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Ott O, Tolppi S, Figueroa-Cruz J, Myagmar K, Unurbuyan K, Tripathi A. Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation. Sci Rep 2024; 14:12564. [PMID: 38822053 DOI: 10.1038/s41598-024-63014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Next-generation sequencing (NGS) is emerging as a powerful tool for molecular diagnostics but remains limited by cumbersome and inefficient sample preparation. We present an innovative automated NGS library preparation system with a simplified mechanical design that exploits both macro- and microfluidic properties for optimizing heat transfer, reaction kinetics, mass transfer, fluid mechanics, adsorption-desorption rates, and molecular thermodynamics. Our approach introduces a unique two-cannula cylindrical capillary system connected to a programmable syringe pump and a Peltier heating element able to execute all steps with high efficiency. Automatic reagent movement, mixing, and magnetic bead-based washing with capillary-based thermal cycling (capillary-PCR) are completely integrated into a single platform. The manual 3-h library preparation process is reduced to less than 15 min of hands-on time via optimally pre-plated reagent plates, followed by less than 6 h of instrument run time during which no user interaction is required. We applied this method to two library preparation assays with different DNA fragmentation requirements (mechanical vs. enzymatic fragmentation), sufficiently limiting consumable use to one cartridge and one 384 well-plate per run. Our platform successfully prepared eight libraries in parallel, generating sequencing data for both human and Escherichia coli DNA libraries with negligible coverage bias compared to positive controls. All sequencing data from our libraries attained Phred (Q) scores > 30, mapping to reference genomes at 99% confidence. The method achieved final library concentrations and size distributions comparable with the conventional manual approach, demonstrating compatibility with downstream sequencing and subsequent data analysis. Our engineering design offers repeatability and consistency in the quality of sequence-able libraries, asserting the importance of mechanical design considerations that employ and optimize fundamental fluid mechanics and heat transfer properties. Furthermore in this work, we provide unique insights into the mechanisms of sample loss within NGS library preparation assays compared with automated adaptations and pinpoint areas in which the principles of thermodynamics, fluid mechanics, and heat transfer can improve future mechanical design iterations.
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Affiliation(s)
- Olivia Ott
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Sabrina Tolppi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Jennifer Figueroa-Cruz
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khaliun Myagmar
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khulan Unurbuyan
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
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Aranega-Bou P, Cornbill C, Rodger G, Bird M, Moore G, Roohi A, Hopkins KL, Hopkins S, Ribeca P, Stoesser N, Lipworth SI. WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae , Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.04.24.23289028. [PMID: 37214917 PMCID: PMC10193520 DOI: 10.1101/2023.04.24.23289028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The authors have withdrawn their manuscript due to becoming aware of methodology issues related to the curation of the training set used to determine cut-off values for Biotyper cluster assignation and lack of replicate measurements on different days for the isolates analysed. It is therefore unclear whether the conclusions of the manuscript are founded and no further work is possible to correct these issues as the instrument is no longer available to the authors. If you have any questions, please contact the corresponding author.
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Xiong L, Deng C, Yang G, Shen M, Chen B, Tian R, Zha H, Wu K. Molecular epidemiology and antimicrobial resistance patterns of carbapenem-resistant Acinetobacter baumannii isolates from patients admitted at ICUs of a teaching hospital in Zunyi, China. Front Cell Infect Microbiol 2023; 13:1280372. [PMID: 38106474 PMCID: PMC10722174 DOI: 10.3389/fcimb.2023.1280372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundation for the development of infection prevention and control strategies. This study aimed to determine the antimicrobial susceptibility profile, the molecular epidemiology and conduct homology analysis on CRAB strains isolated from ICUs. Methods The sensitivity to various antimicrobials was determined using the minimum inhibitory concentration (MIC) method, Kirby-Bauer disk diffusion (KBDD), and E-test assays. Resistance genes were identified by polymerase chain reaction (PCR). Molecular typing was performed using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Results Among the 79 isolates collected, they exhibited high resistance to various antimicrobials but showed low resistance to levofloxacin, trimethoprim-sulfamethoxazole, and tetracyclines. Notably, all isolates of A. baumannii were identified as multidrug-resistant A. baumannii (MDR-AB). The bla OXA-51-like, adeJ, and adeG genes were all detected, while the detection rates of bla OXA-23-like (97.5%), adeB (93.67%), bla ADC (93.67%), qacEΔ1-sul1 (84.81%) were higher; most of the Ambler class A and class B genes were not detected. MLST analysis on the 79 isolates identified five sequence types (STs), which belonged to group 3 clonal complexes 369. ST1145Ox was the most frequently observed ST with a count of 56 out of 79 isolates (70.89%). MLST analysis for non-sensitive tigecycline isolates, which were revealed ST1145Ox and ST1417Ox as well. By using the MLVA assay, the 79 isolates could be grouped into a total of 64 distinct MTs with eleven clusters identified in them. Minimum spanning tree analysis defined seven different MLVA complexes (MCs) labeled MC1 to MC6 along with twenty singletons. The locus MLVA-AB_2396 demonstrated the highest Simpson's diversity index value at 0.829 among all loci tested in this study while also having one of the highest variety of tandem repeat species. Conclusion The molecular diversity and clonal affinities within the genomes of the CRAB strains were clearly evident, with the identification of ST1144Ox, ST1658Ox, and ST1646Oxqaq representing novel findings.
