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Crofts TS, Gasparrini AJ, Dantas G. Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol 2017; 15:422-434. [PMID: 28392565 DOI: 10.1038/nrmicro.2017.28] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities. As the study of antibiotic resistance advances, it is important to incorporate this comprehensive approach to better inform global antibiotic resistance surveillance and antibiotic development. It is increasingly becoming apparent that although not all resistance genes are likely to geographically and phylogenetically disseminate, the threat presented by those that are is serious and warrants an interdisciplinary research focus. In this Review, we highlight seminal work in the resistome field, discuss recent advances in the studies of resistomes, and propose a resistome paradigm that can pave the way for the improved proactive identification and mitigation of emerging antibiotic resistance threats.
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Affiliation(s)
- Terence S Crofts
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Andrew J Gasparrini
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences &Systems Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, Missouri 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine.,Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, Missouri 63110, USA.,Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA
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102
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A Programmable Digital Microfluidic Assay for the Simultaneous Detection of Multiple Anti-Microbial Resistance Genes. MICROMACHINES 2017. [PMCID: PMC6189955 DOI: 10.3390/mi8040111] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The rapid emergence of antimicrobial resistant bacteria requires the development of new diagnostic tests. Nucleic acid-based assays determine antimicrobial susceptibility by detecting genes that encode for the resistance. In this study, we demonstrate rapid and simultaneous detection of three genes that confer resistance in bacteria to extended spectrum β-lactam and carbapenem antibiotics; CTX-M-15, KPC and NDM-1. The assay uses isothermal DNA amplification (recombinase polymerase amplification, RPA) implemented on a programmable digital microfluidics (DMF) platform. Automated dispensing protocols are used to simultaneously manipulate 45 droplets of nL volume containing sample DNA, reagents, and controls. The droplets are processed and mixed under electronic control on the DMF devices with positive amplification measured by fluorescence. The assay on these devices is significantly improved with a Time to Positivity (TTP) half that of the benchtop assay.
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103
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Maurer FP, Christner M, Hentschke M, Rohde H. Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs. Infect Dis Rep 2017; 9:6839. [PMID: 28458798 PMCID: PMC5391540 DOI: 10.4081/idr.2017.6839] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/30/2016] [Accepted: 01/12/2017] [Indexed: 12/11/2022] Open
Abstract
Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.
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Affiliation(s)
- Florian P Maurer
- Institute of Medical Microbiology, Virology and Hygiene.,Antibiotic Stewardship Team, University Medical Centre Hamburg-Eppendorf, Hamburg
| | | | | | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene
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104
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Nowakiewicz A, Ziółkowska G, Zięba P, Gnat S, Trościańczyk A, Adaszek Ł. Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis. PLoS One 2017; 12:e0171160. [PMID: 28135327 PMCID: PMC5279778 DOI: 10.1371/journal.pone.0171160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/15/2017] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to characterize multidrug resistant E. faecalis strains from pigs of local origin and to analyse the relationship between resistance and genotypic and proteomic profiles by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI -TOF MS). From the total pool of Enterococcus spp. isolated from 90 pigs, we selected 36 multidrug resistant E. faecalis strains, which represented three different phenotypic resistance profiles. Phenotypic resistance to tetracycline, macrolides, phenicols, and lincomycin and high-level resistance to aminoglycosides were confirmed by the occurrence of at least one corresponding resistance gene in each strain. Based on the analysis of the genotypic and phenotypic resistance of the strains tested, five distinct resistance profiles were generated. As a complement of this analysis, profiles of virulence genes were determined and these profiles corresponded to the phenotypic resistance profiles. The demonstration of resistance to a wide panel of antimicrobials by the strains tested in this study indicates the need of typing to determine the spread of resistance also at the local level. It seems that in the case of E. faecalis, type and scope of resistance strongly determines the genotypic pattern obtained with the ADSRRS-fingerprinting method. The ADSRRS-fingerprinting analysis showed consistency of the genetic profiles with the resistance profiles, while analysis of data with the use of the MALDI- TOF MS method did not demonstrate direct reproduction of the clustering pattern obtained with this method. Our observations were confirmed by statistical analysis (Simpson’s index of diversity, Rand and Wallace coefficients). Even though the MALDI -TOF MS method showed slightly higher discrimination power than ADSRRS-fingerprinting, only the latter method allowed reproduction of the clustering pattern of isolates based on phenotypic resistance and analysis of resistance and virulence genes (Wallace coefficient 1.0). This feature seems to be the most useful for epidemiological purposes and short-term analysis.
