title: Molecular epidemiologic analysis of a Pneumocystis pneumonia outbreak among renal transplant patients.
abstract: Between 18 November and 3 December 2011, five renal transplant patients at the Department of Nephrology, Toho University Omori Medical Centre, Tokyo, were diagnosed with Pneumocystis pneumonia (PCP). We used molecular epidemiologic methods to determine whether the patients were infected with the same strain of Pneumocystis jirovecii. DNA extracted from the residual bronchoalveolar lavage fluid from the five outbreak cases and from another 20 cases of PCP between 2007 and 2014 were used for multilocus sequence typing to compare the genetic similarity of the P. jirovecii. DNA base sequencing by the Sanger method showed some regions where two bases overlapped and could not be defined. A next-generation sequencer was used to analyse the types and ratios of these overlapping bases. DNA base sequences of P. jirovecii in the bronchoalveolar lavage fluid from four of the five PCP patients in the 2011 outbreak and from another two renal transplant patients who developed PCP in 2013 were highly homologous. The Sanger method revealed 14 genomic regions where two differing DNA bases overlapped and could not be identified. Analyses of the overlapping bases by a next-generation sequencer revealed that the differing types of base were present in almost identical ratios. There is a strong possibility that the PCP outbreak at the Toho University Omori Medical Centre was caused by the same strain of P. jirovecii. Two different types of base present in some regions may be due to P. jirovecii's being a diploid species.
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
authors.forename: N
authors.initials: N
authors.lastname: Urabe
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan. Electronic address: yishii@med.toho-u.ac.jp.
authors.forename: Y
authors.initials: Y
authors.lastname: Ishii
authors.affiliation: Department of Nephrology Medicine, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Hyodo
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Aoki
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Yoshizawa
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Saga
authors.affiliation: Laboratory of Molecular Cell Biology, School of Pharmacy, Nihon University, Funabashi, Chiba, Japan.
authors.forename: S Y
authors.initials: SY
authors.lastname: Murayama
authors.affiliation: Department of Nephrology Medicine, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Sakai
authors.affiliation: Department of Respiratory Medicine, Toho University Omori Medical Centre, Otaku, Tokyo, Japan.
authors.forename: S
authors.initials: S
authors.lastname: Homma
authors.affiliation: Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Tateda
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology; D003428:Cross Infection / Q000453:epidemiology*; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D004196:Disease Outbreaks; D005260:Female; D006761:Hospitals; D006801:Humans; D016867:Immunocompromised Host; D016030:Kidney Transplantation; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D058889:Molecular Typing; D058885:Multilocus Sequence Typing; D016533:Mycological Typing Techniques; D045363:Pneumocystis carinii / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D011020:Pneumonia, Pneumocystis / Q000453:epidemiology*; D017422:Sequence Analysis, DNA; D014041:Tokyo / Q000453:epidemiology
chemical_list: D004271:DNA, Fungal
keywords: Multilocus sequence typing; Pneumocystis pneumonia; next-generation sequencer; outbreak; renal transplant patients