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Affiliation(s)
- Lin Xiong
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Chengmin Deng
- Scientific Research Center, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Guangwu Yang
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Meijing Shen
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Benhai Chen
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Rengui Tian
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - He Zha
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
- Scientific Research Center, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, China
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Scheier TC, Franz J, Boumasmoud M, Andreoni F, Chakrakodi B, Duvnjak B, Egli A, Zingg W, Ramette A, Wolfensberger A, Kouyos RD, Brugger SD. Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation. Microbiol Spectr 2023; 11:e0098423. [PMID: 37737606 PMCID: PMC10581122 DOI: 10.1128/spectrum.00984-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.
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Affiliation(s)
- T. C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - J. Franz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - M. Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zürich, Zurich, Switzerland
| | - F. Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - B. Chakrakodi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - B. Duvnjak
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - A. Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - W. Zingg
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - A. Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - A. Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - R. D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
| | - S. D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Zurich, Switzerland
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Seo KW, Do KH, Jung CM, Lee SW, Lee YJ, Lim SK, Lee WK. Comparative genetic characterisation of third-generation cephalosporin-resistant Escherichia coli isolated from integrated and conventional pig farm in Korea. J Glob Antimicrob Resist 2023; 34:74-82. [PMID: 37394034 DOI: 10.1016/j.jgar.2023.06.010] [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: 02/15/2023] [Revised: 06/09/2023] [Accepted: 06/26/2023] [Indexed: 07/04/2023] Open
Abstract
OBJECTIVES Pig-farming systems consist of integrated or conventional farms, and many antimicrobials are used to treat bacterial infections. The objective of this study was to compare characteristics of third-generation cephalosporin resistance and extended-spectrum β-lactamase (ESBL)/pAmpC β-lactamase-producing Escherichia coli between integrated and conventional farms. METHODS Third-generation cephalosporin-resistant E. coli was collected from integrated and conventional pig farms from 2021 to 2022. Polymerase chain reaction and DNA sequencing were performed for the detection of β-lactamase-encoding genes, molecular analysis, and identification of genetic relationships. To determine the transferability of β-lactamase genes, conjugation assays were conducted. RESULTS Antimicrobial resistance rates were higher in conventional farms than in integrated farms; ESBL- and pAmpC-lactamase-producing E. coli rates were higher in conventional farms (9.8%) than in integrated farms (3.4%). Fifty-two (6.5%) isolates produced ESBL/pAmpC β-lactamase genes. Isolates from integrated farms harboured CTX-15 (3 isolates), CTX-55 (9 isolates), CTX-229 (1 isolate), or CMY-2 (1 isolate) genes; isolates from conventional farms harboured CTX-1 (1 isolate), CTX-14 (6 isolates), CTX-15 (2 isolates), CTX-27 (3 isolates), CTX-55 (14 isolates), CTX-229 (1 isolate), and CMY-2 (11 isolates) genes. Of the 52 ESBL/pAmpC β-lactamase-producing E. coli isolates, class 1 integrons with 11 different gene cassette arrangements were detected in 39 (75.0%) isolates, and class 2 integrons were detected in 3 isolates. The most common sequence type in both integrated and conventional farms was ST5229, followed by ST101, and then ST10. CONCLUSION Third-generation cephalosporin-resistant patterns and molecular characteristics differed between integrated and conventional farms. Our findings suggest that continuous monitoring of third-generation cephalosporin resistance on pig farms is necessary to prevent the dissemination of resistant isolates.
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Affiliation(s)
- Kwang Won Seo
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - Kyung-Hyo Do
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - Chang Min Jung
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea; Onnuri Animals Hospital, Cheonan, Korea
| | - Seong Won Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea; Boehringer Ingelheim Animal Health Korea Ltd., Seoul, Korea
| | - Young Ju Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu, Korea
| | - Suk-Kyung Lim
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, Gimcheon, Korea
| | - Wan-Kyu Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea; GutBiomeTech, Cheongju, Korea.
