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Hartley C, Morrisette T, Malloy K, Steed LL, Dixon T, Garner SS. Successful Eradication of a Highly Resistant Elizabethkingia anophelis Species in a Premature Neonate With Bacteremia and Meningitis. Pediatr Infect Dis J 2023; 42:e461-e465. [PMID: 37851968 DOI: 10.1097/inf.0000000000004132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Elizabethkingia anophelis is a Gram-negative bacillus that can exhibit highly resistant phenotypes against most antibiotics with evidence of efficacy and safety in the neonatal population. Given the limited antimicrobial options, clinicians may be forced into challenging treatment scenarios when faced with central nervous system infections in premature neonates caused by E. anophelis . We report a case of successful treatment of hospital-acquired meningitis and bacteremia caused by E. anophelis at 11 days of life in a male infant born at 29 weeks, 1 day gestation and birth weight of 1.41 kg. Therapy consisted of vancomycin, dose adjusted to maintain goal troughs of 15-20 mg/L, and rifampin 10 mg/kg/dose every 12 hours, with ciprofloxacin 15 mg/kg/dose every 12 hours and trimethoprim/sulfamethoxazole 5 mg/kg/dose every 12 hours added due to antimicrobial susceptibilities and unsatisfactory response, for a total of 21 days. Following initiation of this multidrug regimen, repeat cultures were negative, laboratory parameters improved [with exception of elevated cerebrospinal fluid (CSF) white blood cell count], the patient remained otherwise stable, and there were no adverse effects noted from therapy. Complications after treatment included the requirement of bilateral hearing aids and the development of hydrocephalus necessitating ventriculoperitoneal shunt placement. To our knowledge, we report the first case of meningitis in a premature neonate initially identified as E. anophelis in the United States treated with this regimen which led to successful microbiologic eradication with no antimicrobial safety concerns.
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Affiliation(s)
- Christopher Hartley
- From the Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina
| | - Taylor Morrisette
- From the Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina
- Department of Clinical Pharmacy & Outcomes Sciences, Medical University of South Carolina College of Pharmacy, Charleston, South Carolina
- Department of Pharmacy Services, Medical University of South Carolina Health, Charleston, South Carolina
| | - Katherine Malloy
- From the Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina
| | - Lisa L Steed
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Terry Dixon
- Division of Infectious Diseases, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina
| | - Sandra S Garner
- From the Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina
- Department of Clinical Pharmacy & Outcomes Sciences, Medical University of South Carolina College of Pharmacy, Charleston, South Carolina
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Lee YL, Hsueh PR. Emerging infections in vulnerable hosts: Stenotrophomonas maltophilia and Elizabethkingia anophelis. Curr Opin Infect Dis 2023; 36:481-494. [PMID: 37548375 DOI: 10.1097/qco.0000000000000953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
PURPOSE OF REVIEW This systematic review aimed to explore the recent trends in the epidemiology, risk factors, and antimicrobial susceptibility of two emerging opportunistic pathogens, Stenotrophomonas maltophilia and Elizabethkingia anophelis . RECENT FINDINGS Since 2020, numerous outbreaks of S. maltophilia and E. anophelis have been reported worldwide. Most of these outbreaks have been associated with healthcare facilities, although one outbreak caused by E. anophelis in France was considered a community-associated infection. In terms of antimicrobial susceptibility, trimethoprim/sulfamethoxazole (TMP-SMZ), levofloxacin, and minocycline have exhibited good efficacy against S. maltophilia . Additionally, cefiderocol and a combination of aztreonam and avibactam have shown promising results in in vitro susceptibility testing. For E. anophelis , there is currently no consensus on the optimal treatment. Although some studies have reported good efficacy with rifampin, TMP-SMZ, piperacillin/tazobactam, and cefoperazone/sulbactam, minocycline had the most favourable in vitro susceptibility rates. Cefiderocol may serve as an alternative due to its low minimum inhibitory concentration (MIC) against E. anophelis . The role of vancomycin in treatment is still uncertain, although several successful cases with vancomycin treatment, even with high MIC values, have been reported. SUMMARY Immunocompromised patients are particularly vulnerable to infections caused by S. maltophilia and E. anophelis , but the optimal treatment strategy remains inconclusive. Further research is necessary to determine the most effective use of conventional and novel antimicrobial agents in combatting these multidrug-resistant pathogens.
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Affiliation(s)
- Yu-Lin Lee
- Department of Internal Medicine, Chung Shan Medical University Hospital
- School of Medicine, Chung Shan Medical University
- PhD Program in Medical Biotechnology, National Chung-Hsing University
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital
- School of Medicine
- PhD Program for Aging, School of Medicine, China Medical University, Taichung
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
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Kim KR, Shim KN, Choe AR, Lee MJ, Park YH, Song EM, Tae CH, Jung SA. A Case of Intramural Gastric Wall Abscess, a Rare Disease Successfully Treated with Endoscopic Incision and Drainage. Gut Liver 2023; 17:949-953. [PMID: 36700301 PMCID: PMC10651380 DOI: 10.5009/gnl220009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 01/27/2023] Open
Abstract
Gastric wall abscess is a rare condition characterized by a purulent inflammatory process resulting in the formation of a pocket of pus in the stomach. As the mucosa is usually intact, it requires various tools such as endoscopic ultrasonography or computed tomography for the differential diagnosis to rule out more common subepithelial tumors. Even after the diagnosis, the treatment for gastric wall abscess was previously restricted to surgical resection in combination with antibiotics. Currently, in order to avoid unnecessary surgery, the alternative method of initial treatment with an endoscopic approach is recommended. It also helps to choose appropriate antibiotics with confirmation of the pathogen by drainage. There are few reports that describe the detailed processing of the endoscopic drainage, and there is no consensus on the treatment. The pathogens that cause gastric wall abscess are usually Streptococci, Staphylococci, and Escherichia coli. There is only one case reported to be caused by Candida albicans. This is the first report of Elizabethkingia anopheles as the pathogen of the gastric wall abscess. Here, we report a case of gastric wall abscess in a 75-year-old man, safely treated by endoscopic drainage and antibiotics, confirmed by isolating the contents of the abscess.
