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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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Celik C, Kalin G, Cetinkaya Z, Ildiz N, Ocsoy I. Recent Advances in Colorimetric Tests for the Detection of Infectious Diseases and Antimicrobial Resistance. Diagnostics (Basel) 2023; 13:2427. [PMID: 37510171 PMCID: PMC10377832 DOI: 10.3390/diagnostics13142427] [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: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Diagnosis of infection-causing microorganisms with sensitive, rapid, selective and economical diagnostic tests is critical to start the right treatment. With these tests, the spread of infections can be prevented. In addition to that, the detection of antimicrobial resistance also makes a significant contribution to public health. In recent years, different types of diagnostic tests have been developed as alternatives to traditional diagnostic tests used in clinics. In particular, colorimetric tests, which minimize the need for an instrument, have advantages owing to their cost effectiveness, rapid response and naked-eye detection and practical use. In this review, we especially focused on pH indicators and nanomaterial-based colorimetric tests in detection of infection-causing microorganisms and antimicrobial resistance.
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Affiliation(s)
- Cagla Celik
- Pharmacy Services Program, Vocational School of Health Services, Hitit University, Corum 19000, Turkey
| | - Gamze Kalin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | | | - Nilay Ildiz
- Medical Imaging Department, Vocational School of Health Services, Bandırma Onyedi Eylul University, Bandirma 10200, Turkey
| | - Ismail Ocsoy
- Department of Analytical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [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: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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Jing X, Hu Y, Wu T, Zhang X, Luo S, Wang W, Min X, Sun R, Zeng J. A rapid method for detecting and distinguishing metallo-β-lactamase-and serine carbapenemase-producing Enterobacteriales using MALDI-TOF MS. Front Microbiol 2023; 13:1096987. [PMID: 36713184 PMCID: PMC9880429 DOI: 10.3389/fmicb.2022.1096987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction Carbapenemase-producing Enterobacteriales (CPE) are a major health threat worldwide, and therefore the development of rapid detection methods is needed. Here, we established a method to distinguish metallo-β-lactamase and serine carbapenemases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with ethylenediaminetetraacetic acid (EDTA) and phenylboronic acid (PB). Methods To assess the specificity and sensitivity of the method, 110 carbapenemase-producing and 72 carbapenemase-negative Enterobacteriales isolates were collected, among which 51 strains produced only metallo-β-lactamase, 55 strains only serine carbapenemases, and four strains both metallo-β-lactamase and serine carbapenemases. In the proposed MALDI-TOF MS method, imipenem (IPM) and the bacterial strains to be tested were mixed, EDTA and/or PB was added, and the mixture was incubated for 4 h. The carbapenemase type was confirmed by the IPM waveform spectrum before and after incubation. Results Based on the presence, absence, and recovery of the IPM-cyano-4-hydroxy-cinnamic acid-specific waveform peak near 479 m/z, the detection sensitivity and specificity of the method were 98.2 and 100%, respectively. Discussion Although CPE detection by MALDI-TOF MS has been studied previously, our method distinguishes between metallo-β-lactamase and serine carbapenemases, which will be very helpful for the clinical selection of antibiotics.
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Affiliation(s)
- Xiaopeng Jing
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Yanyan Hu
- Clinical Microbiology Laboratory, School of Medicine, 2nd Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Tingting Wu
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Xing Zhang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Shaofeng Luo
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Wei Wang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Xiaochun Min
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Ruiling Sun
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China
| | - Ji Zeng
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, China,*Correspondence: Ji Zeng,
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Li L, Tan J, Zhang C, Ding X, Wu T, Shi Y, Chen T, Huang C, Qu Y, Zhao Z, Xu Y. One Lead to Numerous: A DNA Concatemer-based Fluorescence Aptasensor for Selective and Sensitive Acinetobacter Baumannii Detection. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bonini A, Carota AG, Poma N, Vivaldi FM, Biagini D, Bottai D, Lenzi A, Tavanti A, Di Francesco F, Lomonaco T. Emerging Biosensing Technologies towards Early Sepsis Diagnosis and Management. BIOSENSORS 2022; 12:894. [PMID: 36291031 PMCID: PMC9599348 DOI: 10.3390/bios12100894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Sepsis is defined as a systemic inflammatory dysfunction strictly associated with infectious diseases, which represents an important health issue whose incidence is continuously increasing worldwide. Nowadays, sepsis is considered as one of the main causes of death that mainly affects critically ill patients in clinical settings, with a higher prevalence in low-income countries. Currently, sepsis management still represents an important challenge, since the use of traditional techniques for the diagnosis does not provide a rapid response, which is crucial for an effective infection management. Biosensing systems represent a valid alternative due to their characteristics such as low cost, portability, low response time, ease of use and suitability for point of care/need applications. This review provides an overview of the infectious agents associated with the development of sepsis and the host biomarkers suitable for diagnosis and prognosis. Special focus is given to the new emerging biosensing technologies using electrochemical and optical transduction techniques for sepsis diagnosis and management.
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Affiliation(s)
- Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Angela Gilda Carota
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Noemi Poma
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Federico Maria Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Denise Biagini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Daria Bottai
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Alessio Lenzi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56100 Pisa, Italy
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tommaso Lomonaco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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Yoon EJ, Jeong SH. MALDI-TOF Mass Spectrometry Technology as a Tool for the Rapid Diagnosis of Antimicrobial Resistance in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10080982. [PMID: 34439032 PMCID: PMC8388893 DOI: 10.3390/antibiotics10080982] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the antimicrobial resistance (AMR) in microorganisms. Primarily, antimicrobial susceptibility testing is able to be carried out either by comparing the area under curve of MALDI spectra of bacteria grown in media with antimicrobial drugs or by identifying the shift peaks of bacteria grown in media including 13C isotope with antimicrobial drugs. Secondly, the antimicrobial resistance is able to be determined through identifying (i) the antimicrobial-resistant clonal groups based on the fingerprints of the clone, (ii) the shift peak of the modified antimicrobial drug, which is inactivated by the resistance determinant, (iii) the shift peak of the modified antimicrobial target, (iv) the peak specific for the antimicrobial determinant, and (v) the biomarkers that are coproduced proteins with AMR determinants. This review aims to present the current usage of the MALDI-TOF MS technique for diagnosing antimicrobial resistance in bacteria, varied approaches for AMR diagnostics using the methodology, and the future applications of the methods for the accurate and rapid identification of AMR in infection-causing bacterial pathogens.