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Udaondo Z, Abram K, Kothari A, Jun SR. Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas. Microbiol Spectr 2023; 11:e0490122. [PMID: 36995227 PMCID: PMC10269635 DOI: 10.1128/spectrum.04901-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kaleb Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Atul Kothari
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Tao S, Zhou D, Chen H, Li N, Zheng L, Fang Y, Xu Y, Jiang Q, Liang W. Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains. Front Microbiol 2023; 14:1177841. [PMID: 37168121 PMCID: PMC10165109 DOI: 10.3389/fmicb.2023.1177841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Dongdong Zhou
- Department of General Medicine, Ningbo First Hospital, Ningbo, China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Na Li
- Bengbu Medical College, Bengbu, China
| | - Lin Zheng
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Qi Jiang
- Department of Gastroenterology, Ningbo First Hospital, Ningbo, China
- *Correspondence: Qi Jiang,
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, China
- Wei Liang,
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Kumar S, Anwer R, Azzi A. Molecular typing methods & resistance mechanisms of MDR Klebsiella pneumoniae. AIMS Microbiol 2023; 9:112-130. [PMID: 36891535 PMCID: PMC9988409 DOI: 10.3934/microbiol.2023008] [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: 11/20/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
The emergence and transmission of carbapenem-resistant Klebsiella pneumoniae (CRKP) have been recognized as a major public health concern. Here, we investigated the molecular epidemiology and its correlation with the mechanisms of resistance in CRKP isolates by compiling studies on the molecular epidemiology of CRKP strains worldwide. CRKP is increasing worldwide, with poorly characterized epidemiology in many parts of the world. Biofilm formation, high efflux pump gene expression, elevated rates of resistance, and the presence of different virulence factors in various clones of K. pneumoniae strains are important health concerns in clinical settings. A wide range of techniques has been implemented to study the global epidemiology of CRKP, such as conjugation assays, 16S-23S rDNA, string tests, capsular genotyping, multilocus sequence typing, whole-genome sequencing-based surveys, sequence-based PCR, and pulsed-field gel electrophoresis. There is an urgent need to conduct global epidemiological studies on multidrug-resistant infections of K. pneumoniae across all healthcare institutions worldwide to develop infection prevention and control strategies. In this review, we discuss different typing methods and resistance mechanisms to explore the epidemiology of K. pneumoniae pertaining to human infections.
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Affiliation(s)
- Sunil Kumar
- Department of Microbiology, Kampala International University, Western Campus, Ishaka, Uganda
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Arezki Azzi
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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Vuichard-Gysin D, Sommerstein R, Kronenberg A, Buetti N, Eder M, Piezzi V, Gardiol C, Schlegel M, Harbarth S, Widmer A. High adherence to national IPC guidelines as key to sustainable VRE control in Swiss hospitals: a cross-sectional survey. Antimicrob Resist Infect Control 2022; 11:19. [PMID: 35090563 PMCID: PMC8795934 DOI: 10.1186/s13756-022-01051-9] [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: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Vancomycin resistant enterococci (VRE) are on the rise in many European hospitals. In 2018, Switzerland experienced its largest nosocomial VRE outbreak. The national center for infection prevention (Swissnoso) elaborated recommendations for controlling this outbreak and published guidelines to prevent epidemic and endemic VRE spread. The primary goal of this study was to evaluate adherence to this new guideline and its potential impact on the VRE epidemiology in Swiss acute care hospitals. Methods In March 2020, Swissnoso distributed a survey among all Swiss acute care hospitals. The level of adherence as well as changes of infection prevention and control (IPC) strategies in the years 2018 and 2019 after publication of the national guidelines were asked along with an inventory on VRE surveillance and outbreaks. Results Data of 97/146 (66%) participants were available, representing 81.6% of all acute care beds operated in Switzerland in 2019. The vast majority—72/81 (88%) responding hospitals—have entirely or largely adopted our new national guideline. 38/51 (74.5%) hospitals which experienced VRE cases were significantly more likely to have changed their IPC strategies than those 19/38 (50%) hospitals without VRE cases p = 0.017). The new IPC guidelines included (1) introduction of targeted admission screening in 89.5%, (2) screening of close contacts of VRE cases in 56%, and (3) contact precaution for suspected VRE cases 58% of these hospitals. 52 (54%) hospitals reported 569 new VRE cases in 2018 including 14 bacteremia, and 472 new cases in 2019 with 10 bacteremia. The ten largest outbreaks encountered between 2018 and 2019 included 671 VRE cases, of which most (93.4%) consisted of colonization events, 29 (4.3%) infections and 15 (2.2%) bacteremia. Conclusion Wide adoption of this VRE control guideline seemed to have a positive effect on VRE containment in Swiss acute care hospitals over two years, even if its long-term impact on the VRE epidemiology remains to be evaluated. Broad dissemination and strict implementation of a uniform national guideline may therefore serve as model for other countries to fight VRE epidemics on a national level. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01051-9.
