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Hu S, Xu H, Meng X, Bai X, Xu J, Ji J, Ying C, Chen Y, Shen P, Zhou Y, Zheng B, Xiao Y. Population genomics of emerging Elizabethkingia anophelis pathogens reveals potential outbreak and rapid global dissemination. Emerg Microbes Infect 2022; 11:2590-2599. [PMID: 36197077 DOI: 10.1080/22221751.2022.2132880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Elizabethkingia anophelis is an emerging species and have increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the E. anophelis geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of E. anophelis pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original E. anophelis shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair mutY gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI E. anophelis was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of E. anophelis causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of E. anophelis populations will generate further knowledge for optimizing future prevent global outbreak infections.
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Affiliation(s)
- Shaohua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohua Meng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangxiang Bai
- Bioinformatics Institute, Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Junli Xu
- Bioinformatics Institute, Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chaoqun Ying
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunxiao Zhou
- Department of Obstetrics & Gynecology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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2
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Hu S, Lv Y, Xu H, Zheng B, Xiao Y. Biofilm formation and antibiotic sensitivity in Elizabethkingia anophelis. Front Cell Infect Microbiol 2022; 12:953780. [PMID: 35967866 PMCID: PMC9366890 DOI: 10.3389/fcimb.2022.953780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Elizabethkingia anophelis has recently gained global attention and is emerging as a cause of life-threatening nosocomial infections. The present study aimed to investigate the association between antimicrobial resistance and the ability to form biofilm among E. anophelis isolated from hospitalized patients in China. Over 10 years, a total of 197 non-duplicate E. anophelis strains were collected. Antibiotic susceptibility was determined by the standard agar dilution method as a reference assay according to the Clinical and Laboratory Standards Institute. The biofilm formation ability was assessed using a culture microtiter plate method, which was determined using a crystal violet assay. Culture plate results were cross-checked by scanning electron microscopy imaging analysis. Among the 197 isolates, all were multidrug-resistant, and 20 were extensively drug-resistant. Clinical E. anophelis showed high resistance to current antibiotics, and 99% of the isolates were resistant to at least seven antibiotics. The resistance rate for aztreonam, ceftazidime, imipenem, meropenem, trimethoprim-sulfamethoxazole, cefepime, and tetracycline was high as 100%, 99%, 99%, 99%, 99%, 95%, and 90%, respectively. However, the isolates exhibited the highest susceptibility to minocycline (100%), doxycycline (96%), and rifampin (94%). The biofilm formation results revealed that all strains could form biofilm. Among them, the proportions of strong, medium, and weak biofilm-forming strains were 41%, 42%, and 17%, respectively. Furthermore, the strains forming strong or moderate biofilm presented a statistically significant higher resistance than the weak formers (p < 0.05), especially for piperacillin, piperacillin-tazobactam, cefepime, amikacin, and ciprofloxacin. Although E. anophelis was notoriously resistant to large antibiotics, minocycline, doxycycline, and rifampin showed potent activity against this pathogen. The data in the present report revealed a positive association between biofilm formation and antibiotic resistance, which will provide a foundation for improved therapeutic strategies against E. anophelis infections in the future.
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Affiliation(s)
- Shaohua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Lv
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
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Hem S, Jarocki VM, Baker DJ, Charles IG, Drigo B, Aucote S, Donner E, Burnard D, Bauer MJ, Harris PNA, Wyrsch ER, Djordjevic SP. Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100083. [PMID: 34988536 PMCID: PMC8703026 DOI: 10.1016/j.crmicr.2021.100083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of closely related (< 50 SNV) clinical and environmental aquatic Elizabethkingia anophelis isolates. Identification of a provisional novel species Elizabethkingia umaracha. Novel blaGOB and blaB carbapenemases and extended spectrum β-lactamase blaCME alleles identified in Elizabethkingia spp. Analysis of the global phylogeny and pangenome of Elizabethkingia spp. Identification of novel ICE elements carrying uncharacterised genetic cargo in 67 / 94 (71.3%) of the aquatic environments Elizabethkingia spp.
Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal blaB, blaGOB and blaCME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (blaBand blaGOB) and extended-spectrum serine‑β-lactamase (blaCME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.