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Affiliation(s)
- Kyung Rok Kim
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Ki Nam Shim
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - A Reum Choe
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Min Jong Lee
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Ye Hyun Park
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Eun Mi Song
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Chung Hyun Tae
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Sung Ae Jung
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
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Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
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Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
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Mallinckrodt L, Huis In 't Veld R, Rosema S, Voss A, Bathoorn E. Review on infection control strategies to minimize outbreaks of the emerging pathogen Elizabethkingia anophelis. Antimicrob Resist Infect Control 2023; 12:97. [PMID: 37679842 PMCID: PMC10486102 DOI: 10.1186/s13756-023-01304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Elizabethkingia anophelis is a multi-drug resistant emerging opportunistic pathogen with a high mortality rate, causing healthcare-associated outbreaks worldwide. METHODS We report a case of E. anophelis pleuritis, resulting from transmission through lung transplantation, followed by a literature review of outbreak reports and strategies to minimize E. anophelis transmission in healthcare settings. RESULTS From 1990 to August 2022, 14 confirmed E. anophelis outbreak cohorts and 21 cohorts with suspected E. anophelis outbreaks were reported in literature. A total of 80 scientific reports with recommendations on diagnostics and infection control measures were included and summarized in our study. CONCLUSION Strategies to prevent and reduce spread of E. anophelis include water-free patient rooms, adequate hygiene and disinfection practices, and optimized diagnostic techniques for screening, identification and molecular typing.
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Affiliation(s)
- Lisa Mallinckrodt
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Gelre Hospital, Apeldoorn, The Netherlands
| | - Robert Huis In 't Veld
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Nascimento APA, de Farias BO, Gonçalves-Brito AS, Magaldi M, Flores C, Quidorne CS, Montenegro KS, Bianco K, Clementino MM. Phylogenomics analysis of multidrug-resistant Elizabethkingia anophelis in industrial wastewater treatment plant. J Appl Microbiol 2023; 134:lxad215. [PMID: 37715335 DOI: 10.1093/jambio/lxad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023]
Abstract
AIMS This study investigated the phylogenetic relatedness of multidrug-resistant Elizabethkingia anophelis recovered from an industrial wastewater treatment plant (WWTPi). METHODS AND RESULTS The wastewater samples were plated in brain heart infusion agar (4 mg/L ceftazidime, 8 mg/L meropenem, and 2 mg/L polimixin). Four isolates recovered from four stages of WWTPi (influent, aeration, decantation, and treated effluent) were identified and evaluated of susceptibility profiles in the VITEK 2 system. These strains identified as E. meningoseptica were confirmed to be E. anophelis by whole genomic sequencing (Miseq-Illumina) and showed antimicrobial resistance genes of β-lactams, aminoglycosides, and tetracycline's classes. The ribosomal multilocus sequence typing showed that they belong to the rST 65620 together with clinical strains. The phylogenomic tree revealed the similarity of our strains to those belonging to sublineage 11 and the single nucleotide polymorphism analysis confirmed that they belong to a single clade. CONCLUSIONS To the best of our knowledge, this is the first study reporting the persistence of multidrug-resistant E. anophelis sublineage 11 along the wastewater treatment.
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Affiliation(s)
- Ana Paula Alves Nascimento
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Beatriz Oliveira de Farias
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Andressa Silva Gonçalves-Brito
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Mariana Magaldi
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Claudia Flores
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Camila Silva Quidorne
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Kaylanne S Montenegro
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Kayo Bianco
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- COVID-19 Monitoring Network in Wastewater, Santo André, São Paulo, 09210-580, Brazil
| | - Maysa Mandetta Clementino
- National Institute of Quality Control in Health-INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- Fiocruz Genomic Network, Oswaldo Cruz Foundation-FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
- COVID-19 Monitoring Network in Wastewater, Santo André, São Paulo, 09210-580, Brazil
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Genomic and phylogenetic characterization of Elizabethkingia anophelis strains: The first two cases of life-threatening infection in Japan. J Infect Chemother 2023; 29:376-383. [PMID: 36682607 DOI: 10.1016/j.jiac.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Elizabethkingia anophelis causes meningitis, bloodstream infections, and respiratory infections in immunocompromised individuals. We examined two E. anophelis strains isolated from the first life-threatening cases caused by this species in Japan to determine the phylogenetic origin and genomic features of them. METHODS We performed whole genome-based analysis to clarify the genetic relationship for the two strains (EK0004 and EK0079) and Elizabethkingia sp. strains isolated from worldwide and to characterize the genomic features such as the prevalence of virulence- and antimicrobial resistance (AMR)-related genes. PATIENTS A 29-year-old man with hepatosplenic T-cell lymphoma and a 52-year-old man with systemic lupus erythematosus developed fatal bacteremia and meningitis due to E. anophelis, respectively. RESULTS Two strains, EK0004 and EK0079, were genetically different but most closely related to the strains isolated from the largest outbreak in Wisconsin, USA from 2015 to 2016, and the strain isolated from cerebrospinal fluid of a patient in Florida, USA in 1982, respectively. The two strains contained AMR-related genes such as those encoding for an extended-spectrum β-lactamase and multiple metallo-β-lactamases and several virulence-related genes such as capsular polysaccharide synthesis gene clusters. CONCLUSIONS Although further functional analyses are required to understand the virulence of these clones, these finding suggests that enough caution of E. anophelis infection in immunocompromised patients is required since the number of infections by this species is increasing outside Japan.