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Li T, Yang Y, Yan R, Lan P, Liu H, Fu Y, Hua X, Jiang Y, Zhou Z, Yu Y. Comparing Core-genome MLST with PFGE and MLST for cluster analysis of Carbapenem-resistant Acinetobacter baumannii. J Glob Antimicrob Resist 2022; 30:148-151. [PMID: 35732264 DOI: 10.1016/j.jgar.2022.06.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/11/2022] [Accepted: 06/11/2022] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES Carbapenem-resistant Acinetobacter baumannii (CRAB) is a prevalent pathogen contributing to hospital infections. Pulsed-field gel electrophoresis, multilocus sequence typing and core-genome MLST are frequently used methods to illuminate the nosocomial transmission of CRAB. In this study, we compared the discriminatory power of the three typing methods. METHODS Antimicrobial susceptibility tests were performed by the broth microdilution and Vitek2 methods. PFGE, MLST and cgMLST were conducted to determine the clonality and phylogenetic relationship of the strains. Whole-genome sequence data were acquired by an Illumina HiSeq 2000, and cgMLST was analysed by the Ridom SeqSphere+ v7.2.3 software. RESULTS A total of 149 carbapenem-resistant A. baumannii isolates had 15 different PFGE profiles (A-O type), and 73 of the isolates had related subtypes (A1 and A2) accounting for the majority of type A isolates. The maximum-likelihood phylogenetic analysis based on the cgMLST genes grouped the same PFGE clonal pattern A into 9 different clusters. ST_Pasteur grouped all the strains into ST2, whereas ST_Oxford grouped the PFGE clonal pattern A isolates into 6 STs. In addition, the gdhB allele in the ST_Oxford scheme had two copies in 5 strains, which complicated the ST_Oxford typing. CONCLUSIONS In conclusion, cgMLST was more discriminant than PFGE and MLST. CgMLST is the most suitable and comprehensive method for genotyping A. baumannii in surveillance and epidemiological research.
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Affiliation(s)
- Tingting Li
- Department of Cinical Laboratory, The First People's Hospital of Linhai, Taizhou, Zhejiang, 318000, China
| | - Yunxing Yang
- Department of Clinical Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Rushuang Yan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Peng Lan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Haiyang Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China.
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11
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Segal E, Bar Yosef S, Axel A, Keller N, Shlaeffer F, Amir A, Efroni G, Haberman Y. Outbreak of Sepsis Following Surgery: Utilizing 16S RNA Sequencing To Detect the Source of Infection. Cureus 2022; 14:e22487. [PMID: 35371778 PMCID: PMC8944214 DOI: 10.7759/cureus.22487] [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] [Accepted: 02/22/2022] [Indexed: 11/06/2022] Open
Abstract
Background Nosocomial infections are a significant health concern. Following surgery, infections are most commonly associated with the surgical site, yet there are other potential sources for infections after surgical interventions. Identification of the source of infections can be very challenging. Methodology An outbreak of postoperative infections following surgery led to intensive care unit (ICU) admission of patients immediately after the surgical procedure. The blood cultures of two patients were positive for Citrobacter freundii. The only connection between all cases was the anesthesiologist. An epidemiological inquiry could not definitively identify the source of the outbreak. Therefore, we utilized an RNA sequencing technique to evaluate the microbiome of the anesthesiologist and compared the results to bacteria cultured from the bloodstream of the two patients. Results The anesthesiologist’s microbiome contained amplicons that were identical to those of the bacteria in the patient’s bloodstream. Because Citrobacter freundii is an uncommon source of bloodstream infections, and in the normal human microbiome, the results establish the source of a cluster of infections to the anesthesiologist. Conclusions In cases of nosocomial infections, when conventional microbiological techniques do not clearly establish the source of the infection, using 16S RNA sequencing should be considered.