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Affiliation(s)
- Aneta Nowakiewicz
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
- * E-mail:
| | - Grażyna Ziółkowska
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
| | | | - Sebastian Gnat
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
| | - Aleksandra Trościańczyk
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
| | - Łukasz Adaszek
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Lublin, Poland
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105
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Dunne Jr WM, Jaillard M, Rochas O, Van Belkum A. Microbial genomics and antimicrobial susceptibility testing. Expert Rev Mol Diagn 2017; 17:257-269. [DOI: 10.1080/14737159.2017.1283220] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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106
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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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107
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Malmberg C, Yuen P, Spaak J, Cars O, Tängdén T, Lagerbäck P. A Novel Microfluidic Assay for Rapid Phenotypic Antibiotic Susceptibility Testing of Bacteria Detected in Clinical Blood Cultures. PLoS One 2016; 11:e0167356. [PMID: 27974860 PMCID: PMC5156554 DOI: 10.1371/journal.pone.0167356] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/12/2016] [Indexed: 12/19/2022] Open
Abstract
Background Appropriate antibiotic therapy is critical in the management of severe sepsis and septic shock to reduce mortality, morbidity and health costs. New methods for rapid antibiotic susceptibility testing are needed because of increasing resistance rates to standard treatment. Aims The purpose of this study was to evaluate the performance of a novel microfluidic method and the potential to directly apply this method on positive blood cultures. Methods Minimum inhibitory concentrations (MICs) of ciprofloxacin, ceftazidime, tigecycline and/or vancomycin for Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Staphylococcus aureus were determined using a linear antibiotic concentration gradient in a microfluidic assay. Bacterial growth along the antibiotic gradient was monitored using automated time-lapse photomicrography and growth inhibition was quantified by measuring greyscale intensity changes in the images. In addition to pure culture MICs, vancomycin MICs were determined for S. aureus from spiked and clinical blood cultures following a short centrifugation step. The MICs were compared with those obtained with the Etest and for S. aureus and vancomycin also with macrodilution. Results The MICs obtained with the microfluidic assay showed good agreement internally as well as with the Etest and macrodilution assays, although some minor differences were noted between the methods. The time to possible readout was within the range of 2 to 5 h. Conclusions The examined microfluidic assay has the potential to provide rapid and accurate MICs using samples from positive clinical blood cultures and will now be tested using other bacterial species and antibiotics.
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Affiliation(s)
- Christer Malmberg
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
- Gradientech AB, Uppsala, Sweden
- * E-mail: (CM); (PY)
| | - Pikkei Yuen
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
- * E-mail: (CM); (PY)
| | | | - Otto Cars
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Pernilla Lagerbäck
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
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108
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Selective Pressure Promotes Tetracycline Resistance of Chlamydia Suis in Fattening Pigs. PLoS One 2016; 11:e0166917. [PMID: 27893834 PMCID: PMC5125646 DOI: 10.1371/journal.pone.0166917] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
In pigs, Chlamydia suis has been associated with respiratory disease, diarrhea and conjunctivitis, but there is a high rate of inapparent C. suis infection found in the gastrointestinal tract of pigs. Tetracycline resistance in C. suis has been described in the USA, Italy, Switzerland, Belgium, Cyprus and Israel. Tetracyclines are commonly used in pig production due to their broad-spectrum activity and relatively low cost. The aim of this study was to isolate clinical C. suis samples in cell culture and to evaluate their antibiotic susceptibility in vitro under consideration of antibiotic treatment on herd level. Swab samples (n = 158) identified as C. suis originating from 24 farms were further processed for isolation, which was successful in 71% of attempts with a significantly higher success rate from fecal swabs compared to conjunctival swabs. The farms were divided into three treatment groups: A) farms without antibiotic treatment, B) farms with prophylactic oral antibiotic treatment of the whole herd consisting of trimethoprime, sulfadimidin and sulfathiazole (TSS), or C) farms giving herd treatment with chlortetracycline with or without tylosin and sulfadimidin (CTS). 59 isolates and their corresponding clinical samples were selected and tested for the presence or absence of the tetracycline resistance class C gene [tet(C)] by conventional PCR and isolates were further investigated for their antibiotic susceptibility in vitro. The phenotype of the investigated isolates was either classified as tetracycline sensitive (Minimum inhibitory concentration [MIC] < 2 μg/ml), intermediate (2 μg/ml ≤ MIC < 4 μg/ml) or resistant (MIC ≥ 4 μg/ml). Results of groups and individual pigs were correlated with antibiotic treatment and time of sampling (beginning/end of the fattening period). We found clear evidence for selective pressure as absence of antibiotics led to isolation of only tetracycline sensitive or intermediate strains whereas tetracycline treatment resulted in a greater number of tetracycline resistant isolates.