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Yang YS, Huang TW, Huang YC, Huang WC, Hsu SY, Wu HC, Chen FJ, Shang HS, Sytwu HK, Kuo SC. In vitro and in vivo efficacy of minocycline-based therapy for Elizabethkingia anophelis and the impact of reduced minocycline susceptibility. Int J Antimicrob Agents 2022; 60:106678. [PMID: 36184015 DOI: 10.1016/j.ijantimicag.2022.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/23/2022] [Accepted: 09/25/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Elizabethkingia anophelis is inherently resistant to multiple antibiotics, except minocycline. This study aimed to determine the in vitro and in vivo efficacy of minocycline monotherapy and combination therapy against susceptible strains and the impact of reduced minocycline susceptibility. METHODS Three clinical isolates and one laboratory-induced mutant with reduced minocycline susceptibility were included. Time-kill and checkerboard assays were used to assess in vitro efficacy and synergy, respectively. Galleria mellonella infection and mouse pneumonia models were used to assess in vivo efficacy, and a mouse thigh infection model was used to determine the bacterial load. RESULTS Minocycline monotherapy exerted a modest inhibitory effect on three clinical minocycline-susceptible E. anophelis isolates in vitro, but delayed G. mellonella death and improved infected mouse survival; it also significantly reduced the in vivo bacterial load. Minocycline had decreased efficacy on G. mellonella and mice infected by the mutant with reduced minocycline susceptibility. Genome comparison revealed several spontaneous mutations associated with reduced minocycline susceptibility. Among eight antibiotics tested in combination with minocycline, rifampin consistently showed in vitro synergy. The addition of rifampin (1 mg/L) reduced the mutant prevention concentration of minocycline from 2-4 mg/L to < 0.5 mg/L. However, compared with monotherapy, the combination of rifampin and minocycline did not further reduce the bacterial load or improve the survival of G. mellonella or mice. CONCLUSION Minocycline monotherapy was in vivo effective against susceptible E. anophelis. Reduced minocycline susceptibility due to spontaneous mutation decreased its therapeutic efficacy. In combination with rifampin, it prevented the in vitro emergence of reduced susceptibility but did not provide additional in vivo survival benefit.
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Affiliation(s)
- Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Tzu-Wen Huang
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ying-Chi Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Wei-Cheng Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Shu-Yuan Hsu
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan; National Yang Ming Chiao Tung University, Department of Biological Science & Technology
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan
| | - Shu-Chen Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli County, Taiwan; National Yang Ming Chiao Tung University, Department of Biological Science & Technology.
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Dean K, Coaster N, Young K, Mitchell J. Development and application of a dose-response model for Elizabethkingia spp. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2022; 43:1496-1507. [PMID: 36161308 DOI: 10.1111/risa.14013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Elizabethkingia spp. are common environmental pathogens responsible for infections in more vulnerable populations. Although the exposure routes of concern are not well understood, some hospital-associated outbreaks have indicated possible waterborne transmission. In order to facilitate quantitative microbial risk assessment (QMRA) for Elizabethkingia spp., this study fit dose-response models to frog and mice datasets that evaluated intramuscular and intraperitoneal exposure to Elizabethkingia spp. The frog datasets could be pooled, and the exact beta-Poisson model was the best fitting model with optimized parameters α = 0.52 and β = 86,351. Using the exact beta-Poisson model, the dose of Elizabethkingia miricola resulting in a 50% morbidity response (LD50 ) was estimated to be approximately 237,000 CFU. The model developed herein was used to estimate the probability of infection for a hospital patient under a modeled exposure scenario involving a contaminated medical device and reported Elizabethkingia spp. concentrations isolated from hospital sinks after an outbreak. The median exposure dose was approximately 3 CFU/insertion event, and the corresponding median risk of infection was 3.4E-05. The median risk estimated in this case study was lower than the 3% attack rate observed in a previous outbreak, however, there are noted gaps pertaining to the possible concentrations of Elizabethkingia spp. in tap water and the most likely exposure routes. This is the first dose-response model developed for Elizabethkingia spp. thus enabling future risk assessments to help determine levels of risk and potential effective risk management strategies.
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Affiliation(s)
- Kara Dean
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Natalie Coaster
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Kyana Young
- Department of Engineering, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jade Mitchell
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, Michigan, USA
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Brooks L, Subramanian S, Dranow DM, Mayclin SJ, Myler PJ, Asojo OA. Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum. Acta Crystallogr F Struct Biol Commun 2022; 78:306-312. [PMID: 35924598 PMCID: PMC9350836 DOI: 10.1107/s2053230x22007555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Elizabethkingia bacteria cause opportunistic infections in neonates, the elderly and the immunocompromised with mortality rates of up to 40%. The high-resolution structures of glutamyl-tRNA synthetase (GluRS) from E. meningosepticum and E. anopheles reveal similarities to bacterial GluRSs that can be exploited to accelerate rational drug discovery for these globally important emerging infectious Gram-negative bacteria. Elizabethkingia bacteria are globally emerging pathogens that cause opportunistic and nosocomial infections, with up to 40% mortality among the immunocompromised. Elizabethkingia species are in the pipeline of organisms for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include the structure–function analysis of potential therapeutic targets. Glutamyl-tRNA synthetase (GluRS) is essential for tRNA aminoacylation and is under investigation as a bacterial drug target. The SSGCID produced, crystallized and determined high-resolution structures of GluRS from E. meningosepticum (EmGluRS) and E. anopheles (EaGluRS). EmGluRS was co-crystallized with glutamate, while EaGluRS is an apo structure. EmGluRS shares ∼97% sequence identity with EaGluRS but less than 39% sequence identity with any other structure in the Protein Data Bank. EmGluRS and EaGluRS have the prototypical bacterial GluRS topology. EmGluRS and EaGluRS have similar binding sites and tertiary structures to other bacterial GluRSs that are promising drug targets. These structural similarities can be exploited for drug discovery.
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Antimicrobial Susceptibility of Elizabethkingia Species: Report from a Reference Laboratory. J Clin Microbiol 2022; 60:e0254121. [PMID: 35510517 DOI: 10.1128/jcm.02541-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Elizabethkingia species are Gram-negative bacilli that were most recently linked to a cluster of infections in the Midwestern United States from 2016 to 2017. Inappropriate empirical and directed antibiotic selection for this organism is common among providers and is an independent risk factor for mortality. Trends in antimicrobial susceptibility profiles of Elizabethkingia species from a referral laboratory over a 10-year period were reviewed. Identification methods used over time varied and included biochemical panels, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and 16S rRNA gene sequencing. Agar dilution was used to conduct antimicrobial susceptibility testing. One hundred seventy-four clinical isolates were included. The lower respiratory tract (20/37; 54%) was the most common specimen source in pediatric patients, whereas blood isolates (62/137; 45%) constituted the most prevalent source in adults. Among the identified species, Elizabethkingia meningoseptica (72/121; 59%) constituted the majority. All Elizabethkingia species tested against minocycline were susceptible (18/18; 100%), and 90% of isolates tested against trimethoprim-sulfamethoxazole (TMP-SMX) (117/130) were susceptible. Of the 12 Elizabethkingia miricola isolates, most of the tested isolates were susceptible to piperacillin-tazobactam (11/12; 92%) and levofloxacin (11/12; 92%), whereas the Elizabethkingia anophelis isolates most often tested susceptible to piperacillin-tazobactam (13/14; 93%). In this study, Elizabethkingia species showed high rates of in vitro susceptibility to minocycline and TMP-SMX. Further studies are needed to investigate the clinical implications of species-level differences in antimicrobial susceptibilities in this genus.