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12
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Greninger AL, Zerr DM. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 2021; 10:S88-S95. [PMID: 34951469 PMCID: PMC8755322 DOI: 10.1093/jpids/piab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Corresponding Author: Alexander L. Greninger MD, PhD, MS, MPhil, 1616 Eastlake Ave East Suite 320, Seattle, WA 98102, USA. E-mail:
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, USA,Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, USA
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13
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Thomas RE, Thomas BC. Reducing Biofilm Infections in Burn Patients' Wounds and Biofilms on Surfaces in Hospitals, Medical Facilities and Medical Equipment to Improve Burn Care: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:13195. [PMID: 34948803 PMCID: PMC8702030 DOI: 10.3390/ijerph182413195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022]
Abstract
Biofilms in burns are major problems: bacterial communities rapidly develop antibiotic resistance, and 60% of burn mortality is attributed to biofilms. Key pathogens are Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and multidrug-resistant Acinetobacter baumanii. Purpose: identify current and novel interventions to reduce biofilms on patients' burns and hospital surfaces and equipment. Medline and Embase were searched without date or language limits, and 31 possible interventions were prioritised: phages, nano-silver, AgSD-NLs@Cur, Acticoat and Mepilex silver, acetic acid, graphene-metal combinations, CuCo2SO4 nanoparticles, Chlorhexidene acetate nanoemulsion, a hydrogel with moxifloxacin, carbomer, Chitosan and Boswellia, LED light therapy with nano-emodin or antimicrobial blue light + Carvacrol to release reactive oxygen species, mannosidase + trypsin, NCK-10 (a napthalene compound with a decyl chain), antimicrobial peptide PV3 (includes two snake venoms), and polypeptides P03 and PL2. Most interventions aimed to penetrate cell membranes and reported significant reductions in biofilms in cfu/mL or biofilm mass or antibiotic minimal inhibitory concentrations or bacterial expression of virulence or quorum sensing genes. Scanning electron microscopy identified important changes in bacterial surfaces. Patients with biofilms need isolating and treating before full admission to hospital. Cleaning and disinfecting needs to include identifying biofilms on keyboards, tablets, cell phones, medical equipment (especially endoscopes), sinks, drains, and kitchens.
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Affiliation(s)
- Roger E. Thomas
- Department of Family Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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14
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Chong DWQ, Jayaraj VJ, Ng CW, Sam IC, Said MA, Ahmad Zaki R, Hairi NN, Nik Farid ND, Hoe VCW, Isahak M, Ponnampalavanar S, Syed Omar SF, Kamaruzzaman SB, Ong HC, Hasmukharay K, Hasnan N, Kamarulzaman A, Chan YF, Chong YM, Rampal S. Propagation of a hospital-associated cluster of COVID-19 in Malaysia. BMC Infect Dis 2021; 21:1238. [PMID: 34886794 PMCID: PMC8655495 DOI: 10.1186/s12879-021-06894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hospitals are vulnerable to COVID-19 outbreaks. Intrahospital transmission of the disease is a threat to the healthcare systems as it increases morbidity and mortality among patients. It is imperative to deepen our understanding of transmission events in hospital-associated cases of COVID-19 for timely implementation of infection prevention and control measures in the hospital in avoiding future outbreaks. We examined the use of epidemiological case investigation combined with whole genome sequencing of cases to investigate and manage a hospital-associated cluster of COVID-19 cases. METHODS An epidemiological investigation was conducted in a University Hospital in Malaysia from 23 March to 22 April 2020. Contact tracing, risk assessment, testing, symptom surveillance, and outbreak management were conducted following the diagnosis of a healthcare worker with SARS-CoV-2 by real-time PCR. These findings were complemented by whole genome sequencing analysis of a subset of positive cases. RESULTS The index case was symptomatic but did not fulfill the initial epidemiological criteria for routine screening. Contact tracing suggested epidemiological linkages of 38 cases with COVID-19. Phylogenetic analysis excluded four of these cases. This cluster included 34 cases comprising ten healthcare worker-cases, nine patient-cases, and 15 community-cases. The epidemic curve demonstrated initial intrahospital transmission that propagated into the community. The estimated median incubation period was 4.7 days (95% CI: 3.5-6.4), and the serial interval was 5.3 days (95% CI: 4.3-6.5). CONCLUSION The study demonstrated the contribution of integrating epidemiological investigation and whole genome sequencing in understanding disease transmission in the hospital setting. Contact tracing, risk assessment, testing, and symptom surveillance remain imperative in resource-limited settings to identify and isolate cases, thereby controlling COVID-19 outbreaks. The use of whole genome sequencing complements field investigation findings in clarifying transmission networks. The safety of a hospital population during this COVID-19 pandemic may be secured with a multidisciplinary approach, good infection control measures, effective preparedness and response plan, and individual-level compliance among the hospital population.
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Affiliation(s)
- Diane Woei-Quan Chong
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ministry of Health Malaysia, 62590 Putrajaya, Malaysia
| | - Vivek Jason Jayaraj
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Ministry of Health Malaysia, 62590 Putrajaya, Malaysia
| | - Chiu-Wan Ng
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mas Ayu Said
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rafdzah Ahmad Zaki
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Noran Naqiah Hairi
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nik Daliana Nik Farid
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Victor Chee-Wai Hoe
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Marzuki Isahak
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | | | - Hang-Cheng Ong
- Ministry of Health Malaysia, 62590 Putrajaya, Malaysia
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kejal Hasmukharay
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nazirah Hasnan
- Department of Rehabilitation Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sanjay Rampal
- Centre for Epidemiology and Evidence-based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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15
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Karlsson PA, Tano E, Jernberg C, Hickman RA, Guy L, Järhult JD, Wang H. Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden. Front Microbiol 2021; 12:664665. [PMID: 34054769 PMCID: PMC8155512 DOI: 10.3389/fmicb.2021.664665] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.
