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Pathogens in COPD exacerbations identified by comprehensive real-time PCR plus older methods.

Shimizu K, Yoshii Y, Morozumi M, Chiba N, Ubukata K, Uruga H, Hanada S, Saito N, Kadota T, Ito S, Wakui H, Takasaka N, Minagawa S, Kojima J, Hara H, Numata T, Kawaishi M, Saito K, Araya J, Kaneko Y, Nakayama K, Kishi K, Kuwano K - Int J Chron Obstruct Pulmon Dis (2015)

Bottom Line: We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture.Infections were viral in 17 of 50 exacerbations (34%).Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.

View Article: PubMed Central - PubMed

Affiliation: Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan.

ABSTRACT
Respiratory infection is a major cause of exacerbation in chronic obstructive pulmonary disease (COPD). Infectious contributions to exacerbations remain incompletely described. We therefore analyzed respiratory tract samples by comprehensive real-time polymerase chain reaction (PCR) in combination with conventional methods. We evaluated multiple risk factors for prolonged hospitalization to manage COPD exacerbations, including infectious agents. Over 19 months, we prospectively studied 46 patients with 50 COPD exacerbations, collecting nasopharyngeal swab and sputum samples from each. We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture. Infectious etiologies of COPD exacerbations were identified in 44 of 50 exacerbations (88%). Infections were viral in 17 of 50 exacerbations (34%). COPD exacerbations caused by Gram-negative bacilli, including enteric and nonfermenting organisms, were significantly associated with prolonged hospitalization for COPD exacerbations. Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.

No MeSH data available.


Related in: MedlinePlus

Percentages of pathogens underlying COPD exacerbations.Notes: *Viruses were as follows: Parainfluenza virus, four cases (8%); influenza virus, three cases (6%); RSV, three cases (6%). **Combined virus and bacterial infections were as follows: influenza virus + Streptococcus pneumoniae, two cases (4%); influenza virus + Mycoplasma pneumoniae, one case (1%); influenza virus + Haemophilus influenzae + M. pneumoniae, one case (1%); RSV + S. pneumoniae, one case (2%); rhinovirus + S. pneumoniae + H. influenzae, one case (2%). ***Mixed bacterial infections were as follows: S. pneumoniae + H. influenzae, one case (2%); Pseudomonas aeruginosa + Citrobactor freundii, one case (2%); P. aeruginosa + Staphylococcus aureus, one case (2%); Enterobacter cloacae + S. aureus, one case (2%); Stenotrophomonas maltophilia + Acinetobacter baumannii, one case (2%); E. cloacae + H. influenzae, one case (2%); S. aureus + H. influenzae, one case (2%); Klebsiella pneumoniae + H. influenzae, one case (2%); E. cloacae + C. pneumoniae, one case (2%). ****Other bacteria were as follows: Proteus mirabilis, one case (2%); Serratia marcesens, one case (2%).Abbreviations: COPD, chronic obstructive pulmonary disease; RSV, respiratory syncytial virus.
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f2-copd-10-2009: Percentages of pathogens underlying COPD exacerbations.Notes: *Viruses were as follows: Parainfluenza virus, four cases (8%); influenza virus, three cases (6%); RSV, three cases (6%). **Combined virus and bacterial infections were as follows: influenza virus + Streptococcus pneumoniae, two cases (4%); influenza virus + Mycoplasma pneumoniae, one case (1%); influenza virus + Haemophilus influenzae + M. pneumoniae, one case (1%); RSV + S. pneumoniae, one case (2%); rhinovirus + S. pneumoniae + H. influenzae, one case (2%). ***Mixed bacterial infections were as follows: S. pneumoniae + H. influenzae, one case (2%); Pseudomonas aeruginosa + Citrobactor freundii, one case (2%); P. aeruginosa + Staphylococcus aureus, one case (2%); Enterobacter cloacae + S. aureus, one case (2%); Stenotrophomonas maltophilia + Acinetobacter baumannii, one case (2%); E. cloacae + H. influenzae, one case (2%); S. aureus + H. influenzae, one case (2%); Klebsiella pneumoniae + H. influenzae, one case (2%); E. cloacae + C. pneumoniae, one case (2%). ****Other bacteria were as follows: Proteus mirabilis, one case (2%); Serratia marcesens, one case (2%).Abbreviations: COPD, chronic obstructive pulmonary disease; RSV, respiratory syncytial virus.

Mentions: Pathogens identified in respiratory samples by comprehensive real-time PCR and conventional methods are listed in Table 2; percentages of pathogens identified are shown in Figure 2. Conventional methods identified the causative pathogens in only 26 (52%) of the 50 exacerbations, while comprehensive real-time PCR together with conventional methods made the identification in 44 (88%) of the 50 exacerbations. Twenty-eight (56%) were attributed to a single-microbe infection, while 16 (32%) were considered polymicrobial infections. The most commonly identified microorganisms were S. pneumoniae, H. influenzae, and FLU (26%, 18%, and 16% of exacerbations, respectively). Among the 8 of 13 S. pneumoniae-related exacerbations that were culture positive, most strains were covered by pneumococcal polysaccharide vaccine (types 3 (2), 11A (2), 15B (1), 16F (1), 33B (1), and 33F (1)) and were not penicillin resistant. However, most strains detected were macrolide resistant (75%).


Pathogens in COPD exacerbations identified by comprehensive real-time PCR plus older methods.

