Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens

Frontiers in Microbiology

Volumn 6, Issue MAY, 2015, Pages

  Shen, Hongwei ^a,b   Zhu, Bingqing ^c   Wang, Shulian ^d   Mo, Haolian ^b   Wang, Ji ^a   Li, Jin ^a   Zhang, Chen ^a   Zeng, Huashu ^b   Guan, Li ^a   Shi, Weixian ^c   Zhang, Yong ^b   Ma, Xuejun ^a  

^a BEIJING HOSPITAL   (China)

^b SHENZHEN CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^c CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^d People's Armed Police Corps General Hospital   (China)

Author keywords

Community acquired pneumonia; Detection; Multiple respiratory pathogens; Resequencing microarray; RPM IVDC1

Indexed keywords

ADOLESCENT; ADULT; AGED; ARTICLE; CHILD; COMMUNITY ACQUIRED PNEUMONIA; DIAGNOSTIC ACCURACY; DNA EXTRACTION; FEMALE; HUMAN; INFANT; MAJOR CLINICAL STUDY; MALE; MICROORGANISM DETECTION; MIDDLE AGED; NASOPHARYNGEAL ASPIRATION; NEWBORN; NONHUMAN; PREDICTIVE VALUE; PRESCHOOL CHILD; PROTEIN EXPRESSION; PROTEIN MICROARRAY; RESPIRATORY TRACT INFECTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCHOOL CHILD; SENSITIVITY AND SPECIFICITY; YOUNG ADULT;

BACTERIA (MICROORGANISMS); HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; KLEBSIELLA PNEUMONIAE; MORAXELLA CATARRHALIS; MYCOPLASMA PNEUMONIAE; NEISSERIA; STAPHYLOCOCCUS; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE;

EID: 84931273673     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00532     Document Type: Article

References (51)