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Affiliation(s)
- Philip A Karlsson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Eva Tano
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | | | - Rachel A Hickman
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden.,Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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16
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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes (Basel) 2020; 11:genes11121504. [PMID: 33327465 PMCID: PMC7764966 DOI: 10.3390/genes11121504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.
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17
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Opperman CJ, Marais GJK, Naidoo M, Hsiao M, Samodien N. Response to a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 cases at a diagnostic laboratory. Afr J Lab Med 2020; 9:1307. [PMID: 32934912 PMCID: PMC7479365 DOI: 10.4102/ajlm.v9i1.1307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/06/2020] [Indexed: 11/03/2022] Open
Abstract
Introduction We report on the first documented cluster of Coronavirus Disease 2019 cases amongst diagnostic laboratory staff and outline some of the initial and ongoing steps that are being implemented to manage and prevent the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in our laboratory. Case presentation On 24 April 2020, three staff members of a tertiary diagnostic laboratory in Groote Schuur Hospital, Cape Town, South Africa, tested positive for SARS-CoV-2. Within seven days, a further nine cases were identified, which suggested an outbreak and prompted a full investigation. Management and outcome A multifaceted strategic approach was adopted to halt the spread of SARS-CoV-2 in our laboratory. Interventions focused on simultaneously establishing appropriate risk mitigation and stratification strategies through the upscaling of infection prevention and control measures, whilst minimising disruption to service delivery. Conclusion Laboratory Coronavirus Disease 2019 outbreaks have the potential to cripple a laboratory's testing capacity. Contingency planning and risk assessments should occur early, and interventions should be modified according to each laboratory's available resources and infrastructure.
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Affiliation(s)
- Christoffel J Opperman
- Division of Medical Microbiology, National Health Laboratory Service, University of Cape Town, Cape Town, South Africa
| | - Gert J K Marais
- Division of Medical Virology, National Health Laboratory Service, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Michelle Naidoo
- Division of Medical Virology, National Health Laboratory Service, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Marvin Hsiao
- Division of Medical Virology, National Health Laboratory Service, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Nazlee Samodien
- Division of Medical Microbiology, National Health Laboratory Service, University of Cape Town, Cape Town, South Africa
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18
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Latorre-Pérez A, Villalba-Bermell P, Pascual J, Vilanova C. Assembly methods for nanopore-based metagenomic sequencing: a comparative study. Sci Rep 2020; 10:13588. [PMID: 32788623 PMCID: PMC7423617 DOI: 10.1038/s41598-020-70491-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023] Open
Abstract
Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.
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Gona F, Comandatore F, Battaglia S, Piazza A, Trovato A, Lorenzin G, Cichero P, Biancardi A, Nizzero P, Moro M, Cirillo DM. Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis. Microb Genom 2020; 6:e000347. [PMID: 32149598 PMCID: PMC7276701 DOI: 10.1099/mgen.0.000347] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
In this work we compared the most frequently used Klebsiella pneumoniae typing methods: PFGE, cgMLST and coreSNP. We evaluated the discriminatory power of the three methods to confirm or exclude nosocomial transmission on K. pneumoniae strains isolated from January to December 2017, in the framework of the routine surveillance for multidrug-resistant organisms at the San Raffaele Hospital, in Milan. We compared the results of the different methods to the results of epidemiological investigation. Our results showed that cgMLST and coreSNP are more discriminant than PFGE, and that both approaches are suitable for transmission analyses. cgMLST appeared to be inferior to coreSNP in the K. pneumoniae CG258 phylogenetic reconstruction. Indeed, we found that the phylogenetic reconstruction based on cgMLST genes wrongly clustered ST258 clade1 and clade2 strains, conversely properly assigned by coreSNP approach. In conclusion, this study provides evidences supporting the reliability of both cgMLST and coreSNP for hospital surveillance programs and highlights the limits of cgMLST scheme genes for phylogenetic reconstructions.
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Affiliation(s)
- Floriana Gona
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, Milan, Italy
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aurora Piazza
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, Milan, Italy
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Lorenzin
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Institute of Microbiology and Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Paola Cichero
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna Biancardi
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Nizzero
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Moro
- Infection Control, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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20
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Perini M, Piazza A, Panelli S, Di Carlo D, Corbella M, Gona F, Vailati F, Marone P, Cirillo DM, Farina C, Zuccotti G, Comandatore F. EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing. Sci Rep 2020; 10:1307. [PMID: 31992749 PMCID: PMC6987216 DOI: 10.1038/s41598-020-57742-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/30/2019] [Indexed: 02/01/2023] Open
Abstract
In this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the consensus sequence. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer pairs on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer pairs on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer pairs. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer pairs required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.
