Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA, Palmer LB, Napolitano LM, O’Grady NP, Bartlett JG, Carratala J, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the infectious diseases society of America and the American Thoracic Society. Clin Infect Dis. 2016;63:e61–111.
Article
PubMed
PubMed Central
Google Scholar
Metlay JP, Waterer GW, Long AC, Anzueto A, Brozek J, Crothers K, Cooley LA, Dean NC, Fine MJ, Flanders SA, et al. Diagnosis and treatment of adults with community-acquired pneumonia. An official clinical practice guideline of the American Thoracic Society and Infectious Diseases Society of America. Am J Respir Crit Care Med. 2019;200:e45–67.
Article
PubMed
PubMed Central
Google Scholar
American Thoracic S, Infectious Diseases Society of A. Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am J Respir Crit Care Med. 2005;171:388–416.
Article
Google Scholar
Chalmers JD, Rother C, Salih W, Ewig S. Healthcare-associated pneumonia does not accurately identify potentially resistant pathogens: a systematic review and meta-analysis. Clin Infect Dis. 2014;58:330–9.
Article
CAS
PubMed
Google Scholar
Gross AE, Van Schooneveld TC, Olsen KM, Rupp ME, Bui TH, Forsung E, Kalil AC. Epidemiology and predictors of multidrug-resistant community-acquired and health care-associated pneumonia. Antimicrob Agents Chemother. 2014;58:5262–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yap V, Datta D, Metersky ML. Is the present definition of health care-associated pneumonia the best way to define risk of infection with antibiotic-resistant pathogens? Infect Dis Clin N Am. 2013;27:1.
Article
Google Scholar
Jones BE, Jones MM, Huttner B, Stoddard G, Brown KA, Stevens VW, Greene T, Sauer B, Madaras-Kelly K, Rubin M, et al. Trends in antibiotic use and nosocomial pathogens in hospitalized veterans with pneumonia at 128 medical centers, 2006–2010. Clin Infect Dis. 2015;61:1403–10.
Article
PubMed
PubMed Central
Google Scholar
Park SC, Kang YA, Park BH, Kim EY, Park MS, Kim YS, Kim SK, Chang J, Jung JY. Poor prediction of potentially drug-resistant pathogens using current criteria of health care-associated pneumonia. Respir Med. 2012;106:1311–9.
Article
PubMed
Google Scholar
Schreiber MP, Chan CM, Shorr AF. Resistant pathogens in nonnosocomial pneumonia and respiratory failure: is it time to refine the definition of health-care-associated pneumonia? Chest. 2010;137:1283–8.
Article
PubMed
Google Scholar
El-Solh AA, Sikka P, Ramadan F, Davies J. Etiology of severe pneumonia in the very elderly. Am J Respir Crit Care Med. 2001;163:645–51.
Article
CAS
PubMed
Google Scholar
El Solh AA, Pietrantoni C, Bhat A, Bhora M, Berbary E. Indicators of potentially drug-resistant bacteria in severe nursing home-acquired pneumonia. Clin Infect Dis. 2004;39:474–80.
Article
PubMed
Google Scholar
Shorr AF, Zilberberg MD, Micek ST, Kollef MH. Prediction of infection due to antibiotic-resistant bacteria by select risk factors for health care-associated pneumonia. Arch Intern Med. 2008;168:2205–10.
Article
PubMed
Google Scholar
Xia LP, Bian LY, Xu M, Liu Y, Tang AL, Ye WQ. 16S rRNA gene sequencing is a non-culture method of defining the specific bacterial etiology of ventilator-associated pneumonia. Int J Clin Exp Med. 2015;8:18560–70.
CAS
PubMed
PubMed Central
Google Scholar
Brito V, Niederman MS. Healthcare-associated pneumonia is a heterogeneous disease, and all patients do not need the same broad-spectrum antibiotic therapy as complex nosocomial pneumonia. Curr Opin Infect Dis. 2009;22:316–25.
Article
PubMed
Google Scholar
Umeki K, Tokimatsu I, Yasuda C, Iwata A, Yoshioka D, Ishii H, Shirai R, Kishi K, Hiramatsu K, Matsumoto B, Kadota J. Clinical features of healthcare-associated pneumonia (HCAP) in a Japanese community hospital: comparisons among nursing home-acquired pneumonia (NHAP), HCAP other than NHAP, and community-acquired pneumonia. Respirology. 2011;16:856–61.
Article
PubMed
Google Scholar
Charlson ME, Pompei P, Ales KL, MacKenzie CR. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J Chronic Dis. 1987;40:373–83.
Article
CAS
PubMed
Google Scholar
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnry J. 2011;17:10–2.
Article
Google Scholar
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.
Article
CAS
PubMed
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Article
CAS
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Plantinga AM, Chen J, Jenq RR, Wu MC. pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis. Bioinformatics. 2019;35:3567–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim KJ, Park J, Park SC, Won S. Phylogenetic tree-based microbiome association test. Bioinformatics. 2020;36:1000–6.