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109
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Pesesky MW, Hussain T, Wallace M, Patel S, Andleeb S, Burnham CAD, Dantas G. Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. Front Microbiol 2016; 7:1887. [PMID: 27965630 PMCID: PMC5124574 DOI: 10.3389/fmicb.2016.01887] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/09/2016] [Indexed: 01/08/2023] Open
Abstract
The time-to-result for culture-based microorganism recovery and phenotypic antimicrobial susceptibility testing necessitates initial use of empiric (frequently broad-spectrum) antimicrobial therapy. If the empiric therapy is not optimal, this can lead to adverse patient outcomes and contribute to increasing antibiotic resistance in pathogens. New, more rapid technologies are emerging to meet this need. Many of these are based on identifying resistance genes, rather than directly assaying resistance phenotypes, and thus require interpretation to translate the genotype into treatment recommendations. These interpretations, like other parts of clinical diagnostic workflows, are likely to be increasingly automated in the future. We set out to evaluate the two major approaches that could be amenable to automation pipelines: rules-based methods and machine learning methods. The rules-based algorithm makes predictions based upon current, curated knowledge of Enterobacteriaceae resistance genes. The machine-learning algorithm predicts resistance and susceptibility based on a model built from a training set of variably resistant isolates. As our test set, we used whole genome sequence data from 78 clinical Enterobacteriaceae isolates, previously identified to represent a variety of phenotypes, from fully-susceptible to pan-resistant strains for the antibiotics tested. We tested three antibiotic resistance determinant databases for their utility in identifying the complete resistome for each isolate. The predictions of the rules-based and machine learning algorithms for these isolates were compared to results of phenotype-based diagnostics. The rules based and machine-learning predictions achieved agreement with standard-of-care phenotypic diagnostics of 89.0 and 90.3%, respectively, across twelve antibiotic agents from six major antibiotic classes. Several sources of disagreement between the algorithms were identified. Novel variants of known resistance factors and incomplete genome assembly confounded the rules-based algorithm, resulting in predictions based on gene family, rather than on knowledge of the specific variant found. Low-frequency resistance caused errors in the machine-learning algorithm because those genes were not seen or seen infrequently in the test set. We also identified an example of variability in the phenotype-based results that led to disagreement with both genotype-based methods. Genotype-based antimicrobial susceptibility testing shows great promise as a diagnostic tool, and we outline specific research goals to further refine this methodology.
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Affiliation(s)
- Mitchell W Pesesky
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine St. Louis, MO, USA
| | - Tahir Hussain
- Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. Louis, MO, USA; Atta ur Rahman School of Applied Biosciences, National University of Sciences and TechnologyIslamabad, Pakistan
| | - Meghan Wallace
- Department of Pathology and Immunology, Washington University School of Medicine St. Louis, MO, USA
| | - Sanket Patel
- Department of Pathology and Immunology, Washington University School of Medicine St. Louis, MO, USA
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology Islamabad, Pakistan
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of MedicineSt. Louis, MO, USA; Department of Pediatrics, Washington University School of MedicineSt. Louis, MO, USA
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of MedicineSt. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. LouisSt. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of MedicineSt. Louis, MO, USA
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110
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Kelley SO. New Technologies for Rapid Bacterial Identification and Antibiotic Resistance Profiling. SLAS Technol 2016; 22:113-121. [PMID: 27879409 DOI: 10.1177/2211068216680207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Conventional approaches to bacterial identification and drug susceptibility testing typically rely on culture-based approaches that take 2 to 7 days to return results. The long turnaround times contribute to the spread of infectious disease, negative patient outcomes, and the misuse of antibiotics that can contribute to antibiotic resistance. To provide new solutions enabling faster bacterial analysis, a variety of approaches are under development that leverage single-cell analysis, microfluidic concentration and detection strategies, and ultrasensitive readout mechanisms. This review discusses recent advances in this area and the potential of new technologies to enable more effective management of infectious disease.