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Elizabethkingia anophelis: An Important Emerging Cause of Neonatal Sepsis and Meningitis in China. Pediatr Infect Dis J 2022; 41:e228-e232. [PMID: 35067644 DOI: 10.1097/inf.0000000000003464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Elizabethkingia anophelis, originally isolated from the midgut of Anopheles gambiae in 2011, is an important cause of sepsis in adults and children and meningitis in newborns, with several reported outbreaks worldwide. Accumulating molecular biological and whole-genome sequencing (WGS) evidence suggests that E. anophelis is the major human pathogen belonging to the genus Elizabethkingia. The source of infection, routes of transmission and pathogenicity of E. anophelis are unclear and should be better understood as the bacterium is capable of causing sepsis and meningitis in newborns, with complications and high mortality rates. Here, we describe two healthy neonates who developed meningitis caused by Elizabethkingia infection. Initial conventional laboratory results revealed that the pathogen was E. meningoseptica; metagenomic findings later confirmed it as E. anophelis. We also summarize reported E. anophelis infections among newborns in China and elsewhere and describe the clinical, pathogenic and genetic characteristics of this bacillus.
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The Evolutionary Trend and Genomic Features of an Emerging Lineage of Elizabethkingia anophelis Strains in Taiwan. Microbiol Spectr 2022; 10:e0168221. [PMID: 35044198 PMCID: PMC8768576 DOI: 10.1128/spectrum.01682-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The incidence of Elizabethkingia anophelis bacteremia increased significantly in a tertiary hospital, Changhua Christian Hospital (CCH) since 2013. The infection density was 1.3 and 8.1 cases per 100,000 patient-days between 2005 and 2012 and 2013 and 2020, respectively (P < 0.05). During an outbreak investigation, a specific lineage of E. anophelis strains was identified by the pulsed-field gel electrophoresis analysis. To evaluate the evolution of the specific E. anophelis lineage, whole-genome sequencing was performed, and unique genomic features (GRs) were determined by comparative genomic analysis. The specific E. anophelis lineage was novel compared to worldwide strains ever reported by cg-MLST phylogenic and whole-genome comparative analysis. Multiplex PCR using primers designed from unique GRs were performed for prevalence screening among isolates from the CCH and nationwide isolates from the Taiwan surveillance of Antimicrobial Resistance (TSAR) Program. The proportion of the specific E. anophelis lineage increased from 7.9% (3/38) during 2005-2012 to 89.2% (223/250) during 2013-2020 (P < 0.05). Although E. anophelis usually confers resistance to multiple antibiotics with limited therapeutic options, the E. anophelis strains in the specific lineage had higher ciprofloxacin resistance (100% [226/226] versus 27.4% [17/62], P < 0.05) and was associated with a higher 14-day mortality rates (33.2% [37/226] versus 16.1% [10/62], P < 0.05) than other strains at CCH. A similarly increasing trend was also found in the national TSAR program during 2002-2018 (p for trend <0.05). We concluded that a novel lineage of E. anophelis strains has emerged dominantly in Taiwan. The genomic features are important for further investigations of epidemiology, resistance, virulence, and appropriate treatment. IMPORTANCEElizabethkingia anophelis is an emerging multidrug resistant pathogen caused several global outbreaks recently. E. anophelis was frequently misidentified as E. meningoseptica in the past by conventional culture methods; therefore, the prevalence was often underestimated. Through revised identification, an increasing trend of E. anophelis infection was noted in a tertiary hospital and a dominant lineage of strains was recognized by genotyping. To our best knowledge, the dominant lineage of E. anophelis is novel in comparison to other worldwide strains by whole-genome comparative analysis and several unique genomic regions were found. The whole-genome sequencing data also demonstrated multiple putative virulence factors and genes associated with multidrug resistance. In our study, we identified a specially evolved E. anophelis in Taiwan with increasing nationwide dominance. This study will assist in further epidemiology surveillance and developing corresponsive infection control policies to restrain it potential of global dissemination.
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Rahaman MM, Sarkar MMH, Rahman MS, Islam MR, Islam I, Saha O, Akter S, Banu TA, Jahan I, Habib MA, Goswami B, Bari L, Malek MA, Khan MS. Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach. J Med Virol 2021; 94:1670-1688. [PMID: 34939673 DOI: 10.1002/jmv.27537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Shahina Akter
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Tanjian Akhtar Banu
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Iffat Jahan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Md Ahasan Habib
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Barna Goswami
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Latiful Bari
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Abdul Malek
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Salim Khan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
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15
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Honavar AG, David A, Amladi A, Thomas L. Multidrug-resistant Elizabethkingia anophelis Septicemia, Meningitis, Ventriculitis, and Hydrocephalus in a Preterm Neonate: A Rare Complication of an Emerging Pathogen. J Pediatr Neurosci 2021; 16:79-81. [PMID: 34316316 PMCID: PMC8276963 DOI: 10.4103/jpn.jpn_45_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/30/2020] [Accepted: 08/06/2020] [Indexed: 11/25/2022] Open
Abstract
Elizabethkingia anophelis is an emerging pathogen causing neonatal meningitis. Here, we describe the challenging course and necessity of a long 14-week duration of antibiotics in a 12-day-old male neonate with E. anophelis septicemia and meningitis. He developed ventriculitis and hydrocephalus, and needed a ventriculoperitoneal shunt. At 5-month follow-up he had developmental delay.