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Affiliation(s)
- Eun-Jeong Yoon
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Korea;
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
- Correspondence:
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Nguyen M, Joshi SG. Carbapenem resistance in Acinetobacter baumannii, and their importance in hospital-acquired infections: a scientific review. J Appl Microbiol 2021; 131:2715-2738. [PMID: 33971055 DOI: 10.1111/jam.15130] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 02/05/2023]
Abstract
Carbapenem is an important therapy for serious hospital-acquired infections and for the care of patients affected by multidrug-resistant organisms, specifically Acinetobacter baumannii; however, with the global increase of carbapenem-resistant A. baumannii, this pathogen has significantly threatened public health. Thus, there is a pressing need to better understand this pathogen in order to develop novel treatments and control strategies for dealing with A. baumannii. In this review, we discuss an overview of carbapenem, including its discovery, development, classification and biological characteristics, and its importance in hospital medicine especially in critical care units. We also describe the peculiarity of bacterial pathogen, A. baumannii, including its commonly reported virulence factors, environmental persistence and carbapenem resistance mechanisms. In closing, we discuss various control strategies for overcoming carbapenem resistance in hospitals and for limiting outbreaks. With the appearance of strains that resist carbapenem, the aim of this review is to highlight the importance of understanding this increasingly problematic healthcare-associated pathogen that creates significant concern in the field of nosocomial infections and overall public health.
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Affiliation(s)
- M Nguyen
- Center for Surgical Infections, Drexel University School of Biomedical Engineering, Science & Health Systems, Philadelphia, PA, USA
| | - S G Joshi
- Center for Surgical Infections, Drexel University School of Biomedical Engineering, Science & Health Systems, Philadelphia, PA, USA.,Institute of Molecular Medicine and Infectious Diseases, Center for Surgical Infections, Drexel University, Philadelphia, PA, USA
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McGee WM, Verma A, Viirtola M, Kronewitter SR, Neil JR, Stephenson JL. Direct detection of OXA-48-like carbapenemase variants with and without co-expression of an extended-spectrum β-lactamase from bacterial cell lysates using mass spectrometry. J Mass Spectrom Adv Clin Lab 2021; 20:25-34. [PMID: 34820668 PMCID: PMC8601005 DOI: 10.1016/j.jmsacl.2021.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Antibiotic-resistant Gram-negative bacteria are of a growing concern globally, especially those producing enzymes conferring resistance. OXA-48-like carbapenemases hydrolyze most β-lactam antibiotics, with typically low-level hydrolysis of carbapenems, but have limited effect on broad-spectrum cephalosporins. These are frequently co-expressed with extended spectrum β-lactamases, especially CTX-M-15, which typically shows high level resistance to broad-spectrum cephalosporins, yet is carbapenem susceptible. The combined resistance profile makes the need for successful detection of these specific resistance determinants imperative for effective antibiotic therapy. OBJECTIVES The objective of this study is to detect and identify OXA-48-like and CTX-M-15 enzymes using mass spectrometry, and to subsequently develop a method for detection of both enzyme types in combination with liquid chromatography. METHODS Cells grown in either broth or on agar were harvested, lysed, and, in some cases buffer-exchanged. Lysates produced from bacterial cells were separated and analyzed via liquid chromatography with mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS). RESULTS The intact proteins of OXA-48, OXA-181, and OXA-232 (collectively OXA-48-like herein) and CTX-M-15 were characterized and detected. Acceptance criteria based on sequence-informative fragments from each protein group were established as confirmatory markers for the presence of the protein(s). A total of 25 isolates were successfully tested for OXA-48 like (2), CTX-M-15 (3), or expression of both (7) enzymes. Thirteen isolates served as negative controls. CONCLUSIONS Here we present a method for the direct and independent detection of both OXA-48-like carbapenemases and CTX-M-15 β-lactamases using LC-MS/MS. The added sensitivity of MS/MS allows for simultaneous detection of at least two co-eluting, co-isolated and co-fragmented proteins from a single mass spectrum.
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Key Words
- ATCC, American Type Culture Collection
- Antimicrobial-resistant organisms
- CDC, Centers for Disease Control and Prevention
- CPO, carbapenemase-producing organism
- CRE, carbapenem-resistant Enterobacterales
- CSD, charge state distribution
- CTX-M-15
- Carbapenem-resistant Enterobacterales
- Carbapenemase
- Carbapenemase-producing organisms
- ESBL, extended-spectrum β-lactamase
- ESI, electrospray ionization
- LC, liquid chromatography
- Liquid chromatography
- MALDI, matrix-assisted laser desorption ionization
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- Mass Spectrometry
- OXA-48
- OXA-48-like
- PCR, polymerase chain reaction
- TOF, time-of-flight (mass spectrometry)
- Tandem mass spectrometry
- m/z, mass-to-charge ratio
- β-Lactamase
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Sharma M, Singhal L, Gautam V, Ray P. Distribution of carbapenemase genes in clinical isolates of Acinetobacter baumannii & a comparison of MALDI-TOF mass spectrometry-based detection of carbapenemase production with other phenotypic methods. Indian J Med Res 2021; 151:585-591. [PMID: 32719232 PMCID: PMC7602923 DOI: 10.4103/ijmr.ijmr_1383_18] [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] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Background & objectives: Carbapenemase-producing Acinetobacter baumannii (CRAB) poses a continuous threat to the current antimicrobial era with its alarming spread in critical care settings. The present study was conducted to evaluate the diagnostic potential of phenotypic methods for carbapenemase [carbapenem-hydrolyzing class D β-lactamases (CHDLs) and metallo-β-lactamases (MBLs)] production, by comparing with molecular detection of genes. Methods: One hundred and fifty clinical CRAB isolates collected between August 2013 and January 2014 were studied. Multiplex PCR was performed to identify the carbapenemases produced (class D blaOXA-51, blaOXA-23, blaOXA-48,blaOXA-58; class B blaVIM, blaNDM-1, blaIMP; class A blaKPC). Each isolate was evaluated for carbapenemase production by studying the pattern of imipenem hydrolysis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results: The most commonly encountered carbapenemase genes were blaOXA-51 (100%), blaOXA-23 (98%), blaVIM (49.3%), blaNDM-1 (18.7%) and blaOXA-58 (2%). MALDI-TOF MS was able to detect 30.6 per cent carbapenemases within three hours (P=0.001 for MBL and P>0.05 for CHDL) and 65.3 per cent within six hours (P=0.001 for MBL and P>0.05 for CHDL). Interpretation & conclusions: MALDI-TOF MS reliably detected carbapenemase activity within a short span of time, thus helping in tailoring patient therapy. MALDI-TOF MS, once optimized, can prove to be a useful tool for timely detection of carbapenemase production by A. baumannii and consequently in directing appropriate antimicrobial therapy.