Shimizu K, Yoshii Y, Morozumi M, Chiba N, Ubukata K, Uruga H, Hanada S, Saito N, Kadota T, Ito S, Wakui H, Takasaka N, Minagawa S, Kojima J, Hara H, Numata T, Kawaishi M, Saito K, Araya J, Kaneko Y, Nakayama K, Kishi K, Kuwano K - Int J Chron Obstruct Pulmon Dis (2015)

Percentages of pathogens underlying COPD exacerbations.Notes: *Viruses were as follows: Parainfluenza virus, four cases (8%); influenza virus, three cases (6%); RSV, three cases (6%). **Combined virus and bacterial infections were as follows: influenza virus + Streptococcus pneumoniae, two cases (4%); influenza virus + Mycoplasma pneumoniae, one case (1%); influenza virus + Haemophilus influenzae + M. pneumoniae, one case (1%); RSV + S. pneumoniae, one case (2%); rhinovirus + S. pneumoniae + H. influenzae, one case (2%). ***Mixed bacterial infections were as follows: S. pneumoniae + H. influenzae, one case (2%); Pseudomonas aeruginosa + Citrobactor freundii, one case (2%); P. aeruginosa + Staphylococcus aureus, one case (2%); Enterobacter cloacae + S. aureus, one case (2%); Stenotrophomonas maltophilia + Acinetobacter baumannii, one case (2%); E. cloacae + H. influenzae, one case (2%); S. aureus + H. influenzae, one case (2%); Klebsiella pneumoniae + H. influenzae, one case (2%); E. cloacae + C. pneumoniae, one case (2%). ****Other bacteria were as follows: Proteus mirabilis, one case (2%); Serratia marcesens, one case (2%).Abbreviations: COPD, chronic obstructive pulmonary disease; RSV, respiratory syncytial virus.
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f2-copd-10-2009: Percentages of pathogens underlying COPD exacerbations.Notes: *Viruses were as follows: Parainfluenza virus, four cases (8%); influenza virus, three cases (6%); RSV, three cases (6%). **Combined virus and bacterial infections were as follows: influenza virus + Streptococcus pneumoniae, two cases (4%); influenza virus + Mycoplasma pneumoniae, one case (1%); influenza virus + Haemophilus influenzae + M. pneumoniae, one case (1%); RSV + S. pneumoniae, one case (2%); rhinovirus + S. pneumoniae + H. influenzae, one case (2%). ***Mixed bacterial infections were as follows: S. pneumoniae + H. influenzae, one case (2%); Pseudomonas aeruginosa + Citrobactor freundii, one case (2%); P. aeruginosa + Staphylococcus aureus, one case (2%); Enterobacter cloacae + S. aureus, one case (2%); Stenotrophomonas maltophilia + Acinetobacter baumannii, one case (2%); E. cloacae + H. influenzae, one case (2%); S. aureus + H. influenzae, one case (2%); Klebsiella pneumoniae + H. influenzae, one case (2%); E. cloacae + C. pneumoniae, one case (2%). ****Other bacteria were as follows: Proteus mirabilis, one case (2%); Serratia marcesens, one case (2%).Abbreviations: COPD, chronic obstructive pulmonary disease; RSV, respiratory syncytial virus.
Mentions: Pathogens identified in respiratory samples by comprehensive real-time PCR and conventional methods are listed in Table 2; percentages of pathogens identified are shown in Figure 2. Conventional methods identified the causative pathogens in only 26 (52%) of the 50 exacerbations, while comprehensive real-time PCR together with conventional methods made the identification in 44 (88%) of the 50 exacerbations. Twenty-eight (56%) were attributed to a single-microbe infection, while 16 (32%) were considered polymicrobial infections. The most commonly identified microorganisms were S. pneumoniae, H. influenzae, and FLU (26%, 18%, and 16% of exacerbations, respectively). Among the 8 of 13 S. pneumoniae-related exacerbations that were culture positive, most strains were covered by pneumococcal polysaccharide vaccine (types 3 (2), 11A (2), 15B (1), 16F (1), 33B (1), and 33F (1)) and were not penicillin resistant. However, most strains detected were macrolide resistant (75%).

Bottom Line: We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture.Infections were viral in 17 of 50 exacerbations (34%).Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.

View Article: PubMed Central - PubMed

Affiliation: Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan.

ABSTRACT
Respiratory infection is a major cause of exacerbation in chronic obstructive pulmonary disease (COPD). Infectious contributions to exacerbations remain incompletely described. We therefore analyzed respiratory tract samples by comprehensive real-time polymerase chain reaction (PCR) in combination with conventional methods. We evaluated multiple risk factors for prolonged hospitalization to manage COPD exacerbations, including infectious agents. Over 19 months, we prospectively studied 46 patients with 50 COPD exacerbations, collecting nasopharyngeal swab and sputum samples from each. We carried out real-time PCR designed to detect six bacterial species and eleven viruses, together with conventional procedures, including sputum culture. Infectious etiologies of COPD exacerbations were identified in 44 of 50 exacerbations (88%). Infections were viral in 17 of 50 exacerbations (34%). COPD exacerbations caused by Gram-negative bacilli, including enteric and nonfermenting organisms, were significantly associated with prolonged hospitalization for COPD exacerbations. Our results support the use of a combination of real-time PCR and conventional methods for determining both infectious etiologies and risk of extended hospitalization.

No MeSH data available.


Related in: MedlinePlus