 8.65%), and rhinovirus (449; 5.98%) (Table 2).

full-text:
Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens | CDC EID

Suggested Citation for this Article

Koon K, Sanders CM, Green J, Malone L, White H, Zayas D, et al. Co-detection of pandemic (H1N1) 2009 virus and other respiratory pathogens. Emerg Infect Dis [serial on the Internet]. 2010 Dec [date cited].
http://www.cdc.gov/EID/content/16/12/1976.htm

DOI: 10.3201/eid1612.091697

Comments to the Authors

Please use the form below to submit correspondence to the authors or contact them at the following address:

Catherine M. Sanders, HudsonAlpha Institute of Biotechnology–Han Lab, 601 Genome Way, Huntsville, AL 35806, USA; email: csanders@hudsonalpha.com