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Affiliation(s)
- Abhijit Goyal Honavar
- Department of Pediatrics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Andrew David
- Department of Pediatrics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Anushri Amladi
- Department of Microbiology, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Leenath Thomas
- Department of Pediatrics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
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16
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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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17
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Burgos-Garay ML, Santiago AJ, Kartforosh L, Kotay S, Donlan RM. Supplemental nutrients stimulate the amplification of carbapenemase-producing Klebsiella pneumoniae (CPKP) in a sink drain in vitro biofilm reactor model. BIOFOULING 2021; 37:465-480. [PMID: 34210218 DOI: 10.1080/08927014.2021.1915998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/25/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Liquid wastes (LW) disposed in hospital handwashing sinks may affect colonization of sink P-traps by carbapenemase-producing Klebsiella pneumoniae (CPKP), causing CPKP dispersal into the patient care environment. This study aimed to determine the effect of LW on biofilm formation and CPKP colonization in a P-Trap model (PTM). PTMs containing polymicrobial biofilms grown in autoclaved municipal tap water (ATW) supplemented with 5% dextrose in water (D5W), nutritional shake (Shake), sugar-based soft drink (Soda), or ATW were inoculated with K. pneumoniae ST258 KPC+ (ST258) or K. pneumoniae CAV1016 (CAV1016) and sampled after 7, 14, and 21 d. Biofilm bio-volume, mean thickness, and heterotrophic plate counts were significantly reduced and roughness coefficient significantly increased by Soda compared with D5W, Shake, or ATW. CPKP were significantly reduced by Soda but significantly amplified by D5W (ST258; CAV1016, 7 d) and Shake (ST258) suggesting that reducing LW disposal in sinks may reduce CPKP dispersal into patient care environments.
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Affiliation(s)
- María L Burgos-Garay
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ariel J Santiago
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Leila Kartforosh
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shireen Kotay
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA
| | - Rodney M Donlan
- Division of Healthcare Quality Promotion, Clinical and Environmental Microbiology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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18
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Larkin PMK, Mortimer L, Malenfant JH, Gaynor P, Contreras DA, Garner OB, Yang S, Allyn P. Investigation of Phylogeny and Drug Resistance Mechanisms of Elizabethkingia anophelis Isolated from Blood and Lower Respiratory Tract. Microb Drug Resist 2021; 27:1259-1264. [PMID: 33656389 DOI: 10.1089/mdr.2020.0263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Elizabethkingia species are environmental bacteria associated with opportunistic infections in vulnerable populations. Traditionally, Elizabethkingia meningoseptica was considered the predominant pathogenic species. However, commercial identification systems have routinely misidentified Elizabethkingia anophelis as E. meningoseptica, leading to a mischaracterization of clinical strains and an underestimation of the role of E. anophelis in human disease. Elizabethkingia spp. harbor multidrug resistance (MDR) genes that pose challenges for treatment. Differentiation between Elizabethkingia spp. is particularly important due to differences in antimicrobial resistance (AMR) and epidemiological investigation. In this study, we describe a case of MDR E. anophelis isolated from the blood and lower respiratory tract of a patient who was successfully treated with minocycline. These isolates were initially misidentified by matrix assisted laser desorption ionization-time of flight as E. meningoseptica, whereas whole genome sequencing (WGS) confirmed the isolates as E. anophelis with the closest related strain being E. anophelis NUHP1, which was implicated in a 2012 outbreak in Singapore. Several AMR genes (blaBlaB, blaBlaGOB, blaCME, Sul2, erm(F), and catB) were identified by WGS, confirming the mechanisms for MDR. This case emphasizes the utility of WGS for correct speciation, elucidation of resistance genes, and relatedness to other outbreak strains. As E. anophelis is associated with a high mortality and has been found in hospital system sinks, WGS is critically important for determining strain relatedness and tracking outbreaks in the hospital setting.
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Affiliation(s)
- Paige M K Larkin
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Leanne Mortimer
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Jason H Malenfant
- Division of Infectious Diseases, UCLA Medical Center, University of California, Los Angeles, Los Angeles, California, USA.,Department of Medicine, UCLA Medical Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Pryce Gaynor
- Division of Infectious Diseases, UCLA Medical Center, University of California, Los Angeles, Los Angeles, California, USA
| | - Deisy A Contreras
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Paul Allyn
- Division of Infectious Diseases, UCLA Medical Center, University of California, Los Angeles, Los Angeles, California, USA
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19
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Teng LC, Wang JM, Lu HY, Mao YC, Lai KL, Tseng CH, Huang YT, Liu PY. Elizabethkingia Intra-Abdominal Infection and Related Trimethoprim-Sulfamethoxazole Resistance: A Clinical-Genomic Study. Antibiotics (Basel) 2021; 10:antibiotics10020173. [PMID: 33572268 PMCID: PMC7915159 DOI: 10.3390/antibiotics10020173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
(1) Background: Elizabethkingia spp. is an emerging nosocomial pathogen which causes mostly blood stream infection and nosocomial pneumonia. Among Elizabethkingia species, Elizabethkingia anophelis is the major pathogen, but misidentification as Elizabethkingia meningoseptica is a common problem. Elizabethkingia also possesses broad antibiotic resistance, resulting in high morbidity and mortality of the infection. The aim of our study was to review Elizabethkingia intra-abdominal infections and investigate resistance mechanisms against TMP/SMX in Elizabethkingia anophelis by whole genome sequencing. (2) Methods: We retrospectively searched records of patients with Elizabethkingia intra-abdominal infection between 1990 and 2019. We also conducted whole genome sequencing for a TMP/SMX-resistant Elizabethkingia anophelis to identify possible mechanisms of resistance. (3) Results: We identified a total of nine cases of Elizabethkingia intra-abdominal infection in a review of the literature, including our own case. The cases included three biliary tract infections, three CAPD-related infection, two with infected ascites, and two postoperation infections. Host factor, indwelling-catheter, and previous invasive procedure, including surgery, play important roles in Elizabethkingia infection. Removal of the catheter is crucial for successful treatment. Genomic analysis revealed accumulated mutations leading to TMP/SMX-resistance in folP. (4) Conclusions: Patients with underlying disease and indwelling catheter are more susceptible to Elizabethkingia intra-abdominal infection, and successful treatment requires removal of the catheter. The emerging resistance to TMP/SMX may be related to accumulated mutations in folP.
