{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T06:44:15Z","timestamp":1772693055387,"version":"3.50.1"},"reference-count":37,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T00:00:00Z","timestamp":1558051200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Helsinki university hospital","award":["TYH 2017244"],"award-info":[{"award-number":["TYH 2017244"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["1285975"],"award-info":[{"award-number":["1285975"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Community-acquired pneumonia (CAP) is a common disease responsible for significant morbidity and mortality. However, the definite etiology of CAP often remains unresolved, suggesting that unknown agents of pneumonia remain to be identified. The recently discovered members of the order Chlamydiales, Chlamydia-related bacteria (CRB), are considered as possible emerging agents of CAP. Parachlamydia acanthamoebae is the most studied candidate. It survives and replicates inside free-living amoeba, which it might potentially use as a vehicle to infect animals and humans. A Mycoplasma pneumoniae outbreak was observed in Kymenlaakso region in Southeastern Finland during August 2017\u2013January 2018. We determined the occurrence of Chlamydiales bacteria and their natural host, free-living amoeba in respiratory specimens collected during this outbreak with molecular methods. Altogether, 22\/278 (7.9%) of the samples contained Chlamydiales DNA. By sequence analysis, majority of the CRBs detected were members of the Parachlamydiaceae family. Amoebal DNA was not detected within the sample material. Our study further proposes that Parachlamydiaceae could be a potential agent causing atypical CAP in children and adolescents.<\/jats:p>","DOI":"10.3390\/microorganisms7050141","type":"journal-article","created":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T11:06:46Z","timestamp":1558091206000},"page":"141","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Parachlamydia acanthamoebae Detected during a Pneumonia Outbreak in Southeastern Finland, in 2017\u20132018"],"prefix":"10.3390","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4428-7536","authenticated-orcid":false,"given":"Kati","family":"Hokynar","sequence":"first","affiliation":[{"name":"Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2911-3212","authenticated-orcid":false,"given":"Satu","family":"Kurkela","sequence":"additional","affiliation":[{"name":"Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2157-4567","authenticated-orcid":false,"given":"Tea","family":"Nieminen","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital, University of Helsinki, FI-00029 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harri","family":"Saxen","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital, University of Helsinki, FI-00029 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3665-5802","authenticated-orcid":false,"given":"Eero J.","family":"Vesterinen","sequence":"additional","affiliation":[{"name":"Department of Ecology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden"},{"name":"Biodiversity Unit, University of Turku, FI-20014 Turku, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Mannonen","sequence":"additional","affiliation":[{"name":"Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Risto","family":"Pietik\u00e4inen","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Kymenlaakso Central Hospital, FI-48210 Kotka, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7413-6793","authenticated-orcid":false,"given":"Mirja","family":"Puolakkainen","sequence":"additional","affiliation":[{"name":"Department of Virology, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,5,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3389\/fmicb.2018.00079","article-title":"Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle","volume":"9","author":"Pillonel","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1080\/10408410601023102","article-title":"Diversity of the parachlamydiae in the environment","volume":"32","author":"Corsaro","year":"2006","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_3","first-page":"1","article-title":"Twenty years of research into Chlamydia-like organisms: A revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae","volume":"73","author":"Vaughan","year":"2015","journal-title":"Pathog. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.micinf.2015.08.007","article-title":"Severe pneumonia due to Parachlamydia acanthamoebae following intranasal inoculation: A mice model","volume":"17","author":"Pilloux","year":"2015","journal-title":"Microbes Infect."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1111\/j.1749-6632.2003.tb07381.x","article-title":"Serological hint suggesting that Parachlamydiaceae are agents of pneumonia in polytraumatized intensive care patients","volume":"990","author":"Greub","year":"2003","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.micinf.2015.09.019","article-title":"Waddlia chondrophila and Chlamydia trachomatis antibodies in screening infertile women for tubal pathology","volume":"17","author":"Verweij","year":"2015","journal-title":"Microbes Infect."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1097\/QCO.0b013e3282f3e6a5","article-title":"Emerging role of Chlamydia and Chlamydia-like organisms in adverse pregnancy outcomes","volume":"21","author":"Baud","year":"2008","journal-title":"Curr. Opin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1111\/j.1574-6968.2008.01099.x","article-title":"Chlamydia-like bacteria in respiratory samples of community-acquired pneumonia patients","volume":"281","author":"Haider","year":"2008","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1007\/s10096-009-0804-7","article-title":"Development of a real-time PCR for the specific detection of Waddlia chondrophila in clinical samples","volume":"28","author":"Goy","year":"2009","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1080\/00365540701558680","article-title":"Simkania negevensis may be a true cause of community acquired pneumonia in children","volume":"40","author":"Paldanius","year":"2008","journal-title":"Scand. J. