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Xu A, Zhu H, Gao B, Weng H, Ding Z, Li M, Weng X, He G. Diagnosis of severe community-acquired pneumonia caused by Acinetobacter baumannii through next-generation sequencing: a case report. BMC Infect Dis 2020; 20:45. [PMID: 31941459 PMCID: PMC6964051 DOI: 10.1186/s12879-019-4733-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/24/2019] [Indexed: 01/07/2023] Open
Abstract
Background Acinetobacter baumannii is a gram-negative aerobic bacillus that is commonly causes of hospital-acquired infections. Community-acquired pneumonia caused by Acinetobacter baumannii (CAP-Ab) is rare but fatal if diagnosis and treatment are delayed. Conventional culture of clinical specimens is the main method for clinical diagnosis of A. baumannii infections which may suffer from limited positive rate and is time consuming. Timely and precise diagnosis of CAP-Ab remains challenging. Case presentation A 66-year-old man with 24 h history of acute fever and dyspnea was admitted to our hospital. He was diagnosed as severe community acquired pneumonia (CAP), septic shock, respiratory failure and acute kidney injury. Next-generation sequencing (NGS) was performed on the patient’s sputum and blood, which identified numerous A. baumannii nucleotide sequences in the sample of sputum and led to the rapid diagnosis and treatment of community acquired pneumonia caused by A. baumannii. This result was confirmed by subsequent sputum culture. Conclusions This case described that the successful application of the next generation sequencing assisting the speedy diagnosis of A. baumannii infection provides a new idea for the timely diagnosis of CAP-Ab and highlights that NGS is a promising tool in rapid etiological diagnosis of acute and severe infectious diseases.
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Affiliation(s)
- Ancong Xu
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Hong Zhu
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Bingqi Gao
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Haixu Weng
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Zhangna Ding
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Mianmian Li
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China
| | - Xing Weng
- BGI-Shenzhen, Shenzhen, 518083, Guandong, China
| | - Guoxin He
- The Third Affiliated Hospital of Wenzhou Medical University, 108 Wansong Road, Wenzhou, 325200, Zhejiang, China.
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Son YW, Jung IY, Ahn MY, Jeon YD, Ann HW, Ahn JY, Ku NS, Han SH, Choi JY, Song YG, Kim JM. A Case of Community-Acquired Pneumonia Caused by Multidrug-Resistant Acinetobacter baumannii in Korea. Infect Chemother 2017; 49:297-300. [PMID: 29299898 PMCID: PMC5754342 DOI: 10.3947/ic.2017.49.4.297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/08/2017] [Indexed: 11/24/2022] Open
Abstract
Acinetobacter baumannii is an aerobic Gram-negative coccobacillus that causes nosocomial pneumonia in patients on mechanical ventilation or previously treated with broad-spectrum antibiotics. Nevertheless, community-acquired pneumonia (CAP) caused by A. baumannii, especially multi-drug resistant (MDR) strains, is rare. We experienced the first case of CAP caused by MDR A. baumannii in Korea in a 78-year-old man. This case shows that MDR A. baumannii can cause CAP in Korea.
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Affiliation(s)
- Young Woong Son
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mi Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Yong Duk Jeon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hea Won Ann
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Young Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea.