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Affiliation(s)
- Megha Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Unresolved issues in the identification and treatment of carbapenem-resistant Gram-negative organisms. Curr Opin Infect Dis 2020; 33:482-494. [PMID: 33009141 DOI: 10.1097/qco.0000000000000682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Carbapenem-resistant organisms (CROs), including Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacterales, are a threat worldwide. This review will cover mechanisms of resistance within CROs and challenges with identification and treatment of these organisms while pointing out unresolved issues and ongoing challenges. RECENT FINDINGS The treatment of CROs has expanded through newer therapeutic options. Guided utilization through genotypic and phenotypic testing is necessary in order for these drugs to target the appropriate mechanisms of resistance and select optimal antibiotic therapy. SUMMARY Identification methods and treatment options need to be precisely understood in order to limit the spread and maximize outcomes of CRO infections.
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García-Betancur JC, Appel TM, Esparza G, Gales AC, Levy-Hara G, Cornistein W, Vega S, Nuñez D, Cuellar L, Bavestrello L, Castañeda-Méndez PF, Villalobos-Vindas JM, Villegas MV. Update on the epidemiology of carbapenemases in Latin America and the Caribbean. Expert Rev Anti Infect Ther 2020; 19:197-213. [PMID: 32813566 DOI: 10.1080/14787210.2020.1813023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Carbapenemases are β-lactamases able to hydrolyze a wide range of β-lactam antibiotics, including carbapenems. Carbapenemase production in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter spp., with and without the co-expression of other β-lactamases is a serious public health threat. Carbapenemases belong to three main classes according to the Ambler classification: class A, class B, and class D. AREAS COVERED Carbapenemase-bearing pathogens are endemic in Latin America. In this review, we update the status of carbapenemases in Latin America and the Caribbean. EXPERT OPINION Understanding the current epidemiology of carbapenemases in Latin America and the Caribbean is of critical importance to improve infection control policies limiting the dissemination of multi-drug-resistant pathogens and in implementing appropriate antimicrobial therapy.
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Affiliation(s)
| | - Tobias Manuel Appel
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque . Bogotá, Colombia
| | - German Esparza
- Programa de Aseguramiento de Calidad. PROASECAL SAS, Bogotá, Colombia
| | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP , São Paulo, Brazil
| | | | | | - Silvio Vega
- Complejo Hospitalario Metropolitano , Ciudad de Panamá, Panama
| | - Duilio Nuñez
- Infectious Diseases División, IPS Hospital Central , Asunción, Paraguay
| | - Luis Cuellar
- Servicio de Infectologia, Instituto Nacional de Enfermedades Neoplasicas , Lima, Peru
| | | | - Paulo F Castañeda-Méndez
- Department of Infectious Diseases, Hospital San Angel Inn Universidad , Ciudad de México, Mexico
| | | | - María Virginia Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque . Bogotá, Colombia.,Centro Médico Imbanaco . Cali, Colombia
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13
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Direct detection of intact Klebsiella pneumoniae carbapenemase variants from cell lysates: Identification, characterization and clinical implications. CLINICAL MASS SPECTROMETRY 2020; 17:12-21. [PMID: 34820520 DOI: 10.1016/j.clinms.2020.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022]
Abstract
Introduction Carbapenemase-producing organisms (CPOs) are a growing threat to human health. Among the enzymes conferring antibiotic resistance produced by these organisms, Klebsiella pneumoniae carbapenemase (KPC) is considered to be a growing global health threat. Reliable and specific detection of this antibiotic resistance-causing enzyme is critical both for effective therapy and to mitigate further spread. Objectives The objective of this study is to develop an intact protein mass spectrometry-based method for detection and differentiation of clinically-relevant KPC variants directly from bacterial cell lysates. The method should be specific for any variant expressed in multiple bacterial species, limit false positive results and be rapid in nature to directly influence clinical outcomes. Methods Lysates obtained directly from bacterial colonies were used for intact protein detection using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Bottom-up and top-down proteomic methods were used to characterize the KPC protein targets of interest. Comparisons between KPC-producing and KPC-non-producing isolates from a wide variety of species were also performed. Results Characterization of the mature KPC protein revealed an unexpected signal peptide cleavage site preceding an AXA signal peptide motif, modifying the molecular weight (MW) of the mature protein. Taking the additional AXA residues into account allowed for direct detection of the intact protein using top-down proteomic methods. Further validation was performed by transforming a KPC-harboring plasmid into a negative control strain, followed by MS detection of the KPC variant from the transformed cell line. Application of this approach to clearly identify clinically-relevant variants among several species is presented for KPC-2, KPC-3, KPC-4 and KPC-5. Conclusion Direct detection of these enzymes contributes to the understanding of occurrence and spread of these antibiotic-resistant organisms. The ability to detect intact KPC variants via a simple LC-MS/MS approach could have a direct and positive impact on clinical therapy, by providing both direction for epidemiological tracking and appropriate therapy.
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Key Words
- ATCC, American type culture collection
- BLAST, basic local alignment search tool
- CDC, Centers for Disease Control and Prevention
- CPO, carbapenemase-producing organisms
- CSD, charge state distribution
- Carbapenem-resistant Enterobacteriaceae
- Carbapenemase-producing organisms
- ESI, electrospray ionization
- KPC, Klebsiella pneumoniae carbapenemase
- Klebsiella pneumoniae carbapenemase
- LC, liquid chromatography
- MALDI, matrix-assisted laser desorption ionization
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- Mass Spectrometry
- PCR, polymerase chain reaction
- TOF, time-of-flight
- Tandem mass spectrometry
- m/z, mass-to-charge ratio
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Roushani M, Sarabaegi M, Rostamzad A. Novel electrochemical sensor based on polydopamine molecularly imprinted polymer for sensitive and selective detection of Acinetobacter baumannii. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-01936-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Huang TS, Lee SSJ, Lee CC, Chang FC. Detection of carbapenem-resistant Klebsiella pneumoniae on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using supervised machine learning approach. PLoS One 2020; 15:e0228459. [PMID: 32027671 PMCID: PMC7004327 DOI: 10.1371/journal.pone.0228459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a significant pathogen causing healthcare-associated infections. Matrix-assisted laser desorption/ionisation mass spectrometry time-of-flight mass spectrometry (MALDI-TOF MS) is used by clinical microbiology laboratories to address the need for rapid, cost-effective and accurate identification of microorganisms. We evaluated application of machine learning methods for differentiation of drug resistant bacteria from susceptible ones directly using the profile spectra of whole cells MALDI-TOF MS in 46 CRKP and 49 CSKP isolates. METHODS We developed a two-step strategy for data preprocessing consisting of peak matching and a feature selection step before supervised machine learning analysis. Subsequently, five machine learning algorithms were used for classification. RESULTS Random forest (RF) outperformed other four algorithms. Using RF algorithm, we correctly identified 93% of the CRKP and 100% of the CSKP isolates with an overall classification accuracy rate of 97% when 80 peaks were selected as input features. CONCLUSIONS We conclude that CRKPs can be differentiated from CSKPs through RF analysis. We used direct colony method, and only one spectrum for an isolate for analysis, without modification of current protocol. This allows the technique to be easily incorporated into clinical practice in the future.