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Affiliation(s)
- Shana O Kelley
- 1 Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.,2 Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada.,3 Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,4 Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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111
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Ungphakorn W, Malmberg C, Lagerbäck P, Cars O, Nielsen EI, Tängdén T. Evaluation of automated time-lapse microscopy for assessment of in vitro activity of antibiotics. J Microbiol Methods 2016; 132:69-75. [PMID: 27836633 DOI: 10.1016/j.mimet.2016.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/03/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022]
Abstract
This study aimed to evaluate the potential of a new time-lapse microscopy based method (oCelloScope) to efficiently assess the in vitro antibacterial effects of antibiotics. Two E. coli and one P. aeruginosa strain were exposed to ciprofloxacin, colistin, ertapenem and meropenem in 24-h experiments. Background corrected absorption (BCA) derived from the oCelloScope was used to detect bacterial growth. The data obtained with the oCelloScope were compared with those of the automated Bioscreen C method and standard time-kill experiments and a good agreement in results was observed during 6-24h of experiments. Viable counts obtained at 1, 4, 6 and 24h during oCelloScope and Bioscreen C experiments were well correlated with the corresponding BCA and optical density (OD) data. Initial antibacterial effects during the first 6h of experiments were difficult to detect with the automated methods due to their high detection limits (approximately 105CFU/mL for oCelloScope and 107CFU/mL for Bioscreen C), the inability to distinguish between live and dead bacteria and early morphological changes of bacteria during exposure to ciprofloxacin, ertapenem and meropenem. Regrowth was more frequently detected in time-kill experiments, possibly related to the larger working volume with an increased risk of pre-existing or emerging resistance. In comparison with Bioscreen C, the oCelloScope provided additional information on bacterial growth dynamics in the range of 105 to 107CFU/mL and morphological features. In conclusion, the oCelloScope would be suitable for detection of in vitro effects of antibiotics, especially when a large number of regimens need to be tested.
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Affiliation(s)
- Wanchana Ungphakorn
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Christer Malmberg
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Pernilla Lagerbäck
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Otto Cars
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden
| | - Elisabet I Nielsen
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, Uppsala, Sweden.
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112
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Dai J, Hamon M, Jambovane S. Microfluidics for Antibiotic Susceptibility and Toxicity Testing. Bioengineering (Basel) 2016; 3:bioengineering3040025. [PMID: 28952587 PMCID: PMC5597268 DOI: 10.3390/bioengineering3040025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/23/2022] Open
Abstract
The recent emergence of antimicrobial resistance has become a major concern for worldwide policy makers as very few new antibiotics have been developed in the last twenty-five years. To prevent the death of millions of people worldwide, there is an urgent need for a cheap, fast and accurate set of tools and techniques that can help to discover and develop new antimicrobial drugs. In the past decade, microfluidic platforms have emerged as potential systems for conducting pharmacological studies. Recent studies have demonstrated that microfluidic platforms can perform rapid antibiotic susceptibility tests to evaluate antimicrobial drugs’ efficacy. In addition, the development of cell-on-a-chip and organ-on-a-chip platforms have enabled the early drug testing, providing more accurate insights into conventional cell cultures on the drug pharmacokinetics and toxicity, at the early and cheaper stage of drug development, i.e., prior to animal and human testing. In this review, we focus on the recent developments of microfluidic platforms for rapid antibiotics susceptibility testing, investigating bacterial persistence and non-growing but metabolically active (NGMA) bacteria, evaluating antibiotic effectiveness on biofilms and combinatorial effect of antibiotics, as well as microfluidic platforms that can be used for in vitro antibiotic toxicity testing.
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Affiliation(s)
- Jing Dai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Morgan Hamon
- Renal Regeneration Laboratory, VAGLAHS at Sepulveda, North Hills, CA 91343, USA.
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Sachin Jambovane
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA 99354, USA.
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113
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Li H, Balan P, Vertes A. Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2016; 55:15035-15039. [DOI: 10.1002/anie.201607751] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Hang Li
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
| | - Pranav Balan
- Thomas Jefferson High School for Science and Technology; Alexandria VA 22312 USA
| | - Akos Vertes
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
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114
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Li H, Balan P, Vertes A. Molecular Imaging of Growth, Metabolism, and Antibiotic Inhibition in Bacterial Colonies by Laser Ablation Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hang Li
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
| | - Pranav Balan
- Thomas Jefferson High School for Science and Technology; Alexandria VA 22312 USA
| | - Akos Vertes
- Department of Chemistry; The George Washington University; Washington DC 20052 USA
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115
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Rapid Antimicrobial Susceptibility Testing Using Forward Laser Light Scatter Technology. J Clin Microbiol 2016; 54:2701-2706. [PMID: 27558176 DOI: 10.1128/jcm.01475-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/15/2016] [Indexed: 11/20/2022] Open
Abstract
The delayed reporting of antimicrobial susceptibility testing remains a limiting factor in clinical decision-making in the treatment of bacterial infection. This study evaluates the use of forward laser light scatter (FLLS) to measure bacterial growth for the early determination of antimicrobial susceptibility. Three isolates each (two clinical isolates and one reference strain) of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa were tested in triplicate using two commercial antimicrobial testing systems, the Vitek2 and the MicroScan MIC panel, to challenge the BacterioScan FLLS. The BacterioScan FLLS showed a high degree of categorical concordance with the commercial methods. Pairwise comparison with each commercial system serving as a reference standard showed 88.9% agreement with MicroScan (two minor errors) and 72.2% agreement with Vitek (five minor errors). FLLS using the BacterioScan system shows promise as a novel method for the rapid and accurate determination of antimicrobial susceptibility.