1. Anderson, R., Wang, X., Briere, E. C., Katz, L. S., Cohn, A. C., Clark, T. A., et al. (2012). Haemophilus haemolyticus isolates causing clinical disease. J. Clin. Microbiol. 50, 2462-2465. doi: 10.1128/JCM.06575-11.
2. Barnes, D. J., Naraqi, S., and Igo, J. D. (1987). Haemophilus influenzae pneumonia in Melanesian adults: report of 15 cases. Thorax 42, 889-891.
3. Bartlett, J. G., and Mundy, L. M. (1995). Community-acquired pneumonia. N. Engl. J. Med. 333, 1618-1624.
4. Blaschke, A. J. (2011). Interpreting assays for the detection of Streptococcus pneumoniae. Clin. Infect. Dis. 52(Suppl 4), S331-S337. doi: 10.1093/cid/cir048.
5. Boving, M. K., Pedersen, L. N., and Moller, J. K. (2009). Eight-plex PCR and liquid-array detection of bacterial and viral pathogens in cerebrospinal fluid from patients with suspected meningitis. J. Clin. Microbiol. 47, 908-913. doi: 10.1128/JCM.01966-08.
6. Cole, J. M., Schuetz, A. N., Hill, C. E., and Nolte, F. S. (2009). Development and evaluation of a real-time PCR assay for detection of Klebsiella pneumoniae carbapenemase genes. J. Clin. Microbiol. 47, 322-326. doi: 10.1128/JCM.01550-08.
7. Dorigo-Zetsma, J. W., Zaat, S. A., Wertheim-van Dillen, P. M., Spanjaard, L., Rijntjes, J., van Waveren, G., et al. (1999). Comparison of PCR, culture, and serological tests for diagnosis of Mycoplasma pneumoniae respiratory tract infection in children. J. Clin. Microbiol. 37, 14-17.
8. Feizabadi, M. M., Majnooni, A., Nomanpour, B., Fatolahzadeh, B., Raji, N., Delfani, S., et al. (2010). Direct detection of Pseudomonas aeruginosa from patients with healthcare associated pneumonia by real time PCR. Infect. Genet. Evol. 10, 1247-1251. doi: 10.1016/j.meegid.2010.08.008.
9. Fry, A. M., Lu, X., Chittaganpitch, M., Peret, T., Fischer, J., Dowell, S. F., et al. (2007). Human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in Thailand. J. Infect. Dis. 195, 1038-1045. doi: 10.1086/512163.
10. Greiner, O., Day, P. J., Altwegg, M., and Nadal, D. (2003). Quantitative detection of Moraxella catarrhalis in nasopharyngeal secretions by real-time PCR. J. Clin. Microbiol. 41, 1386-1390. doi: 10.1128/JCM.41.4.1386-1390.2003.
11. Greiner, O., Day, P. J., Bosshard, P. P., Imeri, F., Altwegg, M., and Nadal, D. (2001). Quantitative detection of Streptococcus pneumoniae in nasopharyngeal secretions by real-time PCR. J. Clin. Microbiol. 39, 3129-3134. doi: 10.1128/JCM.39.9.3129-3134.2001.
12. Gruson, D., Hilbert, G., Vargas, F., Valentino, R., Bebear, C., Allery, A., et al. (2000). Rotation and restricted use of antibiotics in a medical intensive care unit: impact on the incidence of ventilator-associated pneumonia caused by antibiotic-resistant gram-negative bacteria. Am. J. Respir. Crit. Care Med. 162, 837-843. doi: 10.1164/ajrccm.162.3.9905050.
13. Hamelin, M. E., Cote, S., Laforge, J., Lampron, N., Bourbeau, J., Weiss, K., et al. (2005). Human metapneumovirus infection in adults with community-acquired pneumonia and exacerbation of chronic obstructive pulmonary disease. Clin. Infect. Dis. 41, 498-502. doi: 10.1086/431981.
14. Johansson, N., Kalin, M., Tiveljung-Lindell, A., Giske, C. G., and Hedlund, J. (2010). Etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods. Clin. Infect. Dis. 50, 202-209. doi: 10.1086/648678.
15. Juven, T., Mertsola, J., Waris, M., Leinonen, M., Meurman, O., Roivainen, M., et al. (2000). Etiology of community-acquired pneumonia in 254 hospitalized children. Pediatr. Infect. Dis. J. 19, 293-298. doi: 10.1097/00006454-200004000-00006.
16. Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41:e1. doi: 10.1093/nar/gks808.
17. Ko, W.-C., Paterson, D. L., Sagnimeni, A. J., Hansen, D. S., Von Gottberg, A., Mohapatra, S., et al. (2002). Community-acquired Klebsiella pneumoniae bacteremia: global differences in clinical patterns. Emerg. Infect. Dis. 8, 160-166. doi: 10.3201/eid0802.010025.
18. Kristiansen, P. A., Diomande, F., Ouedraogo, R., Sanou, I., Sangare, L., Ouedraogo, A. S., et al. (2012). Carriage of Neisseria lactamica in 1-to 29-year-old people in Burkina Faso: epidemiology and molecular characterization. J. Clin. Microbiol. 50, 4020-4027. doi: 10.1128/JCM.01717-12.