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Affiliation(s)
- Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Susan Shin-Jung Lee
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Chien Lee
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Fu-Chuen Chang
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung, Taiwan
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16
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Welker M, van Belkum A. One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing? Front Microbiol 2019; 10:2711. [PMID: 31849870 PMCID: PMC6901965 DOI: 10.3389/fmicb.2019.02711] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely – still, the same was true for routine microbial identification a mere 15 years ago.
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Affiliation(s)
- Martin Welker
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| | - Alex van Belkum
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
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17
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A Rapid ATP Bioluminescence-based Test for Detecting Levofloxacin Resistance Starting from Positive Blood Culture Bottles. Sci Rep 2019; 9:13565. [PMID: 31578343 PMCID: PMC6775087 DOI: 10.1038/s41598-019-49358-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023] Open
Abstract
Administering appropriate antimicrobial therapy as early as possible is important for rescuing bacteremic patients. Therefore, rapid antimicrobial susceptibility tests in positive blood culture specimens have been diligently sought. Adenosine triphosphate (ATP) bioluminescence-based methods have been used for rapid antimicrobial susceptibility tests. However, blood culture specimens have not been examined in many studies, possibly due to abundant intracellular ATP in blood corpuscles resulting in false-susceptible results. In this study, we developed a rapid ATP bioluminescence-based method for detecting antibiotic resistance starting from positive blood culture. To minimize background ATP originating from blood corpuscles, specimens were centrifuged and the supernatant diluted with broth, and an ATP-eliminating reagent was then added to the bacterial suspension at the beginning of incubation. This newly devised procedure reduced the background ATP by more than five orders of magnitude. In a pilot study using levofloxacin, no false-susceptible results were observed in 15 clinical specimens. Furthermore, the results indicated that the rapid method provided additional information about bacterial activities with high resolution, in contrast to the less-thorough findings with the conventional turbidity method. Therefore, our approach will contribute to the treatment of infectious diseases as a rapid antimicrobial susceptibility test.
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18
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Neonakis IK, Spandidos DA. Detection of carbapenemase producers by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). Eur J Clin Microbiol Infect Dis 2019; 38:1795-1801. [PMID: 31254128 DOI: 10.1007/s10096-019-03620-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been recently applied in detection of carbapenemase-producing Gram-negative isolates. In the present study, we review the latest developments in this field.
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Affiliation(s)
- Ioannis K Neonakis
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, 71201, Heraklion, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003, Heraklion, Greece
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Anantharajah A, Tossens B, Olive N, Kabamba-Mukadi B, Rodriguez-Villalobos H, Verroken A. Performance Evaluation of the MBT STAR ®-Carba IVD Assay for the Detection of Carbapenemases With MALDI-TOF MS. Front Microbiol 2019; 10:1413. [PMID: 31281303 PMCID: PMC6596351 DOI: 10.3389/fmicb.2019.01413] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Objectives: The increasing rate of carbapenem resistance in Gram-negative bacteria is a major public health problem and rapid detection is essential for infection management. We evaluated the performances of the MBT STAR®-Carba IVD assay (Bruker Daltonics) to detect carbapenemase-producing organisms (CPO) from bacterial colonies and directly from positive blood culture bottles with MALDI-TOF MS. Methods: We analyzed 130 strains with a reduced susceptibility to at least one carbapenem including 109 CPO (6 KPC, 27 NDM, 21 VIM, 1 IMP, 41 OXA-48-like, 8 OXA-23, 2 OXA-24/-40, and 2 OXA-58) and 21 non-CPO. The assay on colonies was performed with all 130 strains while the assay on spiked blood cultures was performed with 45 strains. Samples were prepared with the MBT STAR®-CARBA IVD kit and imipenem hydrolysis by the potential carbapenemase was analyzed with the MBT STAR®-BL module (Bruker Daltonics) on MALDI-TOF MS. Results: Performed on colonies, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 78), Pseudomonas spp. (n = 19) and Acinetobacter spp. (n = 12). All 21 tested non-CPO remained negative resulting in sensitivity and specificity of 100%. Performed on positive blood cultures, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 23) and Pseudomonas spp. (n = 4) but missed 9/12 carbapenemase-producing Acinetobacter spp. However, a prolonged imipenem-incubation time of the strain pellet improved carbapenemase detection. Non-CPO from positive blood culture bottles remained negative (n = 5) with the assay with the exception of one Klebsiella pneumoniae isolate. Conclusion: The MBT STAR®-Carba IVD assay is a highly reliable method for the detection of carbapenemase activity in Gram-negative bacteria. However, time-consuming sample preparation steps and reagent costs need to be considered before implementation in a routine clinical microbiology laboratory.
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Affiliation(s)
- Ahalieyah Anantharajah
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Bastien Tossens
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Nathalie Olive
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Benoit Kabamba-Mukadi
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Hector Rodriguez-Villalobos
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Alexia Verroken
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
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20
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Hadjadj L, Baron SA, Diene SM, Rolain JM. How to discover new antibiotic resistance genes? Expert Rev Mol Diagn 2019; 19:349-362. [PMID: 30895843 DOI: 10.1080/14737159.2019.1592678] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.
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Affiliation(s)
- Linda Hadjadj
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Sophie Alexandra Baron
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Seydina M Diene
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Jean-Marc Rolain
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France.,b IHU Méditerranée Infection , Marseille , France
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Abstract
Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.