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116
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Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF. Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure. Angew Chem Int Ed Engl 2016; 55:9557-61. [PMID: 27357747 PMCID: PMC5215780 DOI: 10.1002/anie.201602763] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/05/2016] [Indexed: 01/11/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.
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Affiliation(s)
- Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Matthew S Curtis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Romney M Humphries
- Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA
| | - Janet A Hindler
- Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
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117
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Sun H, Liu Z, Hu C, Ren K. Cell-on-hydrogel platform made of agar and alginate for rapid, low-cost, multidimensional test of antimicrobial susceptibility. LAB ON A CHIP 2016; 16:3130-3138. [PMID: 27452345 DOI: 10.1039/c6lc00417b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antimicrobial resistance (AMR) is a rapidly increasing threat to the effective treatment of infectious diseases worldwide. The two major remedies include: (1) using narrow-spectrum antibiotics based on rapid diagnosis; and (2) developing new antibiotics. A key part of both remedies is the antimicrobial susceptibility test (AST). However, the current standard ASTs that monitor colony formation are costly and time-consuming and the new strategies proposed are not yet practical to be implemented. Herein, we report a strategy to fabricate whole-hydrogel microfluidic chips using alginate-doped agar. This agar-based microfabrication makes it possible to prepare inexpensive hydrogel devices, and allows a seamless link between microfluidics and conventional agar-based cell culture. Different from common microfluidic systems, in our system the cells are cultured on top of the device, similar to normal agar plate culture; on the other hand, the microfluidic channels inside the hydrogel allow precise generation of linear gradient of drugs, thus giving a better performance than the conventional disk diffusion method. Cells in this system are not exposed to any shear flow, which allows the reliable tracking of individual cells and AST results to be obtained within 2-3 hours. Furthermore, our system could test the synergistic effect of drugs through two-dimensional gradient generation. Finally, the platform could be directly implemented to new drug discovery and other applications wherein a fast, cost-efficient method for studying the response of microorganisms upon drug administration is desirable.
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Affiliation(s)
- Han Sun
- Department of Chemistry,, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Zhengzhi Liu
- Department of Chemistry,, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Chong Hu
- Department of Chemistry,, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Kangning Ren
- Department of Chemistry,, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China. and State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China and HKBU Institute of Research and Continuing Education, Shenzhen, China
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118
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Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF. Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Eugenia M. Khorosheva
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Travis S. Schlappi
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Matthew S. Curtis
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Romney M. Humphries
- Pathology and Laboratory Medicine; University of California, Los Angeles; 10888 Le Conte Avenue, Brentwood Annex Los Angeles CA 90095 USA
| | - Janet A. Hindler
- Pathology and Laboratory Medicine; University of California, Los Angeles; 10888 Le Conte Avenue, Brentwood Annex Los Angeles CA 90095 USA
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
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119
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Otero F, Santiso R, Tamayo M, Fernández JL, Bou G, Lepe JA, McConnell MJ, Gosálvez J, Cisneros JM. Rapid Detection of Antibiotic Resistance in Gram-Negative Bacteria Through Assessment of Changes in Cellular Morphology. Microb Drug Resist 2016; 23:157-162. [PMID: 27259183 DOI: 10.1089/mdr.2016.0023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rapid antimicrobial susceptibility testing has the potential to improve patient outcomes and reduce healthcare-associated costs. In this study, a novel assay based on bacterial cell elongation after exposure to an antibiotic (ceftazidime) was evaluated for its ability to rapidly detect resistance in Gram-negative bacteria. The assay was used to detect resistance in a large collection of strains containing 320 clinical isolates of Acinetobacter baumannii, 171 clinical isolates of Klebsiella pneumoniae, and 212 clinical isolates of Pseudomonas aeruginosa, and the results were compared to those obtained using standard antimicrobial susceptibility testing methods. The assay identified ceftazidime-resistant strains with 100% sensitivity and 100% specificity for A. baumannii, 100% sensitivity and 97.2% specificity for K. pneumoniae, and with 82.3% sensitivity and 100% specificity for P. aeruginosa. Importantly, results were obtained in 1 hour 15 minutes from exponentially growing cultures. This study demonstrates that changes in cell length are highly correlated with phenotypic antibiotic susceptibility determined using standard susceptibility testing methods. This study therefore provides proof-of-concept that changes in cell morphology can be used as the basis for rapid detection of antibiotic resistance and provides the basis for the development of novel rapid diagnostics for the detection of antibiotic resistance.