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Affiliation(s)
- Ling-Chiao Teng
- Section of Infectious Disease, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (L.-C.T.); (C.-H.T.)
| | - Jiunn-Min Wang
- Routine Laboratory, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Hsueh-Yin Lu
- Department of Computer Science and Information Engineering, National Chung Cheng University, Taichung 62102, Taiwan;
| | - Yan-Chiao Mao
- Department of Emergency Medicine, Division of Clinical Toxicology, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
- National Defense Medical Center, School of Medicine, Taipei 11490, Taiwan
| | - Kuo-Lung Lai
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Chien-Hao Tseng
- Section of Infectious Disease, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (L.-C.T.); (C.-H.T.)
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Taichung 62102, Taiwan;
- Correspondence: (Y.-T.H.); (P.-Y.L.)
| | - Po-Yu Liu
- Section of Infectious Disease, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (L.-C.T.); (C.-H.T.)
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence: (Y.-T.H.); (P.-Y.L.)
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20
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Lee YL, Liu KM, Chang HL, Lin JS, Kung FY, Ho CM, Lin KH, Chen YT. A dominant strain of Elizabethkingia anophelis emerged from a hospital water system to cause a three-year outbreak in a respiratory care center. J Hosp Infect 2020; 108:43-51. [PMID: 33157171 DOI: 10.1016/j.jhin.2020.10.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 01/17/2023]
Abstract
BACKGROUND Elizabethkingia species are ubiquitous bacteria but uncommonly cause human infection. An outbreak of Elizabethkingia anophelis bacteraemia was observed in a respiratory care center of a tertiary hospital in Taiwan from 2015 to 2018. METHODS Clinical and environmental isolates were collected for the outbreak investigation. Pulsed-field gel electrophoresis (PFGE) and complete-genome sequencing were conducted to elucidate the mechanism of transmission. FINDINGS The three-year outbreak involved 26 patients with E. anophelis bacteraemia and the incidence significantly increased during the outbreak period compared with that observed from 2010 to 2014 (P<0.05). All 26 clinical isolates during the outbreak period belonged to a cluster by PFGE analysis. In contrast, the PFGE pattern was heterogeneous among comparative historical strains. Hospital tap water was highly contaminated by Elizabethkingia species (18/34, 52.9%); among that, five E. anophelis belonged to the outbreak cluster (5/18, 27.8%). As for the inanimate surface survey, 3.4% sites (4/117) revealed positive growth of E. anophelis including two from feeding tubes/bags and two from sputum suction regulators. All four isolates belonged to the outbreak clone. The outbreak strain had no apparent relationship to currently known E. anophelis strains worldwide through complete-genome sequencing analysis. Specific infection control strategies aimed at water source control and environmental disinfection were implemented subsequently and the outbreak ended in mid-2018. CONCLUSIONS A specific E. anophelis strain was identified from a three-year outbreak. The elucidation of the mechanism of dominance and intra-hospital transmission is crucial for development of corresponsive infection control policies and outbreak control.
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Affiliation(s)
- Y-L Lee
- Department of Internal Medicine, Changhua Christian Hospital, Changhua County, Taiwan; Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City, Taiwan
| | - K-M Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City, Taiwan
| | - H-L Chang
- Department of Internal Medicine, Changhua Christian Hospital, Changhua County, Taiwan; Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City, Taiwan
| | - J-S Lin
- Department of Laboratory Medicine, Changhua Christian Hospital, Changhua County, Taiwan
| | - F-Y Kung
- Department of Laboratory Medicine, Changhua Christian Hospital, Changhua County, Taiwan
| | - C-M Ho
- Department of Clinical Pathology and Laboratory Medicine, Taichung Tzu Chi Hospital, Taichung City, Taiwan
| | - K-H Lin
- Department of Clinical Pathology and Laboratory Medicine, Taichung Tzu Chi Hospital, Taichung City, Taiwan
| | - Y-T Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung City, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan.
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21
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Chen S, Johnson BK, Yu T, Nelson BN, Walker ED. Elizabethkingia anophelis: Physiologic and Transcriptomic Responses to Iron Stress. Front Microbiol 2020; 11:804. [PMID: 32457715 PMCID: PMC7221216 DOI: 10.3389/fmicb.2020.00804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we investigated the global gene expression responses of Elizabethkingia anophelis to iron fluxes in the midgut of female Anopheles stephensi mosquitoes fed sucrose or blood, and in iron-poor or iron-rich culture conditions. Of 3,686 transcripts revealed by RNAseq technology, 218 were upregulated while 112 were down-regulated under iron-poor conditions. Hemolysin gene expression was significantly repressed when cells were grown under iron-rich or high temperature (37°C) conditions. Furthermore, hemolysin gene expression was down-regulated after a blood meal, indicating that E. anophelis cells responded to excess iron and its associated physiological stress by limiting iron loading. By contrast, genes encoding respiratory chain proteins were up-regulated under iron-rich conditions, allowing these iron-containing proteins to chelate intracellular free iron. In vivo studies showed that growth of E. anophelis cells increased 3-fold in blood-fed mosquitoes over those in sucrose-fed ones. Deletion of siderophore synthesis genes led to impaired cell growth in both iron-rich and iron-poor media. Mutants showed more susceptibility to H2O2 toxicity and less biofilm formation than did wild-type cells. Mosquitoes with E. anophelis experimentally colonized in their guts produced more eggs than did those treated with erythromycin or left unmanipulated, as controls. Results reveal that E. anophelis bacteria respond to varying iron concentration in the mosquito gut, harvest iron while fending off iron-associated stress, contribute to lysis of red blood cells, and positively influence mosquito host fecundity.