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Affiliation(s)
- Donna M Wolk
- Clinical Microbiology, Department of Laboratory Medicine, Diagnostic Medicine Institute, Geisinger Health, 100 North Academy Avenue, Danville, PA 17822-1930, USA.
| | - Andrew E Clark
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA
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22
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NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings. Clin Microbiol Rev 2019; 32:32/2/e00115-18. [PMID: 30700432 DOI: 10.1128/cmr.00115-18] [Citation(s) in RCA: 371] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase able to hydrolyze almost all β-lactams. Twenty-four NDM variants have been identified in >60 species of 11 bacterial families, and several variants have enhanced carbapenemase activity. Klebsiella pneumoniae and Escherichia coli are the predominant carriers of bla NDM, with certain sequence types (STs) (for K. pneumoniae, ST11, ST14, ST15, or ST147; for E. coli, ST167, ST410, or ST617) being the most prevalent. NDM-positive strains have been identified worldwide, with the highest prevalence in the Indian subcontinent, the Middle East, and the Balkans. Most bla NDM-carrying plasmids belong to limited replicon types (IncX3, IncFII, or IncC). Commonly used phenotypic tests cannot specifically identify NDM. Lateral flow immunoassays specifically detect NDM, and molecular approaches remain the reference methods for detecting bla NDM Polymyxins combined with other agents remain the mainstream options of antimicrobial treatment. Compounds able to inhibit NDM have been found, but none have been approved for clinical use. Outbreaks caused by NDM-positive strains have been reported worldwide, attributable to sources such as contaminated devices. Evidence-based guidelines on prevention and control of carbapenem-resistant Gram-negative bacteria are available, although none are specific for NDM-positive strains. NDM will remain a severe challenge in health care settings, and more studies on appropriate countermeasures are required.
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Impacts and Challenges of Advanced Diagnostic Assays for Transplant Infectious Diseases. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7121269 DOI: 10.1007/978-1-4939-9034-4_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advanced technologies described in this chapter should allow for full inventories to be made of bacterial genes, their time- and place-dependent expression, and the resulting proteins as well as their outcome metabolites. The evolution of these molecular technologies will continue, not only in the microbial pathogens but also in the context of host-pathogen interactions targeting human genomics and transcriptomics. Their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.
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Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
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Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
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25
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
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26
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Tadros M, Goneau L, Romaschin A, Jarvis M, Matukas L. Rapid detection of resistance to carbapenems and cephalosporins in Enterobacteriaceae using liquid chromatography tandem mass spectrometry. PLoS One 2018; 13:e0206842. [PMID: 30412608 PMCID: PMC6226185 DOI: 10.1371/journal.pone.0206842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
Carbapenemase producing Enterobacteriaceae (CPE) are becoming a global healthcare concern. Current laboratory methods for the detection of CPE include screening followed by confirmatory phenotypic and genotypic tests. These processes would generally take ≥72 hours, which could negatively impact patient care and Infection Control practices. To this end, we developed a protocol for rapid resistance testing (RRT) to detect hydrolysis in a panel of beta lactam antibiotics consisting of ampicillin, cefazolin, cefotaxime and imipenem, using liquid chromatography tandem mass spectrometry. Ninety—nine beta lactamase producing Enterobacteriaceae isolates were used to evaluate the RRT method, 54 isolates were CPE and 45 isolates were Class A or AmpC beta lactamase producing Enterobacteriaceae but not carbapenemase producers. We also tested 10 E.coli isolates that were susceptible to ampicillin, cefazolin, cefotaxime and imipenem. Receiver Operating Characteristic (ROC) Curves analysis showed that imipenem had a sensitivity and a specificity of 100% for crabapenemase detection at hydrolysis cut off values that are greater than 50% and less than or equal to 80%. The RRT protocol can be conducted in a time frame of less than 2 hours. This preliminary study shows that the rapid resistance testing protocol might have utility for the rapid detection of CPE. Additional work with a greater number and variety of beta- lactamase producing Enterobacteriaceae isolates is required to validate these preliminary findings.
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Affiliation(s)
- Manal Tadros
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, St. Michael’s Hospital, Toronto, Ontario, Canada
- * E-mail:
| | - Lee Goneau
- Department of Microbiology, Public Health Ontario, Toronto, Ontario, Canada
| | | | | | - Larissa Matukas
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, St. Michael’s Hospital, Toronto, Ontario, Canada
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Chabriere E, Bassène H, Drancourt M, Sokhna C. MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa. New Microbes New Infect 2018; 26:S83-S88. [PMID: 30402248 PMCID: PMC6205576 DOI: 10.1016/j.nmni.2018.08.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients.
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Affiliation(s)
- E. Chabriere
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Bassène
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
| | - M. Drancourt
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
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28
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Peyclit L, Chanteloup A, Hadjadj L, Rolain JM. Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries. New Microbes New Infect 2018; 26:S52-S64. [PMID: 30402244 PMCID: PMC6205572 DOI: 10.1016/j.nmni.2018.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Surveillance of antibiotic resistance has become a public global concern after the rapid worldwide dissemination of several antibiotic resistance genes. Here we report the role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries. Since the creation of the institute, 95 students and researchers have come from 19 different countries from these areas to characterize 6359 bacterial isolates from 7280 samples from humans (64%), animals (28%) and the environment (8%). Most bacterial isolates studied were Gram-negative bacteria (n = 5588; 87.9%), mostly from Algeria (n = 4190), Lebanon (n = 946), Greece (n = 610), Saudi Arabia (n = 299) and Senegal (n = 278). Antibiotic resistance was diversified with the detection and characterization of extended-spectrum β-lactamases, carbapenemases and resistance to colistin, vancomycin and methicillin. All those studies led to 97 indexed international scientific papers. Over the last 6 years, our institute has created a huge network of collaborations by training students that plays a major role in the surveillance of resistance to antibiotics in these countries.
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Affiliation(s)
| | | | | | - J.-M. Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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Phenotypic Detection of Carbapenemase-Producing Organisms from Clinical Isolates. J Clin Microbiol 2018; 56:JCM.01140-18. [PMID: 30158194 DOI: 10.1128/jcm.01140-18] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The rapid spread of multidrug-resistant Gram-negative organisms constitutes one of the greatest challenges to global health. While Gram-negative organisms have developed several mechanisms to avert the bactericidal effects of commonly prescribed antibiotic agents, the increasing prevalence of carbapenemase-producing organisms (CPO) is particularly concerning given the rapid spread of mobile genetic elements containing carbapenemase genes, the limited treatment options for infections caused by these organisms, and the high mortality rates associated with CPO infections. Understanding if an organism is carbapenemase producing and, if so, the class of carbapenemase(s) produced has treatment implications, as some agents preferentially have activity against specific carbapenemases. Furthermore, CPO disseminate between patients with greater ease than non-CP-carbapenem-resistant organisms and warrant more intensive infection control measures than would be employed in the absence of carbapenemase production. Phenotypic assays currently used in clinical practice to detect CPO consist of the following: (i) growth-based assays which measure carbapenem resistance based on organism growth in the presence of a carbapenem antibiotic (e.g., modified Hodge test and modified carbapenem inactivation method), (ii) hydrolysis methods which detect carbapenem degradation products (e.g., Carba NP test and matrix-assisted laser desorption-ionization time of flight mass spectrometry), and (iii) lateral flow immunoassays which detect carbapenemase enzymes through the use of specific antibodies. Although there is no single phenotypic test that meets all specifications of the ideal test, as we describe in this review, there are a number of tests that are user-friendly, affordable, accurate, and feasible for implementation in clinical microbiology laboratories of all sizes.