PubMed
Google Scholar
Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, Zengler K, Knight R. Establishing microbial composition measurement standards with reference frames. Nat Commun. 2019;10:2719.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kollef MH, Shorr A, Tabak YP, Gupta V, Liu LZ, Johannes RS. Epidemiology and outcomes of health-care-associated pneumonia: results from a large US database of culture-positive pneumonia. Chest. 2005;128:3854–62.
Article
PubMed
Google Scholar
Micek ST, Kollef KE, Reichley RM, Roubinian N, Kollef MH. Health care-associated pneumonia and community-acquired pneumonia: a single-center experience. Antimicrob Agents Chemother. 2007;51:3568–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shindo Y, Sato S, Maruyama E, Ohashi T, Ogawa M, Hashimoto N, Imaizumi K, Sato T, Hasegawa Y. Health-care-associated pneumonia among hospitalized patients in a Japanese community hospital. Chest. 2009;135:633–40.
Article
PubMed
Google Scholar
Chalmers JD, Taylor JK, Singanayagam A, Fleming GB, Akram AR, Mandal P, Choudhury G, Hill AT. Epidemiology, antibiotic therapy, and clinical outcomes in health care-associated pneumonia: a UK cohort study. Clin Infect Dis. 2011;53:107–13.
Article
PubMed
Google Scholar
Park HK, Song JU, Um SW, Koh WJ, Suh GY, Chung MP, Kim H, Kwon OJ, Jeon K. Clinical characteristics of health care-associated pneumonia in a Korean teaching hospital. Respir Med. 2010;104:1729–35.
Article
PubMed
Google Scholar
Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome. 2016;4:7.
Article
PubMed
PubMed Central
Google Scholar
Lipsky BA, Goldberger AC, Tompkins LS, Plorde JJ. Infections caused by nondiphtheria corynebacteria. Rev Infect Dis. 1982;4:1220–35.
Article
CAS
PubMed
Google Scholar
Clariot S, Constant O, Lepeule R, Fihman V, Razazi K, Cook F, Attias A, Merle JC, Hemery F, Levesque E, et al. Clinical relevance and impact of Corynebacterium isolation in lower respiratory tract of critically ill patients requiring mechanical ventilation. Infection. 2020;48:413–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yatera K, Mukae H. Corynebacterium species as one of the major causative pathogens of bacterial pneumonia. Respir Investig. 2020;58:131–3.
Article
PubMed
Google Scholar
Yang K, Kruse RL, Lin WV, Musher DM. Corynebacteria as a cause of pulmonary infection: a case series and literature review. Pneumonia (Nathan). 2018;10:10.
Article
Google Scholar
Yasuda I, Matsuyama H, Ishifuji T, Yamashita Y, Takaki M, Morimoto K, Sekino M, Yanagihara K, Fujii T, Iwaki M, et al. Severe pneumonia caused by toxigenic Corynebacterium ulcerans infection, Japan. Emerg Infect Dis. 2018;24:588–91.
Article
PubMed
PubMed Central
Google Scholar
Yatera K, Noguchi S, Yamasaki K, Kawanami T, Fukuda K, Naito K, Akata K, Kido T, Ishimoto H, Sakamoto N, et al. Determining the possible etiology of hospital-acquired pneumonia using a clone library analysis in Japan. Tohoku J Exp Med. 2017;242:9–17.
Article
PubMed
Google Scholar
de Steenhuijsen Piters WA, Huijskens EG, Wyllie AL, Biesbroek G, van den Bergh MR, Veenhoven RH, Wang X, Trzcinski K, Bonten MJ, Rossen JW, et al. Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients. ISME J. 2016;10:97–108.
Article
PubMed
CAS
Google Scholar
Zakharkina T, Martin-Loeches I, Matamoros S, Povoa P, Torres A, Kastelijn JB, Hofstra JJ, de Wever B, de Jong M, Schultz MJ, et al. The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia. Thorax. 2017;72:803–10.
Article
PubMed
Google Scholar
Bousbia S, Papazian L, Saux P, Forel JM, Auffray JP, Martin C, Raoult D, La Scola B. Repertoire of intensive care unit pneumonia microbiota. PLoS ONE. 2012;7:e32486.
Article
CAS
PubMed
PubMed Central
Google Scholar
Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol. 2016;1:16031.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kitsios GD, Fitch A, Manatakis DV, Rapport SF, Li K, Qin S, Huwe J, Zhang Y, Doi Y, Evankovich J, et al. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients. Front Microbiol. 2018;9:1413.
Article
PubMed
PubMed Central
Google Scholar
Carratala J, Mykietiuk A, Fernandez-Sabe N, Suarez C, Dorca J, Verdaguer R, Manresa F, Gudiol F. Health care-associated pneumonia requiring hospital admission: epidemiology, antibiotic therapy, and clinical outcomes. Arch Intern Med. 2007;167:1393–9.
Article
PubMed
Google Scholar
Dickson RP, Schultz MJ, van der Poll T, Schouten LR, Falkowski NR, Luth JE, Sjoding MW, Brown CA, Chanderraj R, Huffnagle GB, et al. Lung microbiota predict clinical outcomes in critically ill patients. Am J Respir Crit Care Med. 2020;201:555–63.
Article
CAS
PubMed
PubMed Central
Google Scholar