Skip to main content
PMC home page
Elsevier - PMC COVID-19 Collection logoLink to Elsevier - PMC COVID-19 Collection
. 2019 Jul 4;32(6):438–445. doi: 10.3967/bes2019.058

Viral and Bacterial Etiology of Acute Febrile Respiratory Syndrome among Patients in Qinghai, China

Gao Shan LIU a, Hong LI b, Sheng Cang ZHAO b, Rou Jian LU a, Pei Hua NIU a,#, Wen Jie TAN a,#
PMCID: PMC7135780  PMID: 31262389

Abstract

Objective

This study was conducted to investigate the viral and bacterial etiology and epidemiology of patients with acute febrile respiratory syndrome (AFRS) in Qinghai using a commercial routine multiplex-ligation-nucleic acid amplification test (NAT)-based assay.

Methods

A total of 445 nasopharyngeal swabs specimens from patients with AFRS were analyzed using the RespiFinderSmart22kit (PathoFinder BV, Netherlands) and the LightCycler 480 real-time PCR system.

Results

Among the 225 (225/445, 51%) positive specimens, 329 positive pathogens were detected, including 298 (90.58%) viruses and 31 (9%) bacteria. The most commonly detected pathogens were influenza virus (IFV; 37.39%; 123/329), adenovirus (AdV; 17.02%; 56/329), human coronaviruses (HCoVs; 10.94%; 36/329), rhinovirus/enterovirus (RV/EV; 10.03%; 33/329), parainfluenza viruses (PIVs; 8.51%; 28/329), and Mycoplasma pneumoniae (M. pneu; 8.51%; 28/329), respectively. Among the co-infected cases (17.53%; 78/445), IFV/AdV and IFV/M. pneu were the most common co-infections. Most of the respiratory viruses were detected in summer and fall.

Conclusion

In our study, IFV-A was the most common respiratory pathogen among 22 detected pathogens, followed by AdV, HCoV, RV/EV, PIV, and M. pneu. Bacteria appeared less frequently than viruses, and co-infection was the most common phenomenon among viral pathogens. Pathogens were distributed among different age groups and respiratory viruses were generally active in July, September, and November. Enhanced surveillance and early detection can be useful in the diagnosis, treatment, and prevention of AFRS, as well as for guiding the development of appropriate public health strategies.

Key words: Acute febrile respiratory syndrome, Viral and bacterial etiology, Prevalence, Seasonal distribution

Footnotes

This work was supported by State Major Project of Infections Disease Control and Prevention of China [2017ZX10104001-002-003 and 2014ZX10004001-002]; and the National Key Research and Development Program of China [2016YFD0500301 and 2016YFC1200200].

Biographical note of the first author: LIU Gao Shan, male, born in 1990, MD candidate, majoring in public health.

Contributor Information

Pei Hua NIU, Email: peihua.niu@163.com.

Wen Jie TAN, Email: tanwj28@163.com.