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Pellegrino FLPC, Chagas TPG, Alves MS, Carvalho-Assef APD, Chapeaurouge A, Asensi MD. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Applications in Bacteriology: brazilian contributions. HU REVISTA 2018. [DOI: 10.34019/1982-8047.2017.v43.2859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.
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Leulmi Z, Kandouli C, Mihoubi I, Benlabed K, Lezzar A, Rolain JM. First report of bla OXA-24 carbapenemase gene, armA methyltransferase and aac(6')-Ib-cr among multidrug-resistant clinical isolates of Proteus mirabilis in Algeria. J Glob Antimicrob Resist 2018; 16:125-129. [PMID: 30217548 DOI: 10.1016/j.jgar.2018.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Carbapenemase-producing, or carbapenem-resistant, Enterobacteriaceae are an emerging threat to human and animal health because they are resistant to many of the last-line antimicrobials available for treatment of infection. The aim of this study was to analyse the antimicrobial resistance patterns and their encoding genes of Proteus mirabilis isolated in Constantine, Algeria. METHODS A total of 108 Proteus, Morganella and Providencia (PMP) strains were isolated from a large variety of clinical specimens at University Hospital of Constantine in Algeria. Isolates were identified using the API 20E system and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Diagnostic accuracy was determined by independent comparison of each method to phylogenetic analysis based on 16S rRNA gene sequencing. Antimicrobial susceptibility was determined by the standard disk diffusion and Etest methods. The presence of antimicrobial resistance genes was screened for by PCR amplification and sequencing. RESULTS A total of 72 PMP strains were multidrug-resistant (MDR). Among them, one P. mirabilis isolate was resistant to imipenem with a minimum inhibitory concentration (MIC) of ≥12μg/mL. PCR and sequencing showed the presence of various antimicrobial resistance genes, including blaCTX-M-15, blaTEM-1, blaTEM-2, blaPER-1, blaSHV-11, aadA1, aadA2, armA, aac(6')-Ib, aac(6')-Ib-cr, aac(3)-Ia and ant(2″)-I, forming different resistance profiles. Moreover, the blaOXA-24 gene was detected in the imipenem-resistant P. mirabilis strain. CONCLUSION In this study, a MDR P. mirabilis isolate harbouring the blaOXA-24, armA 16S rRNA methylase and aac(6)-Ib-cr genes was found for the first time in Algeria.
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Affiliation(s)
- Zineb Leulmi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, URMITE CNRS-IRD, UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France; Laboratoire Microbiologie, CHU de Constantine, Constantine, Algeria
| | - Chouaib Kandouli
- Laboratoire de Biologie et Environnement, Faculté des Sciences de la Nature et de la Vie, Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | - Ilhem Mihoubi
- Laboratoire de Mycologie, Biotechnologie et de l'Activité Microbienne, Faculté des Sciences de la Nature et de la Vie, Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | - Kaddour Benlabed
- Laboratoire Microbiologie, CHU de Constantine, Constantine, Algeria
| | - Abdeslam Lezzar
- Laboratoire Microbiologie, CHU de Constantine, Constantine, Algeria
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, URMITE CNRS-IRD, UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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Schuster D, Josten M, Janssen K, Bodenstein I, Albert C, Schallenberg A, Gajdiss M, Sib E, Szekat C, Kehl K, Parčina M, Hischebeth GT, Bierbaum G. Detection of methicillin-resistant coagulase-negative staphylococci harboring the class A mec complex by MALDI-TOF mass spectrometry. Int J Med Microbiol 2018; 308:522-526. [DOI: 10.1016/j.ijmm.2018.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/25/2018] [Accepted: 05/07/2018] [Indexed: 11/28/2022] Open
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Li C, Ding S, Huang Y, Wang Z, Shen J, Ling H, Xu Y. Detection of AmpC β-lactamase-producing Gram-negative bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Hosp Infect 2018; 99:200-207. [DOI: 10.1016/j.jhin.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/29/2022]
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Agoba EE, Govinden U, Peer AKC, Osei Sekyere J, Essack SY. ISAba1 Regulated OXA-23 Carbapenem Resistance in Acinetobacter baumannii Strains in Durban, South Africa. Microb Drug Resist 2018; 24:1289-1295. [PMID: 29653481 DOI: 10.1089/mdr.2017.0172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIM This study investigated the molecular mechanisms of resistance to carbapenems and cephalosporins in 24 consecutive, multidrug-resistant Acinetobacter baumannii (MDRAB) isolates collected between January and April 2015 by a private sector laboratory in Durban, South Africa. RESULTS All isolates were resistant to all carbapenems tested. blaOXA-23 and blaOXA-51 genes were found in 23 isolates, while blaOXA-24, blaOXA-48, and blaOXA-58 were absent in all isolates. The most prevalent extended-spectrum β-lactamase was TEM-116 (92%). blaADC was present in 83.3% of isolates, of which two were new variants with three and five amino acid differences compared to Acinetobacter-derived cephalosporinase (ADC)-1, the first at positions 64E → K, 341N → T, and 342R → G and the second at positions 24G → D, 167S → P, 283R → F, 341N → T, and 342R → G, respectively. All isolates were negative for blaPER, blaCMY, blaGES, blaKPC, blaCTX-M, and blaSHV. Metallo-β-lactamase IMP and VIM were absent in all isolates, and NDM-1 was present in 1 isolate. ISAba1 was located upstream blaOXA-23 in all isolates and upstream blaADC (30, 78, 79, 87 and the ADC variants) in 54.2% of the ADC-carrying isolates. None of the isolates had ISAba1 inserted upstream blaOXA-51 gene. Four isolates were clonally related and showed two clusters (A and B), while 20 isolates remained unclustered. There was no direct relationship between the clusters and the hospitals they were isolated from. CONCLUSIONS This study reports the first NDM-1-producing carbapenem resistant Acinetobacter baumannii isolate in South Africa and highlights the presence of OXA-23, the known ADCs (ADC-30, ADC-78, ADC-79, and ADC-87), and two new ADC variants associated with ISAba1 from the private health sector in Durban, South Africa. The complexity and diversity of MDRAB severely limit treatment options.