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1016\/j.micinf.2011.04.012","article-title":"Chlamydia-related bacteria in respiratory samples in Finland","volume":"13","author":"Niemi","year":"2011","journal-title":"Microbes Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1093\/cid\/cir420","article-title":"Parachlamydia and Rhabdochlamydia: Emerging agents of community-acquired respiratory infections in children","volume":"53","author":"Lamoth","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kurkela, S., Puolakkainen, M., Hokynar, K., Nieminen, T., Saxen, H., Mannonen, L., and Pietik\u00e4inen, R. (2019). Mycoplasma pneumoniae outbreak, Southeastern Finland, 2017\u20132018: Molecular epidemiology and laboratory diagnostic lessons. Eur. J. Clin. Microbiol. Infect. Dis., under review.","DOI":"10.1007\/s10096-019-03619-7"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1186\/s40064-015-1457-x","article-title":"Development of a multiplex real-time PCR assay for detection of Mycoplasma pneumoniae, Chlamydia pneumoniae and mutations associated with macrolide resistance in Mycoplasma pneumoniae from respiratory clinical specimens","volume":"4","author":"Nummi","year":"2015","journal-title":"Springerplus"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.micpath.2003.09.001","article-title":"IFN-gamma induced persistent Chlamydia pneumoniae infection in HL and Mono Mac 6 cells: characterization by real-time quantitative PCR and culture","volume":"36","author":"Mannonen","year":"2004","journal-title":"Microb. Pathog."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1128\/JCM.00114-11","article-title":"Development of a new chlamydiales-specific real-time PCR and its application to respiratory clinical samples","volume":"49","author":"Lienard","year":"2011","journal-title":"J. Clin. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Hokynar, K., Sormunen, J.J., Vesterinen, E.J., Partio, E.K., Lilley, T., Timonen, V., Panelius, J., Ranki, A., and Puolakkainen, M. (2016). Chlamydia-Like Organisms (CLOs) in Finnish Ixodes ricinus Ticks and Human Skin. Microorganisms, 4.","DOI":"10.3390\/microorganisms4030028"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1099\/00207713-49-2-415","article-title":"Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms","volume":"49","author":"Everett","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3589","DOI":"10.1128\/JCM.00875-06","article-title":"Multiplex real-time PCR assay for simultaneous detection of Acanthamoeba spp., Balamuthia mandrillaris, and Naegleria fowleri","volume":"44","author":"Qvarnstrom","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3365","DOI":"10.1007\/s00436-016-5097-z","article-title":"Free-living amoebae and their associated bacteria in Austrian cooling towers: A 1-year routine screening","volume":"115","author":"Scheikl","year":"2016","journal-title":"Parasitol. Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5750","DOI":"10.1128\/AEM.00085-06","article-title":"Quantitative detection of the free-living amoeba Hartmannella vermiformis in surface water by using real-time PCR","volume":"72","author":"Kuiper","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1099\/ijs.0.000090","article-title":"Taxogenomics of the order Chlamydiales","volume":"65","author":"Pillonel","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/AEM.02951-16","article-title":"Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats","volume":"83","author":"Hokynar","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Edgar, R.C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform., 5.","DOI":"10.1186\/1471-2105-5-113"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","article-title":"MRBAYES: Bayesian inference of phylogenetic trees","volume":"17","author":"Huelsenbeck","year":"2001","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.cmi.2018.10.015","article-title":"New evidence for domesticated animals as reservoirs of Chlamydia-associated community-acquired pneumonia","volume":"25","author":"Polkinghorne","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1056\/NEJMc1702983","article-title":"Zoonotic Chlamydia caviae Presenting as Community-Acquired Pneumonia","volume":"377","author":"Ramakers","year":"2017","journal-title":"N. Engl. J. Med."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1089\/vbz.2018.2304","article-title":"Chlamydia caviae Causing Community-Acquired Pneumonia: An Emerging Zoonosis","volume":"18","author":"Bilsen","year":"2018","journal-title":"Vector. Borne. Zoonotic. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.3201\/eid0706.010619","article-title":"Legionella-like and other amoebal pathogens as agents of community-acquired pneumonia","volume":"7","author":"Marrie","year":"2001","journal-title":"Emerg. Infect. Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"755","DOI":"10.3201\/eid0906.020613","article-title":"Parachlamydiaceae as rare agents of pneumonia","volume":"9","author":"Greub","year":"2003","journal-title":"Emerg. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5979","DOI":"10.1128\/IAI.71.10.5979-5985.2003","article-title":"Parachlamydia acanthamoebae enters and multiplies within human macrophages and induces their apoptosis [corrected]","volume":"71","author":"Greub","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1016\/j.micinf.2005.12.011","article-title":"Parachlamydia acanthamoebae enters and multiplies within pneumocytes and lung fibroblasts","volume":"8","author":"Casson","year":"2006","journal-title":"Microbes Infect."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1128\/JCM.02302-07","article-title":"New diagnostic real-time PCR for specific detection of Parachlamydia acanthamoebae DNA in clinical samples","volume":"46","author":"Casson","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.nmni.2015.10.002","article-title":"Lack of Chlamydia-related bacteria among patients with community-acquired pneumonia","volume":"8","author":"Garin","year":"2015","journal-title":"New Microbes New Infect."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1894","DOI":"10.1001\/jamainternmed.2014.4887","article-title":"beta-Lactam monotherapy vs beta-lactam-macrolide combination treatment in moderately severe community-acquired pneumonia: A randomized noninferiority trial","volume":"174","author":"Garin","year":"2014","journal-title":"JAMA Intern. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1016\/j.micinf.2015.08.002","article-title":"Antibiotic susceptibility of Neochlamydia hartmanellae and Parachlamydia acanthamoebae in amoebae","volume":"17","author":"Vouga","year":"2015","journal-title":"Microbes Infect."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/5\/141\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:53:06Z","timestamp":1760187186000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/5\/141"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,17]]},"references-count":37,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5]]}},"alternative-id":["microorganisms7050141"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms7050141","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,17]]}}}