| | - Sang Hoon Han
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
| | - Jun Young Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
| | - Young Goo Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,AIDS Research Institue, Yonsei University College of Medicine, Seoul, Korea
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Li P, Yang C, Xie J, Liu N, Wang H, Zhang L, Wang X, Wang Y, Qiu S, Song H. Acinetobacter calcoaceticus from a fatal case of pneumonia harboring bla(NDM-1) on a widely distributed plasmid. BMC Infect Dis 2015; 15:131. [PMID: 25881070 PMCID: PMC4373515 DOI: 10.1186/s12879-015-0870-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We have recovered one bla(NDM-1)-harboring bacterial strain, designated as XM1570, from a sputum sample obtained from a fatal case of pneumonia in China. METHODS Biochemical profiling, 16S rRNA sequencing and antimicrobial susceptibility testing were performed. Conjugation experiments were conducted to determine transmissibility of resistance. Pulsed-field gel electrophoresis and whole genome sequencing were performed to identify strain-specific features. RESULTS The isolate XM1570 was identified as Acinetobacter calcoaceticus. Whole genome sequencing identified two plasmids, pXM1 and pXM2. Comparative analysis showed >99% similarity between XM1570 and A. calcoaceticus PHEA-2. Plasmid pXM1 carried the carbapenemase gene bla(NDM-1) and displayed high homology with previously described plasmids isolated from different Acinetobacter spp., which were collected from human or livestock distributed in China and worldwide. The bla(NDM-1) gene was located on this conjugative plasmid in a transposon-like region flanked by two copies of the insertion sequence ISAba125; and resistance to all tested β-lactams was observed. Transferability of resistance from pXM1 to the transconjugants was identified. Plasmid pXM2 had an insertion sequence ISAba125 and a -35 region of the bla NDM-1 gene promoter but the bla NDM-1 gene was not present. A chromosomally located carbapenemase-encoding gene bla OXA-75 was detected; however, this gene was interrupted by an insertion sequence ISAba22 belonging to IS3 family. CONCLUSIONS Location of bla(NDM-1) on different self-transmissible plasmids could facilitate geographically broad dissemination and host range expansion of the bla(NDM-1) gene via horizontal gene transfer. Our findings of this normally environmental species A. calcoaceticus XM1570 further underline the significant clinical challenge and the essential need for surveillance including molecular methods and plasmid analyses.
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Affiliation(s)
- Peng Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Chaojie Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Jing Xie
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Nan Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | | | - Ling Zhang
- 174th Hospital of PLA, Xiamen, Fujian, China.
| | - Xu Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Yong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 DongDa Street, Fengtai District, Beijing, 100071, China.
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Davis JS, McMillan M, Swaminathan A, Kelly JA, Piera KE, Baird RW, Currie BJ, Anstey NM. A 16-Year Prospective Study of Community-Onset Bacteremic Acinetobacter Pneumonia. Chest 2014; 146:1038-1045. [DOI: 10.1378/chest.13-3065] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Choi JY, Ko EA, Kwon KT, Lee S, Kang CI, Chung DR, Peck KR, Song JH, Ko KS. Acinetobacter sp. isolates from emergency departments in two hospitals of South Korea. J Med Microbiol 2014; 63:1363-1368. [PMID: 25062943 DOI: 10.1099/jmm.0.075325-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 114 Acinetobacter sp. isolates were collected from patients in the emergency departments (EDs) of two Korean hospitals. Most isolates belonged to the Acinetobacter baumannii complex (105 isolates, 92.1 %). Imipenem resistance was found in 39 isolates (34.2 %) of the Acinetobacter sp. isolates, and 6 colistin-resistant isolates were also identified. Species distribution and antimicrobial-resistance rates were different between the two hospitals. In addition, two main clones were identified in the imipenem-resistant A. baumannii isolates from hospital B, but very diverse and novel genotypes were found in those from hospital A. Many Acinetobacter sp. isolates, including the imipenem-resistant A. baumannii, are considered to be associated with the community. The evidence of high antimicrobial resistance and different features in these Acinetobacter sp. isolates between the two EDs suggests the need for continuous testing to monitor changes in epidemiology.
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Affiliation(s)
- Ji-Young Choi
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Eun Ah Ko
- Korean Minjok Leadership Academy, Heongseong, Republic of Korea
| | - Ki Tae Kwon
- Division of Infectious Diseases, Daegu Fatima Hospital, Daegu, Republic of Korea
| | - Shinwon Lee
- Division of Infectious Diseases, Daegu Fatima Hospital, Daegu, Republic of Korea
| | - Choel In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo-Ryeon Chung
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jae-Hoon Song
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea.,Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kwan Soo Ko
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea.,Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Su SY, Chao CM. Acinetobacter calcoaceticus–Acinetobacter baumannii Complex Is Not Equal to A. baumannii. Infect Control Hosp Epidemiol 2013; 34:215-6. [DOI: 10.1086/669076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kang CI, Kang SJ. Reply to Su and Chao. Infect Control Hosp Epidemiol 2013; 34:216-7. [DOI: 10.1086/669078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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