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Affiliation(s)
- Esther Eyram Agoba
- 1 Antimicrobial Research Unit, Discipline of Pharmaceutical Sciences, University of KwaZulu , Natal, Durban, South Africa
| | - Usha Govinden
- 1 Antimicrobial Research Unit, Discipline of Pharmaceutical Sciences, University of KwaZulu , Natal, Durban, South Africa
| | | | - John Osei Sekyere
- 1 Antimicrobial Research Unit, Discipline of Pharmaceutical Sciences, University of KwaZulu , Natal, Durban, South Africa
| | - Sabiha Yusuf Essack
- 1 Antimicrobial Research Unit, Discipline of Pharmaceutical Sciences, University of KwaZulu , Natal, Durban, South Africa
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Chang KC, Chung CY, Yeh CH, Hsu KH, Chin YC, Huang SS, Liu BR, Chen HA, Hu A, Soo PC, Peng WP. Direct detection of carbapenemase-associated proteins of Acinetobacter baumannii using nanodiamonds coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2018; 147:36-42. [PMID: 29499232 DOI: 10.1016/j.mimet.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 12/25/2022]
Abstract
The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR assays need only a few hours but due to its specificity, can only detect known genetic targets encoding carbapenem-resistance genes. Therefore, new approaches to detect carbapenemase-producing A. baumannii are of great importance. Here, we have developed a rapid and novel method using detonation nanodiamonds (DNDs) as a platform for concentration and extraction of A. baumannii carbapenemase-associated proteins prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS) analysis. To concentrate and extract the A. baumannii carbapenemase-associated proteins, we tested several protein precipitation conditions and found a 0.5% trifluoroacetic acid (TFA) solution within the bacterial suspension could result in strong ion signals with DNDs. A total of 66 A. baumannii clinical-isolates including 51 carbapenem-resistant strains and 15 carbapenem-susceptible strains were tested. Our result showed that among the 51 carbapenem-resistant strains 49 strains had a signal at m/z ~40,279 (±87); among the 15 carbapenem-susceptible strains, 4 strains showed a signal at m/z ~40,279. With on-diamond digestion, we confirmed that the captured protein at m/z ~40,279 was related to ADC family extended-spectrum class C beta-lactamase, from A. baumannii. Using this ADC family protein as a biomarker (m/z ~ 40,279) for carbapenem susceptibility testing of A. baumannii, the sensitivity and the specificity could reach 96% and 73% as compared to traditional imipenem susceptibility testing (MIC results). However, the sensitivity and specificity of this method reached 100% as compared to polymerase chain reaction (PCR) result. Our approach could directly detect the carbapenemase-associated proteins of A. baumannii within 90 min and does not require addition of carbapenemase substrate which is required in the MHT or other mass spectrometric methods. For future applications, our method could be efficiently used in the detection of other carbapenemase-producing bacteria.
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Affiliation(s)
- Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan; Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Chin-Yi Chung
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Hsing Yeh
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Kuo-Hsiu Hsu
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Ya-Ching Chin
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Sin-Siang Huang
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Bo-Rong Liu
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Hsi-An Chen
- Department of Physics, National Dong Hwa University, Hualien, Taiwan
| | - Anren Hu
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Hualien, Taiwan.
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Miltgen G, Plésiat P, Mille A, Chatelain P, Fournier D. Detection of carbapenemase activity in Pseudomonas aeruginosa by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). J Microbiol Methods 2018; 145:66-68. [DOI: 10.1016/j.mimet.2017.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 11/29/2022]
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Oviaño M, Ramírez CDLL, Barbeyto LP, Bou G. Rapid direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples by MALDI-TOF MS analysis. J Antimicrob Chemother 2018; 72:1350-1354. [PMID: 28119478 DOI: 10.1093/jac/dkw579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/15/2016] [Indexed: 11/12/2022] Open
Abstract
Objectives Development of an automated MALDI-TOF MS-based method for the rapid, direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples within 90 min of sample reception. Methods A total of 3041 urine samples were processed by flow cytometry, and a cut-off value of ≥1.5 × 10 5 bacteria/mL was used to select samples for the study. Following these criteria, 608 samples were selected for direct bacterial identification. Detection of carbapenemase activity by MALDI-TOF MS analysis was only performed after reliable direct identification of Gram-negative bacilli. A novel protocol was developed for extracting bacteria from urine samples by using the Sepsityper Kit (Bruker Daltonik, Germany). Carbapenem resistance was detected with imipenem as an antibiotic marker and the results were automatically interpreted using the STAR-BL module of MALDI-TOF Biotyper Compass software (Bruker Daltonik, Germany). Results The MALDI-TOF MS-based assay yielded direct reliable identification of 91% (503/553) of the samples. The assay showed 100% sensitivity (30/30) and specificity (454/454) for detecting carbapenemase activity within 90 min of sample reception. Isolates included in the study were further characterized by PCR and sequencing, and bla OXA-48 was detected from all isolates that tested positive in the MALDI-TOF MS-based resistance assay. Conclusions The proposed protocol for the direct analysis of urine samples by MALDI-TOF MS is suitable for use in clinical laboratories to identify bacteria and detect carbapenemase activity, thus saving at least 24-48 h relative to current routine methods.
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Comparison of MALDI-ToF MS with the Rapidec Carba NP test for the detection of carbapenemase-producing Enterobacteriaceae. Eur J Clin Microbiol Infect Dis 2017; 37:149-155. [PMID: 28980084 DOI: 10.1007/s10096-017-3115-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
Although carbapenemase-producing Enterobacteriaceae (CPE) have become a serious public health issue, their detection remains challenging. The aim of this study was to implement a test based on imipenem hydrolysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS), using 65 strains producing or not a carbapenemase. Then, we compared its performance to that of the Rapidec Carba NP test using 20 additional strains. The MS-based test effectively discriminated between CPE and other non-carbapenem-susceptible strains compared to the Rapidec Carba NP test (sensitivity 100% and 92%, specificity 94% and 92%, respectively). The MS-based test gave less difficulty in interpretation than the colorimetric Rapidec Carba NP test. MALDI-ToF gave a result in less than one hour and limited the use of expensive molecular assays. In conclusion, the hydrolysis test based on MALDI-ToF MS can detect clinically relevant CPE isolates in routine practice. This technology, also described to screen for carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii complex strains, also seems to be interesting in routine practice for these pathogens.