REFERENCES

  • 1.Goktas S, Sirin MC. Prevalence and Seasonal Distribution of Respiratory Viruses During the 2014 - 2015 Season in Istanbul. Jundishapur J Microbiol. 2016;9 doi: 10.5812/jjm.39132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.WHO the top 10 global causes of deaths. 2016. http://www.who.int/mediacentre/factsheets/fs310/en/ [2018-5-24].
  • 3.Njouom R, Yekwa EL, Cappy P. Viral etiology of influenza-like illnesses in Cameroon, January-December 2009. J Infect Dis. 2012;206:S29–S35. doi: 10.1093/infdis/jis573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Paba P, Farchi F, Mortati E. Screening of respiratory pathogens by Respiratory Multi Well System (MWS) r-gene assay in hospitalized patients. New Microbiol. 2014;37:231–236. [PubMed] [Google Scholar]
  • 5.Dabisch-Ruthe M, Vollmer T, Adams O. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. 2012;12:163. doi: 10.1186/1471-2334-12-163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Bruijnesteijn van Coppenraet LE, Swanink CM, van Zwet AA. Comparison of two commercial molecular assays for simultaneous detection of respiratory viruses in clinical samples using two automatic electrophoresis detection systems. J Virol Methods. 2010;169:188–192. doi: 10.1016/j.jviromet.2010.07.032. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Paranhos-Baccala G, Komurian-Pradel F, Richard N. Mixed respiratory virus infections. J Clin Virol. 2008;43:407–410. doi: 10.1016/j.jcv.2008.08.010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Brittain-Long R, Westin J, Olofsson S. Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate. J Clin Virol. 2010;47:263–267. doi: 10.1016/j.jcv.2009.12.010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Yu J, Xie Z, Zhang T. Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012-2015. BMC Infect Dis. 2018;18:72. doi: 10.1186/s12879-018-2982-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Liu GS, Niu PH, Zhao SC. Detection of six common human paramyxoviruses in patients with acute febrile respiratory symptoms using a novel multiplex real-time RT-PCR assay. J Med Virol. 2019;91:564–569. doi: 10.1002/jmv.25350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Niu P, Shen J, Zhu N. Two-tube multiplex real-time reverse transcription PCR to detect six human coronaviruses. Virol Sin. 2016;31:85–88. doi: 10.1007/s12250-015-3653-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Zaas AK, Garner BH, Tsalik EL. The current epidemiology and clinical decisions surrounding acute respiratory infections. Trends Mol Med. 2014;20:579–588. doi: 10.1016/j.molmed.2014.08.001. [DOI] [PubMed] [Google Scholar]
  • 13.Pillet S, Lardeux M, Dina J. Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections. PLoS One. 2013;8 doi: 10.1371/journal.pone.0072174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Quick J, Cumley N, Wearn CM. Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing. BMJ Open. 2014;4 doi: 10.1136/bmjopen-2014-006278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Yoshii Y, Shimizu K, Morozumi M. Detection of pathogens by real-time PCR in adult patients with acute exacerbation of bronchial asthma. BMC Pulm Med. 2017;17:150. doi: 10.1186/s12890-017-0494-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Chen H, Weng H, Lin M. The Clinical Significance of FilmArray Respiratory Panel in Diagnosing Community-Acquired Pneumonia. Biomed Res Int. 2017;2017 doi: 10.1155/2017/7320859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Parrott G, Kinjo T, Nabeya D. Evaluation of Anyplex II RV16 and RB5 real-time RT-PCR compared to Seeplex (R) RV15 OneStep ACE and PneumoBacter ACE for the simultaneous detection of upper respiratory pathogens. J Infect Chemother. 2017;23:859–861. doi: 10.1016/j.jiac.2017.07.013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Richter J, Panayiotou C, Tryfonos C. Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus. PLoS One. 2016;11 doi: 10.1371/journal.pone.0147041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Do AH, van Doorn HR, Nghiem MN. Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. PLoS One. 2011;6 doi: 10.1371/journal.pone.0018176. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Brittain-Long R, Nord S, Olofsson S. Multiplex real-time PCR for detection of respiratory tract infections. J Clin Virol. 2008;41:53–56. doi: 10.1016/j.jcv.2007.10.029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Javadi A, Adibi P, Ataei B. Surveillance of acute respiratory infections among outpatients: A pilot study in Isfahan city. J Res Med Sci. 2015;20:115–121. [PMC free article] [PubMed] [Google Scholar]
  • 22.Cicek C, Arslan A, Karakus HS. Prevalence and seasonal distribution of respiratory viruses in patients with acute respiratory tract infections, 2002-2014. Mikrobiyol Bul. 2015;49:188–200. doi: 10.5578/mb.9024. [DOI] [PubMed] [Google Scholar]
  • 23.Yuksel H, Yilmaz O, Akcali S. Common viral etiologies of community acquired lower respiratory tract infections in young children and their relationship with long term complications. Mikrobiyol Bul. 2008;42:429–435. [PubMed] [Google Scholar]
  • 24.Liao X, Hu Z, Liu W. New Epidemiological and Clinical Signatures of 18 Pathogens from Respiratory Tract Infections Based on a 5-Year Study. PLoS One. 2015;10 doi: 10.1371/journal.pone.0138684. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Li Y, Zhou W, Zhao Y. Molecular typing and epidemiology profiles of human adenovirus infection among paediatric patients with severe acute respiratory infection in China. PLoS One. 2015;10 doi: 10.1371/journal.pone.0123234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Seo YB, Cheong HJ, Song JY. Epidemiologic differences of four major respiratory viruses between children, adolescents, and adults in Korea. J Infect Chemother. 2014;20:672–677. doi: 10.1016/j.jiac.2013.07.009. [DOI] [PubMed] [Google Scholar]
  • 27.Fouchier RA, Hartwig NG, Bestebroer TM. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA. 2004;101:6212–6216. doi: 10.1073/pnas.0400762101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Liu WK, Liu Q, Chen DH. Epidemiology of acute respiratory infections in children in Guangzhou: a three-year study. PLoS One. 2014;9 doi: 10.1371/journal.pone.0096674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Jin Y, Zhang RF, Xie ZP. Newly identified respiratory viruses associated with acute lower respiratory tract infections in children in Lanzou, China, from 2006 to 2009. Clin Microbiol Infect. 2012;18:74–80. doi: 10.1111/j.1469-0691.2011.03541.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Pan Y, Zhang Y, Shi W. Human parainfluenza virus infection in severe acute respiratory infection cases in Beijing, 2014-2016: A molecular epidemiological study. Influenza Other Respir Viruses. 2017;11:564–568. doi: 10.1111/irv.12514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Malasao R, Okamoto M, Chaimongkol N. Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013. PLoS One. 2015;10 doi: 10.1371/journal.pone.0142192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Goka EA, Vallely PJ, Mutton KJ. Single and multiple respiratory virus infections and severity of respiratory disease: a systematic review. Paediatr Respir Rev. 2014;15:363–370. doi: 10.1016/j.prrv.2013.11.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Zhang D, He Z, Xu L. Epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern China. Int J Infect Dis. 2014;25:159–164. doi: 10.1016/j.ijid.2014.02.019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Jansen RR, Wieringa J, Koekkoek SM. Frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values. J Clin Microbiol. 2011;49:2631–2636. doi: 10.1128/JCM.02094-10. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biomedical and Environmental Sciences are provided here courtesy of Elsevier

RESOURCES