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Affiliation(s)
- Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Benjamin K. Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Brooke N. Nelson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
- Department of Entomology, Michigan State University, East Lansing, MI, United States
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22
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Nain Z, Abdulla F, Rahman MM, Karim MM, Khan MSA, Sayed SB, Mahmud S, Rahman SMR, Sheam MM, Haque Z, Adhikari UK. Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches. J Biomol Struct Dyn 2019; 38:4850-4867. [PMID: 31709929 DOI: 10.1080/07391102.2019.1692072] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Elizabethkingia anophelis is an emerging human pathogen causing neonatal meningitis, catheter-associated infections and nosocomial outbreaks with high mortality rates. Besides, they are resistant to most antibiotics used in empirical therapy. In this study, therefore, we used immunoinformatic approaches to design a prophylactic peptide vaccine against E. anophelis as an alternative preventive measure. Initially, cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes were predicted from the highest antigenic protein. The CTL and HTL epitopes together had a population coverage of 99.97% around the world. Eventually, six CTL, seven HTL, and two LBL epitopes were selected and used to construct a multi-epitope vaccine. The vaccine protein was found to be highly immunogenic, non-allergenic, and non-toxic. Codon adaptation and in silico cloning were performed to ensure better expression within E. coli K12 host system. The stability of the vaccine structure was also improved by disulphide bridging. In addition, molecular docking and dynamics simulation revealed strong and stable binding affinity between the vaccine and toll-like receptor 4 (TLR4) molecule. The immune simulation showed higher levels of T-cell and B-cell activities which was in coherence with actual immune response. Repeated exposure simulation resulted in higher clonal selection and faster antigen clearance. Nevertheless, experimental validation is required to ensure the immunogenic potency and safety of this vaccine to control E. anophelis infection in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Faruq Abdulla
- Department of Statistics, Faculty of Sciences, Islamic University, Kushtia, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mohammad Minnatul Karim
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Shakil Ahmed Khan
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sifat Bin Sayed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Shafi Mahmud
- Department of Biotechnology and Genetic Engineering, Faculty of Life and Earth Science, Rajshahi University, Rajshahi, Bangladesh
| | - S M Raihan Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Moinuddin Sheam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Zahurul Haque
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
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In vitro activities of imipenem, vancomycin, and rifampicin against clinical Elizabethkingia species producing BlaB and GOB metallo-beta-lactamases. Eur J Clin Microbiol Infect Dis 2019; 38:2045-2052. [PMID: 31352669 DOI: 10.1007/s10096-019-03639-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/11/2019] [Indexed: 01/11/2023]
Abstract
Elizabethkingia genus is emerging in hospitals and resistant to multiple antibiotics. The intrinsic imipenem resistance of Elizabethkingia genus is related to two chromosome-encoded metallo-beta-lactamases (MBLs), BlaB and GOB. This study was aimed to investigate the in vitro activity of imipenem, vancomycin, and rifampicin in clinical Elizabethkingia species. The distribution and heterogeneity of MBLs responsible for imipenem resistance were also evaluated. A total of 167 Elizabethkingia isolates from different patients were collected, including E. anophelis (142), E. meningoseptica (11), and E. miricola (14). All isolates were evaluated by the broth microdilution assay, ethylenediaminetetraacetic acid (EDTA) combination disk test, and EDTA-based microdilution test. The characteristics of BlaB and GOB were evaluated in phylogenetic analysis and heterologous expression experiments. Most of the isolates were susceptible to rifampin (94%), whereas none of the isolates were susceptible to imipenem. Vancomycin showed intermediate effectiveness. EDTA could reduce 4 folds or more minimum inhibitory concentrations (MICs) of imipenem in 105 isolates (62.9%). Of the isolates, the amino acid sequences of BlaB and GOB were divided into 22 and 25 different types, respectively. Phylogenetic analysis showed BlaB and GOB are species-specific proteins. Furthermore, GOB and BlaB from E. anophelis showed higher imipenem hydrolysis efficiency than those from the other two species. Rifampicin remained the most active agent in the current study. The mechanism of Elizabethkingia resistance to imipenem primarily stemmed from MBLs but other mechanisms could also exist, which requires further investigation.
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Snesrud E, McGann P, Walsh E, Ong A, Maybank R, Kwak Y, Campbell J, Jones A, Vore K, Hinkle M, Lesho E. Clinical and Genomic Features of the First Cases of Elizabethkingia anophelis Infection in New York, Including the First Case in a Healthy Infant Without Previous Nosocomial Exposure. J Pediatric Infect Dis Soc 2019; 8:269-271. [PMID: 30107596 DOI: 10.1093/jpids/piy071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/17/2018] [Indexed: 11/14/2022]
Abstract
Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015-2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermined, and experts warned of reemergence. We describe here the first cases of E anophelis infection in New York, including the case of a healthy infant without previous healthcare contact.
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Affiliation(s)
- Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Edward Walsh
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Ana Ong
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Yoon Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jean Campbell
- Microbiology and Molecular Diagnostics, Rochester Regional Health, New York
| | - Anthony Jones
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Kelly Vore
- Infection Prevention, Rochester Regional Health, New York
| | - Mary Hinkle
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Emil Lesho
- Infectious Diseases Unit, Rochester Regional Health, New York
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Abstract
Emerging infectious diseases (EID) and reemerging infectious diseases are increasing globally. Zoonotic diseases are transmitted from animals to humans through direct contact or through food, water, and the environment. Vector-borne diseases are major sources of mortality and morbidity globally. Three mosquito-borne viruses are yellow fever, chikungunya virus, and dengue virus. Recent EIDs include Candida auris, Elizabethkingia anopheles, The Lone Star tick, and avian influenza H7N2. In addition, mcr-1 may contribute to the dissemination of drug resistance to gram-negative bacteria. Nurses play a major role in the identification and prevention of EID within health care settings.
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Affiliation(s)
- Donna Behler McArthur
- University of Arizona College of Nursing and Department of Neurology, College of Medicine, 1305 North Martin Avenue, Tucson, AZ 85721, USA; Vanderbilt University School of Nursing, 461 21st Avenue South, Nashville, TN 37240, USA.