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Affiliation(s)
- Matteo Perini
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy
| | - Aurora Piazza
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy
| | - Marta Corbella
- S.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Floriana Gona
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Francesca Vailati
- Microbiology Institute, A.S.S.T. "Papa Giovanni XXIII", Bergamo, 24127, Italy
| | - Piero Marone
- S.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Claudio Farina
- Microbiology Institute, A.S.S.T. "Papa Giovanni XXIII", Bergamo, 24127, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy
- Department of Pediatrics, V. Buzzi Childrens' Hospital, Università di Milano, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences "L. Sacco", Università di Milano, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20157, Italy.
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Chen PY, Chuang YC, Wang JT, Sheng WH, Chen YC, Chang SC. Predictors for vancomycin resistant Enterococcus faecium transforming from colonization to infection: a case control study. Antimicrob Resist Infect Control 2019; 8:196. [PMID: 31827777 PMCID: PMC6889723 DOI: 10.1186/s13756-019-0647-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Background Little is known about risk factors for subsequent infections among vancomycin resistant Enterococcus faecium (VREfm) colonizers, especially characterized by concordant pulsotypes (CP) of paired colonization and infection-related isolates. Methods This case-control study was conducted at a teaching hospital between 2011 and 2014. Targeted patients received active surveillance culture for VREfm by anal swabs at admission. Cases were those who developed VREfm infection within 180 days after colonization of VREfm. Controls were those colonized with VREfm without subsequent VREfm infection. CP were defined by similarities ≥86.7% using pulsed-field gel electrophoresis between paired colonization and infection-related isolates. Results Ninety-seven cases and 194 controls were enrolled. By conditional multivariable logistic regression analysis, the risk factors for subsequent infection among VREfm colonizers were intensive care unit (ICU) admission (adjusted odds ratio [aOR], 9.32; 95% CI, 3.61–24.02), receipt of central venous catheters (CVC) (aOR, 3.38; 95% CI, 1.30–8.82), and utilization of third- and fourth-generation cephalosporins (aOR, 4.06; 95% CI, 1.79–9.20, and aOR, 5.32; 95% CI, 1.85– 10.29, respectively) (all P ≤ 0.01). Fifty-six (57.7%) of case patients belonged to the CP group, which were associated with ICU admission (aOR, 3.74; 95% CI, 1.38–10.13), and infection developing within 30 days after colonization (aOR, 3.34; 95% CI, 1.25–8.91). Conclusions Among VREfm colonizers, being admitted to ICU and receiving CVC or broad spectrum cephalosporins, were the risk factors for subsequent infections. These findings highlight the importance of conducting more strict infection control measures on specific groups of VREfm colonizers.
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Affiliation(s)
- Pao-Yu Chen
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100.,2Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chung Chuang
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100
| | - Jann-Tay Wang
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100.,3National Institutes of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Wang-Huei Sheng
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100.,4College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yee-Chun Chen
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100.,3National Institutes of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan.,4College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shan-Chwen Chang
- 1Department of Internal Medicine, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei, Taiwan 100.,4College of Medicine, National Taiwan University, Taipei, Taiwan
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22
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Tadros M, Cabrera A, Matukas LM, Muller M. Evaluation of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry and ClinPro Tools as a Rapid Tool for Typing Streptococcus pyogenes. Open Forum Infect Dis 2019; 6:ofz441. [PMID: 31700941 PMCID: PMC6825801 DOI: 10.1093/ofid/ofz441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/03/2019] [Indexed: 11/30/2022] Open
Abstract
Background Timely strain typing of group A Streptococci (GAS) is necessary to guide outbreak recognition and investigation. We evaluated the use of (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) combined with cluster analysis software to rapidly distinguish between related and unrelated GAS isolates in real-time. Methods We developed and validated a typing model using 177 GAS isolates with known emm types. The typing model was created using 43 isolates, which included 8 different emm types, and then validated using 134 GAS isolates of known emm types that were not included in model generation. Results Twelve spectra were generated from each isolate during validation. The overall accuracy of the model was 74% at a cutoff value of 80%. The model performed well with emm types 4, 59, and 74 but showed poor accuracy for emm types 1, 3, 12, 28, and 101. To evaluate the ability of this tool to perform typing in an outbreak situation, we evaluated a virtual outbreak model using a “virtual outbreak strain; emm74” compared with a non-outbreak group or an “outgroup “ of other emm types. External validation of this model showed an accuracy of 91.4%. Conclusions This approach has the potential to provide meaningful information that can be used in real time to identify and manage GAS outbreaks. Choosing isolates characterized by whole genome sequencing rather than emm typing for model generation should improve the accuracy of this approach in rapidly identifying related and unrelated GAS strains.