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Affiliation(s)
- Fátima Otero
- 1 Unidad de Genética, INIBIC-Complejo Hospitalario Universitario A Coruña , A Coruña, Spain .,2 Laboratorio de Genética, Centro Oncológico de Galicia , A Coruña, Spain
| | - Rebeca Santiso
- 1 Unidad de Genética, INIBIC-Complejo Hospitalario Universitario A Coruña , A Coruña, Spain .,2 Laboratorio de Genética, Centro Oncológico de Galicia , A Coruña, Spain
| | - Maria Tamayo
- 1 Unidad de Genética, INIBIC-Complejo Hospitalario Universitario A Coruña , A Coruña, Spain .,2 Laboratorio de Genética, Centro Oncológico de Galicia , A Coruña, Spain
| | - José Luis Fernández
- 1 Unidad de Genética, INIBIC-Complejo Hospitalario Universitario A Coruña , A Coruña, Spain .,2 Laboratorio de Genética, Centro Oncológico de Galicia , A Coruña, Spain
| | - Germán Bou
- 3 Servicio de Microbiología, INIBIC-Complejo Hospitalario Universitario A Coruña , A Coruña, Spain
| | - José Antonio Lepe
- 4 Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospitals Virgen del Rocío and Virgen Macarena, Seville, Spain
| | - Michael J McConnell
- 4 Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospitals Virgen del Rocío and Virgen Macarena, Seville, Spain
| | - Jaime Gosálvez
- 5 Unidad de Genética, Facultad de Biología, Universidad Autónoma de Madrid , Madrid, Spain
| | - José Miguel Cisneros
- 4 Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospitals Virgen del Rocío and Virgen Macarena, Seville, Spain
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120
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Penny C, Grothendick B, Zhang L, Borror CM, Barbano D, Cornelius AJ, Gilpin BJ, Fagerquist CK, Zaragoza WJ, Jay-Russell MT, Lastovica AJ, Ragimbeau C, Cauchie HM, Sandrin TR. A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni. Front Microbiol 2016; 7:818. [PMID: 27303397 PMCID: PMC4885823 DOI: 10.3389/fmicb.2016.00818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/13/2016] [Indexed: 12/13/2022] Open
Abstract
MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: (1) 65 strains resistant to cefoperazone (2) 26 resistant to cefoperazone and beta-lactams (3) 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and (4) 76 strains resistant to cefoperazone, teicoplanin, amphotericin, B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra) of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra). We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson) was applied rather than a peak based (Dice) and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: (1) 5% (2) 9% (3) 10%, and (4) 2%. An additional second categorization was created from the collection consisting of 31 strains resistant to beta-lactams and 141 strains sensitive to beta-lactams. Applying optimal preprocessing parameters, beta-lactam resistance detection was increased by 34%. These results suggest that spectrum processing parameters, which are rarely optimized or adjusted, affect the performance of MALDI-TOF MS-based detection of antibiotic resistance and can be fine-tuned to enhance screening performance.
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Affiliation(s)
- Christian Penny
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology Esch-sur-Alzette, Luxembourg
| | - Beau Grothendick
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix AZ, USA
| | - Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix AZ, USA
| | - Connie M Borror
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix AZ, USA
| | - Duane Barbano
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix AZ, USA
| | - Angela J Cornelius
- Institute of Environmental Science and Research Christchurch, New Zealand
| | - Brent J Gilpin
- Institute of Environmental Science and Research Christchurch, New Zealand
| | - Clifton K Fagerquist
- Agricultural Research Service, United States Department of Agriculture, Albany CA, USA
| | - William J Zaragoza
- Agricultural Research Service, United States Department of Agriculture, Albany CA, USA
| | | | - Albert J Lastovica
- Department of Biotechnology, University of the Western Cape Bellville, South Africa
| | - Catherine Ragimbeau
- Epidemiological Surveillance of Infectious Diseases, Laboratoire National de Santé Dudelange, Luxembourg
| | - Henry-Michel Cauchie
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology Esch-sur-Alzette, Luxembourg
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix AZ, USA
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121
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Steinberger-Levy I, Shifman O, Zvi A, Ariel N, Beth-Din A, Israeli O, Gur D, Aftalion M, Maoz S, Ber R. A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes. Front Microbiol 2016; 7:763. [PMID: 27242774 PMCID: PMC4871873 DOI: 10.3389/fmicb.2016.00763] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/05/2016] [Indexed: 12/22/2022] Open
Abstract
Standard antimicrobial susceptibility tests used to determine bacterial susceptibility to antibiotics are growth dependent and time consuming. The long incubation time required for standard tests may render susceptibility results irrelevant, particularly for patients infected with lethal bacteria that are slow growing on agar but progress rapidly in vivo, such as Yersinia pestis. Here, we present an alternative approach for the rapid determination of antimicrobial susceptibility, based on the quantification of the changes in the expression levels of specific marker genes following exposure to growth-inhibiting concentrations of the antibiotic, using Y. pestis and ciprofloxacin as a model. The marker genes were identified by transcriptomic DNA microarray analysis of the virulent Y. pestis Kimberley53 strain after exposure to specific concentrations of ciprofloxacin for various time periods. We identified several marker genes that were induced following exposure to growth-inhibitory concentrations of ciprofloxacin, and we confirmed the marker expression profiles at additional ciprofloxacin concentrations using quantitative RT-PCR. Eleven candidate marker transcripts were identified, of which four mRNA markers were selected for a rapid quantitative RT-PCR susceptibility test that correctly determined the Minimal Inhibitory Concentration (MIC) values and the categories of susceptibility of several Y. pestis strains and isolates harboring various ciprofloxacin MIC values. The novel molecular susceptibility test requires just 2 h of antibiotic exposure in a 7-h overall test time, in contrast to the 24 h of antibiotic exposure required for a standard microdilution test.