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Comparison of imipenem and meropenem antibiotics for the MALDI-TOF MS detection of carbapenemase activity. J Microbiol Methods 2017; 137:30-33. [DOI: 10.1016/j.mimet.2017.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 11/18/2022]
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Evaluation of a modified meropenem hydrolysis assay on a large cohort of KPC and VIM carbapenemase-producing Enterobacteriaceae. PLoS One 2017; 12:e0174908. [PMID: 28384185 PMCID: PMC5383100 DOI: 10.1371/journal.pone.0174908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/27/2017] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. The introduction of rapid and sensitive methods for the detection of carbapenemase-producing bacteria is of increasing importance. The carbapenemase production can be detected using non-molecular methods (such as the modified Hodge test, the synergy test, the Carba NP test and the antibiotic hydrolysis assays) and DNA-based methods. In this study, we propose a modified version of a previously described meropenem hydrolysis assay (MHA) by MALDI-TOF MS for the phenotypic detection in 2h of carbapenemase-producing Enterobacteriaceae. The MHA was successfully applied to detect carbapenemase activity in 981 well-characterized Enterobacteriaceae strains producing KPC or VIM carbapenemases, and in 146 carbapenem fully susceptible strains. This assay, applied also to NDM and OXA-48-producing strains and to CRE with resistance mechanisms other than carbapenemase production, has proved to be able to distinguish between carbapenemase-producing and -nonproducing Enterobacteriaceae. As already stated and as observed in our hands, MHA by MALDI-TOF MS analysis is independent from the type of carbapenemases involved, it is faster and easier to perform/interpret than culture-based methods. On the other hand, it cannot detect other carbapenem resistance mechanisms, such as porin alterations and efflux mechanisms.
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Mellouk FZ, Bakour S, Meradji S, Al-Bayssari C, Bentakouk MC, Zouyed F, Djahoudi A, Boutefnouchet N, Rolain JM. First Detection of VIM-4-Producing Pseudomonas aeruginosa and OXA-48-Producing Klebsiella pneumoniae in Northeastern (Annaba, Skikda) Algeria. Microb Drug Resist 2017; 23:335-344. [DOI: 10.1089/mdr.2016.0032] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Fatma Zohra Mellouk
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
- Laboratoire de Biochimie et de Microbiologie Appliquée, Département de Biochimie, Université Badji Mokhtar-Annaba, Annaba, Algérie
| | - Sofiane Bakour
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Sameh Meradji
- Laboratoire de Biochimie et de Microbiologie Appliquée, Département de Biochimie, Université Badji Mokhtar-Annaba, Annaba, Algérie
| | - Charbel Al-Bayssari
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | | | - Fatiha Zouyed
- Laboratoire central d'EPH EL Hadjar, Annaba, Algérie
| | | | - Nafissa Boutefnouchet
- Laboratoire de Biochimie et de Microbiologie Appliquée, Département de Biochimie, Université Badji Mokhtar-Annaba, Annaba, Algérie
| | - Jean Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Knox J, Palombo E. Performance of a MALDI-TOF MS-based imipenem hydrolysis assay incorporating zinc sulfate. Diagn Microbiol Infect Dis 2017; 87:258-260. [DOI: 10.1016/j.diagmicrobio.2016.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/21/2016] [Accepted: 11/27/2016] [Indexed: 11/25/2022]
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Bialvaei AZ, Kafil HS, Asgharzadeh M, Yousef Memar M, Yousefi M. Current methods for the identification of carbapenemases. J Chemother 2017; 28:1-19. [PMID: 26256147 DOI: 10.1179/1973947815y.0000000063] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.
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Affiliation(s)
- Abed Zahedi Bialvaei
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | - Hossein Samadi Kafil
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | | | - Mohammad Yousef Memar
- c Infectious Disease and Tropical Medicine Research Center , Tabriz University of Medical Sciences , Iran
| | - Mehdi Yousefi
- d Immunology Research Center , Tabriz University of Medical Sciences , Iran
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Abouseada N, Raouf M, El-Attar E, Moez P. Matrix-assisted Laser Desorption Ionisation Time-of-flight Mass Spectrometry Rapid Detection of Carbapenamase Activity in Acinetobacter baumannii Isolates. Indian J Med Microbiol 2017; 35:85-89. [PMID: 28303824 DOI: 10.4103/0255-0857.202335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Mezger A, Nilsson M, Andersson DI. Rapid Antibiotic Susceptibility Testing for Urinary Tract Infections. Methods Mol Biol 2017; 1616:147-153. [PMID: 28600767 DOI: 10.1007/978-1-4939-7037-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antibiotic susceptibility testing is important to guide clinicians in their choice of antibiotic used for treatment of bacterial infections. Current methods are time-consuming and more rapid alternatives are needed. Here, we describe a novel rapid method for antibiotic susceptibility testing which combines phenotypic and genotypic measurements. The use of padlock probes and rolling circle amplification allows for fast and precise determination of antibiotic susceptibilities as well as species identification.
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Affiliation(s)
- Anja Mezger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 256, Uppsala, 751 05, Sweden.
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Lin HR, Hu A, Lai MJ, Chiang CW, Liao CC, Chang KC. Rapid and sensitive detection of carbapenemase activity in Acinetobacter baumannii using superficially porous liquid chromatography-tandem mass spectrometry. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 49:910-917. [DOI: 10.1016/j.jmii.2015.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 07/13/2015] [Accepted: 08/04/2015] [Indexed: 12/17/2022]
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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Fritzenwanker M, Imirzalioglu C, Chakraborty T, Wagenlehner FM. Modern diagnostic methods for urinary tract infections. Expert Rev Anti Infect Ther 2016; 14:1047-1063. [DOI: 10.1080/14787210.2016.1236685] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods. Clin Microbiol Rev 2016; 29:1-27. [PMID: 26511484 DOI: 10.1128/cmr.00108-14] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Carbapenemases have become a significant mechanism for broad-spectrum β-lactam resistance in Enterobacteriaceae and other Gram-negative bacteria such as Pseudomonas and Acinetobacter spp. Intestinal carriage of carbapenemase-producing organisms (CPOs) is an important source of transmission. Isolation of carriers is one strategy that can be used to limit the spread of these bacteria. In this review, we critically examine the clinical performance, advantages, and disadvantages of methods available for the detection of intestinal carriage of CPOs. Culture-based methods (Centers for Disease Control and Prevention [CDC] protocols, chromogenic media, specialized agars, and double-disk synergy tests) for detecting carriage of CPOs are convenient due to their ready availability and low cost, but their limited sensitivity and long turnaround time may not always be optimal for infection control practices. Contemporary nucleic acid amplification techniques (NAATs) such as real-time PCR, hybridization assays, loop-mediated isothermal amplification (LAMP), or a combined culture and NAAT approach may provide fast results and/or added sensitivity and specificity compared with culture-based methods. Infection control practitioners and clinical microbiologists should be aware of the strengths and limitations of available methods to determine the most suitable approach for their medical facility to fit their infection control needs.
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