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Affiliation(s)
- Manal Tadros
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Division of Microbiology, Unity Health Toronto, Toronto, Ontario, Canada
| | - Ana Cabrera
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.,Division of Microbiology, Pathology and Laboratory Medicine, London Health Sciences Centre, London, Ontario, Canada
| | - Larissa M Matukas
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Division of Microbiology, Unity Health Toronto, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Division of Infectious Diseases, Unity Health Toronto, Toronto, Ontario, Canada
| | - Matthew Muller
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Division of Infectious Diseases, Unity Health Toronto, Toronto, Ontario, Canada
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23
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Krutova M, Wilcox MH, Kuijper EJ. A two-step approach for the investigation of a Clostridium difficile outbreak by molecular methods. Clin Microbiol Infect 2019; 25:1300-1301. [PMID: 31369805 DOI: 10.1016/j.cmi.2019.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/19/2019] [Accepted: 07/20/2019] [Indexed: 11/25/2022]
Affiliation(s)
- M Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD).
| | - M H Wilcox
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD); Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, United Kingdom
| | - E J Kuijper
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD); Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
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Abstract
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing how physicians diagnose and treat infectious disease, with applications spanning a wide range of areas, including antimicrobial resistance, the microbiome, human host gene expression (transcriptomics) and oncology. Here, we focus on the challenges of implementing mNGS in the clinical laboratory and address potential solutions for maximizing its impact on patient care and public health.
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Affiliation(s)
- Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Steven A Miller
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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25
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Blondeau LD, Rubin JE, Deneer H, Kanthan R, Sanche S, Hamula C, Blondeau JM. Forensic, investigative and diagnostic microbiology: similar technologies but different priorities. Future Microbiol 2019; 14:553-558. [PMID: 31148476 DOI: 10.2217/fmb-2019-0088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Joseph E Rubin
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Harry Deneer
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Rani Kanthan
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Stephen Sanche
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Camille Hamula
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
| | - Joseph M Blondeau
- University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Pathology & Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Clinical Microbiology, Royal University Hospital & Saskatchewan Health Authority, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada.,Department of Ophthalmology, University of Saskatchewan, Saskatoon, SK, S7N 0W8, Canada
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An epidemiological and molecular study regarding the spread of vancomycin-resistant Enterococcus faecium in a teaching hospital in Bogotá, Colombia 2016. BMC Infect Dis 2019; 19:258. [PMID: 30876395 PMCID: PMC6419805 DOI: 10.1186/s12879-019-3877-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background Enterococcus faecium is ranked worldwide as one of the top ten pathogens identified in healthcare-associated infections (HAI) and is classified as one of the high priority pathogens for research and development of new antibiotics worldwide. Due to molecular biology techniques’ higher costs, the approach for identifying and controlling infectious diseases in developing countries has been based on clinical and epidemiological perspectives. Nevertheless, after an abrupt vancomycin-resistant Enterococcus faecium dissemination in the Méderi teaching hospital, ending up in an outbreak, further measures needed to be taken into consideration. The present study describes the vancomycin-resistant Enterococcus faecium pattern within Colombian’s largest installed-bed capacity hospital in 2016. Methods Thirty-three vancomycin-resistant Enterococcus faecium isolates were recovered during a 5-month period in 2016. Multilocus variable-number tandem-repeat analysis was used for molecular typing to determine clonality amongst strains. A modified time-place-sequence algorithm was used to trace VREfm spread patterns during the outbreak period and estimate transmission routes. Results Four clonal profiles were identified. Chronological clonal profile follow-up suggested a transitional spread from profile “A” to profile “B”, returning to a higher prevalence of “A” by the end of the study. Antibiotic susceptibility indicated high-level vancomycin-resistance in most isolates frequently matching vanA gene identification. Discussion Transmission analysis suggested cross-contamination via healthcare workers. Despite epidemiological control of the outbreak, post-outbreak isolates were still being identified as having outbreak-related clonal profile (A), indicating reduction but not eradication of this clonality. This study supports the use of combined molecular and epidemiological strategies in an approach to controlling infectious diseases. It contributes towards a more accurate evaluation of the effectiveness of the epidemiological measures taken regarding outbreak control and estimates the main cause related to the spread of this microorganism. Electronic supplementary material The online version of this article (10.1186/s12879-019-3877-7) contains supplementary material, which is available to authorized users.
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