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Affiliation(s)
- Sopheak Hem
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Veronica M Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich, United Kingdom.,Norwich Medical School, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Sarah Aucote
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Ethan R Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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Kuo SC, Tan MC, Huang WC, Wu HC, Chen FJ, Liao YC, Wang HY, Shiau YR, Lauderdale TL. Susceptibility of Elizabethkingia spp. to commonly tested and novel antibiotics and concordance between broth microdilution and automated testing methods. J Antimicrob Chemother 2021; 76:653-658. [PMID: 33258923 DOI: 10.1093/jac/dkaa499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/27/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES We aimed to determine susceptibilities of Elizabethkingia spp. to 25 commonly tested and 8 novel antibiotics, and to compare the performance of different susceptibility testing methods. METHODS Clinical isolates of Elizabethkingia spp., Chryseobacterium spp. and Flavobacterium spp. collected during 2002-18 (n = 210) in a nationwide surveillance programme in Taiwan were speciated by 16S rRNA sequencing. MICs were determined by broth microdilution. The broth microdilution results of 18 common antibiotics were compared with those obtained by the VITEK 2 automated system. RESULTS Among the Elizabethkingia spp. identified (n = 108), Elizabethkingia anophelis was the most prevalent (n = 90), followed by Elizabethkingia meningoseptica (n = 7) and Elizabethkingia miricola cluster [E. miricola (n = 6), Elizabethkingia bruuniana (n = 3) and Elizabethkingia ursingii (n = 2)]. Most isolates were recovered from respiratory or blood specimens from hospitalized, elderly patients. PFGE showed two major and several minor E. anophelis clones. All isolates were resistant to nearly all the tested β-lactams. Doxycycline, minocycline and trimethoprim/sulfamethoxazole inhibited >90% of Elizabethkingia spp. Rifampin inhibited E. meningoseptica (100%) and E. anophelis (81.1%). Fluoroquinolones and tigecycline were active against E. meningoseptica and E. miricola cluster isolates. Novel antibiotics, including imipenem/relebactam, meropenem/vaborbactam, ceftazidime/avibactam, cefepime/zidebactam, delafloxacin, eravacycline and omadacycline were ineffective but lascufloxacin inhibited half of Elizabethkingia spp. The very major discrepancy rates of VITEK 2 were >1.5% for ciprofloxacin, moxifloxacin and vancomycin. Major discrepancy rates were >3% for amikacin, tigecycline, piperacillin/tazobactam and trimethoprim/sulfamethoxazole. CONCLUSIONS MDR, absence of standard interpretation criteria and poor intermethod concordance necessitate working guidelines to facilitate future research of emerging Elizabethkingia spp.
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Affiliation(s)
- Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Mei-Chen Tan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Wei-Cheng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Hui-Ying Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Yih-Ru Shiau
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
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A real-time PCR assay for detection of emerging infectious Elizabethkingia miricola. Mol Cell Probes 2020; 52:101571. [PMID: 32289377 DOI: 10.1016/j.mcp.2020.101571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 11/22/2022]
Abstract
Elizabethkingia miricola, a Gram-negative bacillus, is emerging as a life-threatening pathogen in both humans and animals. However, no specific and rapid diagnostic method exists to detect E. miricola. Here, we established a real-time PCR assay for the rapid, sensitive, and specific detection of E. miricola with a wide dynamic range of 108 copies/μL to 102 copies/μL. The detection limit of the real-time assay was 145 copies/μL, which was 100 times more sensitive than conventional PCR. All clinical isolates E. miricola from different host species yield very close Tm (80.25 ± 0.25 °C). Additionally, no cross-reaction or false positives were observed in the assay for non-target bacterial species. The performance of this assay was primarily assessed by testing frog tissue samples. Overall, our study provided a real-time PCR assay, which is a rapid, sensitive, and specific diagnostic method that could be used for early diagnosis and epidemiological investigation of E. miricola.
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Lin JN, Lai CH, Yang CH, Huang YH. Elizabethkingia Infections in Humans: From Genomics to Clinics. Microorganisms 2019; 7:microorganisms7090295. [PMID: 31466280 PMCID: PMC6780780 DOI: 10.3390/microorganisms7090295] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
The genus Elizabethkingia has recently emerged as a cause of life-threatening infections in humans, particularly in immunocompromised patients. Several new species in the genus Elizabethkingia have been proposed in the last decade. Numerous studies have indicated that Elizabethkingia anophelis, rather than Elizabethkingia meningoseptica, is the most prevalent pathogen in this genus. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry systems with an extended spectrum database could reliably identify E. anophelis and E. meningoseptica, but they are unable to distinguish the remaining species. Precise species identification relies on molecular techniques, such as housekeeping gene sequencing and whole-genome sequencing. These microorganisms are usually susceptible to minocycline but resistant to most β-lactams, β-lactam/β-lactam inhibitors, carbapenems, and aminoglycosides. They often exhibit variable susceptibility to piperacillin, piperacillin-tazobactam, fluoroquinolones, and trimethoprim-sulfamethoxazole. Accordingly, treatment should be guided by antimicrobial susceptibility testing. Target gene mutations are markedly associated with fluoroquinolone resistance. Knowledge on the genomic characteristics provides valuable insights into in these emerging pathogens.
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Affiliation(s)
- Jiun-Nong Lin
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan.
- Department of Critical Care Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan.
| | - Chung-Hsu Lai
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, Meiho University, Pingtung 912, Taiwan
| | - Yi-Han Huang
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 824, Taiwan
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