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Affiliation(s)
- Ida Steinberger-Levy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Naomi Ariel
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - David Gur
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Sharon Maoz
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
| | - Raphael Ber
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness-Ziona, Israel
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122
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Banerjee R, Humphries R. Clinical and laboratory considerations for the rapid detection of carbapenem-resistant Enterobacteriaceae. Virulence 2016; 8:427-439. [PMID: 27168451 DOI: 10.1080/21505594.2016.1185577] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Carbapenem resistance among the Enterobacteriaceae has become a significant clinical and public health dilemma. Rapid administration of effective antimicrobials and implementation of supplemental infection control practices is required to both improve patient outcomes and limit the spread of these highly resistant organisms. However, carbapenem-resistant Enterobacteriaceae (CRE)-infected patients are predominantly identified by routine culture methods, which take days to perform. Rapid genomic and phenotypic methods are currently available to accelerate the identification of carbapenemase-producing CRE. Effective use of these technologies is reliant on close collaboration between clinical microbiology, infection prevention, antimicrobial stewardship and infectious diseases specialists. This review discusses the performance characteristics of these technologies to date, and describes strategies for their optimal implementation.
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Affiliation(s)
- Ritu Banerjee
- a Department of Pediatric and Adolescent Medicine , Mayo Clinic , Rochester , MN , USA
| | - Romney Humphries
- b Department of Pathology and Laboratory Medicine , University of California , Los Angeles , CA , USA
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123
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Navarro F, Coll P. Speeding up antimicrobial susceptibility testing. Enferm Infecc Microbiol Clin 2016; 34:331-3. [PMID: 27004427 DOI: 10.1016/j.eimc.2016.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 11/15/2022]
Affiliation(s)
- Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.
| | - Pere Coll
- Departament de Genètica i de Microbiología, Universitat Autònoma de Barcelona, Institut d'Investigacions Biomèdiques Sant Pau, Barcelona, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
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124
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Jiang L, Boitard L, Broyer P, Chareire AC, Bourne-Branchu P, Mahé P, Tournoud M, Franceschi C, Zambardi G, Baudry J, Bibette J. Digital antimicrobial susceptibility testing using the MilliDrop technology. Eur J Clin Microbiol Infect Dis 2016; 35:415-22. [DOI: 10.1007/s10096-015-2554-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/10/2015] [Indexed: 01/30/2023]
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125
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Antibiograma rápido en Microbiología Clínica. Enferm Infecc Microbiol Clin 2016; 34:61-8. [DOI: 10.1016/j.eimc.2014.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/25/2014] [Accepted: 11/15/2014] [Indexed: 11/22/2022]
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126
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Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy. Eur J Clin Microbiol Infect Dis 2015; 34:2385-94. [PMID: 26407621 PMCID: PMC4655009 DOI: 10.1007/s10096-015-2492-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/14/2015] [Indexed: 01/21/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the oCelloScope system, to perform rapid AST. The oCelloScope system demonstrated a very high accuracy (96 % overall agreement) when determining the resistance profiles of four reference strains, nine clinical isolates, including multi-drug-resistant isolates, and three positive blood cultures. AST of clinical isolates (168 antimicrobial agent–organism combinations) demonstrated 3.6 % minor, no major and 1.2 % very major errors of the oCelloScope system compared to conventional susceptibility testing, as well as a rapid and correct phenotypic detection of strains with methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) profiles. The net average time-to-result was 108 min, with 95 % of the results being available within 180 min. In conclusion, this study strongly indicates that the oCelloScope system holds considerable potential as an accurate and sensitive AST method with short time-to-result, enabling same-day targeted antimicrobial therapy, facilitating antibiotic stewardship and better patient management. A full-scale validation of the oCelloScope system including more isolates is necessary to assess the impact of using it for AST.