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McTaggart LR, Stapleton PJ, Eshaghi A, Soares D, Brisse S, Patel SN, Kus JV. Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada. Access Microbiol 2019; 1:e000017. [PMID: 32974512 PMCID: PMC7470347 DOI: 10.1099/acmi.0.000017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/21/2019] [Indexed: 11/18/2022] Open
Abstract
Bioinformatic analysis of whole genome sequence (WGS) data is emerging as a tool to provide powerful insights for clinical microbiology. We used WGS data to investigate the genetic diversity of clinical isolates of the bacterial pathogen Elizabethkingia anophelis to query the existence of a single-strain outbreak in Ontario, Canada. The Public Health Ontario Laboratory (PHOL) provides reference identification of clinical isolates of bacteria for Ontario and prior to 2016 had not identified E. anophelis. In the wake of the Wisconsin outbreak of 2015–2016 for which a source was never elucidated, the identification of E. anophelis from clinical specimens from five Ontario patients gave reason to question the presence of an outbreak. Genomic comparisons based on core genome multi-locus sequence typing conclusively refuted the existence of an outbreak, since the 5 Ontario isolates were genetically dissimilar, representing at least 3 distinct sub-lineages scattered among a set of 39 previously characterized isolates. Further interrogation of the genomic data revealed multiple antimicrobial resistance genes. Retrospective reidentification via rpoB sequence analysis of 22 clinical isolates of Elizabethkingia spp. collected by PHOL from 2010 to 2018 demonstrated that E. anophelis was isolated from clinical specimens as early as 2010. The uptick in E. anophelis in Ontario was not due to an outbreak or increased incidence of the pathogen, but rather enhanced laboratory identification techniques and improved sequence databases. This study demonstrates the usefulness of WGS analysis as a public health tool to quickly rule out the existence of clonally related case clusters of bacterial pathogens indicative of single-strain outbreaks.
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Affiliation(s)
- Lisa R. McTaggart
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
| | - Patrick J. Stapleton
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - AliReza Eshaghi
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
| | - Deirdre Soares
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, F-75724 Paris, France
| | - Samir N. Patel
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Julianne V. Kus
- Public Health Ontario, 661 University Avenue, Toronto, ON, Canada M5G 1M1
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- *Correspondence: Julianne V. Kus,
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In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. mSphere 2019; 4:4/2/e00040-19. [PMID: 30944210 PMCID: PMC6449604 DOI: 10.1128/msphere.00040-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE. Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis. IMPORTANCEElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
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Jian MJ, Cheng YH, Chung HY, Cheng YH, Yang HY, Hsu CS, Perng CL, Shang HS. Fluoroquinolone resistance in carbapenem-resistant Elizabethkingia anophelis: phenotypic and genotypic characteristics of clinical isolates with topoisomerase mutations and comparative genomic analysis. J Antimicrob Chemother 2019; 74:1503-1510. [DOI: 10.1093/jac/dkz045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/15/2018] [Accepted: 01/11/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
MDR Elizabethkingia anophelis strains are implicated in an increasing number of healthcare-associated infections worldwide, including a recent cluster of E. anophelis infections in the Midwestern USA associated with significant morbidity and mortality. However, there is minimal information on the antimicrobial susceptibilities of E. anophelis strains or their antimicrobial resistance to carbapenems and fluoroquinolones.
Objectives
Our aim was to examine the susceptibilities and genetic profiles of clinical isolates of E. anophelis from our hospital, characterize their carbapenemase genes and production of MBLs, and determine the mechanism of fluoroquinolone resistance.
Methods
A total of 115 non-duplicated isolates of E. anophelis were examined. MICs of antimicrobial agents were determined using the Sensititre 96-well broth microdilution panel method. QRDR mutations and MBL genes were identified using PCR. MBL production was screened for using a combined disc test.
Results
All E. anophelis isolates harboured the blaGOB and blaB genes with resistance to carbapenems. Antibiotic susceptibility testing indicated different resistance patterns to ciprofloxacin and levofloxacin in most isolates. Sequencing analysis confirmed that a concurrent GyrA amino acid substitution (Ser83Ile or Ser83Arg) in the hotspots of respective QRDRs was primarily responsible for high-level ciprofloxacin/levofloxacin resistance. Only one isolate had no mutation but a high fluoroquinolone MIC.
Conclusions
Our study identified a strong correlation between antibiotic susceptibility profiles and mechanisms of fluoroquinolone resistance among carbapenem-resistant E. anophelis isolates, providing an important foundation for continued surveillance and epidemiological analyses of emerging E. anophelis opportunistic infections. Minocycline or ciprofloxacin has the potential for treatment of severe E. anophelis infections.
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Affiliation(s)
- Ming-Jr Jian
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Hsuan Cheng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Yi Yang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Sin Hsu
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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Jian MJ, Cheng YH, Perng CL, Shang HS. Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species. PeerJ 2018; 6:e5608. [PMID: 30225179 PMCID: PMC6139017 DOI: 10.7717/peerj.5608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/19/2018] [Indexed: 12/02/2022] Open
Abstract
Objectives Several Elizabethkingia species often exhibit extensive antibiotic resistance, causing infections associated with severe morbidity and high mortality rates worldwide. In this study, we determined fluoroquinolone susceptibility profiles of clinical Elizabethkingia spp. isolates and investigated the resistance mechanisms. Methods In 2017–2018, 131 Elizabethkingia spp. isolates were recovered from specimens collected at tertiary care centers in northern Taiwan. Initial species identification using the Vitek MS system and subsequent verification by 16S rRNA sequencing confirmed the presence of Elizabethkingia anophelis (n = 111), E. miricola (n = 11), and E. meningoseptica (n = 9). Fluoroquinolone susceptibility was determined using the microbroth dilution method, and fluoroquinolone resistance genes were analyzed by sequencing. Results Among Elizabethkingia spp. isolates, 91% and 77% were resistant to ciprofloxacin and levofloxacin, respectively. The most prevalent alterations were two single mutations in GyrA, Ser83Ile, and Ser83Arg, detected in 76% of the isolates exhibiting fluoroquinolone MIC between 8 and 128 μg/ml. Another GyrA single mutation, Asp87Asn, was identified in two quinolone-resistant E. miricola strains. None of the isolates had alterations in GyrB, ParC, or ParE. We developed a high-resolution melting assay for rapid identification of the prevalent gyrA gene mutations. The genetic relationship between the isolates was evaluated by random amplified polymorphic DNA PCR that yielded diverse pulsotypes, indicating the absence of any temporal or spatial overlap among the patients during hospitalization. Conclusion Our analysis of fluoroquinolone-resistant Elizabethkingia spp. isolates provides information for further research on the variations of the resistance mechanism and potential clinical guidance for infection management.
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Affiliation(s)
- Ming-Jr Jian
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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