19. Kumar, S., Wang, L., Fan, J., Kraft, A., Bose, M. E., Tiwari, S., et al. (2008). Detection of 11 common viral and bacterial pathogens causing community-acquired pneumonia or sepsis in asymptomatic patients by using a multiplex reverse transcription-PCR assay with manual (enzyme hybridization) or automated (electronic microarray) detection. J. Clin. Microbiol. 46, 3063-3072. doi: 10.1128/JCM.00625-08.
20. Leski, T. A., Lin, B., Malanoski, A. P., and Stenger, D. A. (2012). Application of resequencing microarrays in microbial detection and characterization. Future Microbiol. 7, 625-637. doi: 10.2217/fmb.12.30.
21. Leski, T. A., Lin, B., Malanoski, A. P., Wang, Z., Long, N. C., Meador, C. E., et al. (2009). Testing and validation of high density resequencing microarray for broad range biothreat agents detection. PLoS ONE 4:e6569. doi: 10.1371/journal.pone.0006569.
22. Lin, B., Blaney, K. M., Malanoski, A. P., Ligler, A. G., Schnur, J. M., Metzgar, D., et al. (2007). Using a resequencing microarray as a multiple respiratory pathogen detection assay. J. Clin. Microbiol. 45, 443-452. doi: 10.1128/JCM.01870-06.
23. Lin, B., Malanoski, A. P., Wang, Z., Blaney, K. M., Long, N. C., Meador, C. E., et al. (2009). Universal detection and identification of avian influenza virus by use of resequencing microarrays. J. Clin. Microbiol. 47, 988-993. doi: 10.1128/JCM.01346-08.
24. Lin, B., Wang, Z., Vora, G. J., Thornton, J. A., Schnur, J. M., Thach, D. C., et al. (2006). Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res. 16, 527-535. doi: 10.1101/gr.4337206.
25. Liu, Y., Chen, M., Zhao, T., Wang, H., Wang, R., Liu, Q., et al. (2006). [A multicentre study on the pathogenic agents in 665 adult patients with community-acquired pneumonia in cities of China]. Zhonghua Jie He He Hu Xi Za Zhi 29, 3-8.
26. Louie, L., Simor, A. E., Louie, M., McGeer, A., and Low, D. E. (1998). Diagnosis of group A streptococcal necrotizing fasciitis by using PCR to amplify the streptococcal pyrogenic exotoxin B gene. J. Clin. Microbiol. 36, 1769-1771.
27. Luo, R. F., Scahill, M. D., and Banaei, N. (2010). Comparison of single-copy and multicopy real-time PCR targets for detection of Mycobacterium tuberculosis in paraffin-embedded tissue. J. Clin. Microbiol. 48, 2569-2570. doi: 10.1128/JCM.02449-09.
28. Malanoski, A. P., Lin, B., Wang, Z., Schnur, J. M., and Stenger, D. A. (2006). Automated identification of multiple micro-organisms from resequencing DNA microarrays. Nucleic Acids Res. 34, 5300-5311. doi: 10.1093/nar/gkl565.
29. Moes, E., Vijgen, L., Keyaerts, E., Zlateva, K., Li, S., Maes, P., et al. (2005). A novel pancoronavirus RT-PCR assay: freffluent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium. BMC Infect. Dis. 5:6. doi: 10.1186/1471-2334-5-6.
30. Mukundan, D., Ecevit, Z., Patel, M., Marrs, C. F., and Gilsdorf, J. R. (2007). Pharyngeal colonization dynamics of Haemophilus influenzae and Haemophilus haemolyticus in healthy adult carriers. J. Clin. Microbiol. 45, 3207-3217. doi: 10.1128/JCM.00492-07.
31. Mundy, L. M., Auwaerter, P. G., Oldach, D., Warner, M. L., Burton, A., Vance, E., et al. (1995). Community-acquired pneumonia: impact of immune status. Am. J. Respir. Crit. Care Med. 152(4 Pt 1), 1309-1315.
32. Murakami, K., Minamide, W., Wada, K., Nakamura, E., Teraoka, H., and Watanabe, S. (1991). Identification of methicillin-resistant strains of staphylococci by polymerase chain reaction. J. Clin. Microbiol. 29, 2240-2244.
33. Murphy, T. F., Brauer, A. L., Sethi, S., Kilian, M., Cai, X., and Lesse, A. J. (2007). Haemophilus haemolyticus: a human respiratory tract commensal to be distinguished from Haemophilus influenzae. J. Infect. Dis. 195, 81-89. doi: 10.1086/509824.
34. Nascimento-Carvalho, C. M. (2001). Etiology of childhood community acquired pneumonia and its implications for vaccination. Braz. J. Infect. Dis. 5, 87-97. doi: 10.1590/S1413-86702001000200007.
35. Pillai, A., Mitchell, J. L., Hill, S. L., and Stockley, R. A. (2000). A case of Haemophilus parainfluenzae pneumonia. Thorax 55, 623-624. doi: 10.1136/thorax.55.7.623.
36. Rudan, I., Boschi-Pinto, C., Biloglav, Z., Mulholland, K., and Campbell, H. (2008). Epidemiology and etiology of childhood pneumonia. Bull. World Health Organ. 86, 408-416. doi: 10.2471/BLT.07.048769.
37. Rudan, I., O'Brien, K. L., Nair, H., Liu, L., Theodoratou, E., Qazi, S., et al. (2013). Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries. J. Glob. Health 3:010401. doi: 10.7189/jogh.03.010401.
38. Ruimy, R., Dos-Santos, M., Raskine, L., Bert, F., Masson, R., Elbaz, S., et al. (2008). Accuracy and potential usefulness of triplex real-time PCR for improving antibiotic treatment of patients with blood cultures showing clustered gram-positive cocci on direct smears. J. Clin. Microbiol. 46, 2045-2051. doi: 10.1128/JCM.02250-07.
39. Shen, H., Shi, W., Wang, J., Wang, M., Li, J., Zhang, C., et al. (2013). Development of a new resequencing pathogen microarray based assay for detection of broad-spectrum respiratory tract viruses in patients with community-acquired pneumonia. PLoS ONE 8:e75704. doi: 10.1371/journal.pone.0075704.
40. Sistek, V., Boissinot, M., Boudreau, D. K., Huletsky, A., Picard, F. J., and Bergeron, M. G. (2012). Development of a real-time PCR assay for the specific detection and identification of Streptococcus pseudopneumoniae using the recA gene. Clin. Microbiol. Infect. 18, 1089-1096. doi: 10.1111/j.1469-0691.2011.03684.x.
41. Spuesens, E. B., Fraaij, P. L., Visser, E. G., Hoogenboezem, T., Hop, W. C., van Adrichem, L. N., et al. (2013). Carriage of Mycoplasma pneumoniae in the upper respiratory tract of symptomatic and asymptomatic children: an observational study. PLoS Med. 10:e1001444. doi: 10.1371/journal.pmed.1001444.
42. Trouillet, J. L., Chastre, J., Vuagnat, A., Joly-Guillou, M. L., Combaux, D., Dombret, M. C., et al. (1998). Ventilator-associated pneumonia caused by potentially drug-resistant bacteria. Am. J. Respir. Crit. Care Med. 157, 531-539.
43. Tsolia, M. N., Psarras, S., Bossios, A., Audi, H., Paldanius, M., Gourgiotis, D., et al. (2004). Etiology of community-acquired pneumonia in hospitalized school-age children: evidence for high prevalence of viral infections. Clin. Infect. Dis. 39, 681-686. doi: 10.1086/422996.
44. Uyeki, T. M., and Cox, N. J. (2013). Global concerns regarding novel influenza A (H7N9) virus infections. N. Engl. J. Med. 368, 1862-1864. doi: 10.1056/NEJMp1304661.
45. Vaneechoutte, M., Verschraegen, G., Claeys, G., Weise, B., and Van den Abeele, A. M. (1990). Respiratory tract carrier rates of Moraxella (Branhamella) catarrhalis in adults and children and interpretation of the isolation of M. catarrhalis from sputum. J. Clin. Microbiol. 28, 2674-2680.
46. van Ketel, R. J., de Wever, B., and van Alphen, L. (1990). Detection of Haemophilus influenzae in cerebrospinal fluids by polymerase chain reaction DNA amplification. J. Med. Microbiol. 33, 271-276.
47. Welte, T., Torres, A., and Nathwani, D. (2012). Clinical and economic burden of community-acquired pneumonia among adults in Europe. Thorax 67, 71-79. doi: 10.1136/thx.2009.129502.
48. Wessels, E., Schelfaut, J. J., Bernards, A. T., and Claas, E. C. (2012). Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J. Clin. Microbiol. 50, 1171-1177. doi: 10.1128/JCM.06609-11.
49. Winchell, J. M., Thurman, K. A., Mitchell, S. L., Thacker, W. L., and Fields, B. S. (2008). Evaluation of three real-time PCR assays for detection of Mycoplasma pneumoniae in an outbreak investigation. J. Clin. Microbiol. 46, 3116-3118. doi: 10.1128/JCM.00440-08.
50. Woo, P. C., Lau, S. K., Chu, C. M., Chan, K. H., Tsoi, H. W., Huang, Y., et al. (2005). Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J. Virol. 79, 884-895. doi: 10.1128/JVI.79.2.884-895.2005.
51. Young, M. (1924). The influence of weather conditions on the mortality from Bronchitis and Pneumonia in children. J. Hyg. 23, 151-175. doi: 10.1017/S002217240000855X.