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127
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Pump-free gradient-based micro-device enables quantitative and high-throughput bacterial growth inhibition analysis. Biomed Microdevices 2015; 17:67. [DOI: 10.1007/s10544-015-9971-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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128
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Proton Nuclear Magnetic Resonance Spectroscopy as a Technique for Gentamicin Drug Susceptibility Studies with Escherichia coli ATCC 25922. J Clin Microbiol 2015; 53:2433-8. [PMID: 25972417 DOI: 10.1128/jcm.00604-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/06/2015] [Indexed: 01/15/2023] Open
Abstract
Antimicrobial drug susceptibility tests involving multiple time-consuming steps are still used as reference methods. Today, there is a need for the development of new automated instruments that can provide faster results and reduce operating time, reagent costs, and labor requirements. Nuclear magnetic resonance (NMR) spectroscopy meets those requirements. The metabolism and antimicrobial susceptibility of Escherichia coli ATCC 25922 in the presence of gentamicin have been analyzed using NMR and compared with a reference method. Direct incubation of the bacteria (with and without gentamicin) into the NMR tube has also been performed, and differences in the NMR spectra were obtained. The MIC, determined by the reference method found in this study, would correspond with the termination of the bacterial metabolism observed with NMR. Experiments carried out directly into the NMR tube enabled the development of antimicrobial drug susceptibility tests to assess the effectiveness of the antibiotic. NMR is an objective and reproducible method for showing the effects of a drug on the subject bacterium and can emerge as an excellent tool for studying bacterial activity in the presence of different antibiotic concentrations.
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129
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March Rosselló GA, García-Loygorri Jordán de Urries MC, Gutiérrez Rodríguez MP, Simarro Grande M, Orduña Domingo A, Bratos Pérez MÁ. A two-hour antibiotic susceptibility test by ATP-bioluminescence. Enferm Infecc Microbiol Clin 2015; 34:334-9. [PMID: 25979598 DOI: 10.1016/j.eimc.2015.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 11/15/2022]
Abstract
The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours.
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Affiliation(s)
| | | | | | - María Simarro Grande
- Departamento de Microbiología, Facultad de Medicina, Universidad de Valladolid, Spain
| | - Antonio Orduña Domingo
- Departamento de Microbiología, Facultad de Medicina, Universidad de Valladolid, Spain; Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, Spain
| | - Miguel Ángel Bratos Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Valladolid, Spain; Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, Spain
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130
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Detection of vancomycin resistances in enterococci within 3 ½ hours. Sci Rep 2015; 5:8217. [PMID: 25645753 PMCID: PMC4314646 DOI: 10.1038/srep08217] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/29/2014] [Indexed: 12/26/2022] Open
Abstract
Vancomycin resistant enterococci (VRE) constitute a challenging problem in health care institutions worldwide. Novel methods to rapidly identify resistances are highly required to ensure an early start of tailored therapy and to prevent further spread of the bacteria. Here, a spectroscopy-based rapid test is presented that reveals resistances of enterococci towards vancomycin within 3.5 hours. Without any specific knowledge on the strain, VRE can be recognized with high accuracy in two different enterococci species. By means of dielectrophoresis, bacteria are directly captured from dilute suspensions, making sample preparation very easy. Raman spectroscopic analysis of the trapped bacteria over a time span of two hours in absence and presence of antibiotics reveals characteristic differences in the molecular response of sensitive as well as resistant Enterococcus faecalis and Enterococcus faecium. Furthermore, the spectroscopic fingerprints provide an indication on the mechanisms of induced resistance in VRE.
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131
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Lubbers BV, Turnidge J. Antimicrobial susceptibility testing for bovine respiratory disease: Getting more from diagnostic results. Vet J 2015; 203:149-54. [DOI: 10.1016/j.tvjl.2014.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/25/2014] [Accepted: 12/09/2014] [Indexed: 12/23/2022]
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132
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Alcaine SD, Pacitto D, Sela DA, Nugen SR. Phage & phosphatase: a novel phage-based probe for rapid, multi-platform detection of bacteria. Analyst 2015; 140:7629-36. [DOI: 10.1039/c5an01181g] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A bacteriophage-based biosensing platform forE. coliis proposed. The bacteriophage T7 was genetically engineered to carry the alkaline phosphatase genephoA. The overexpression of the gene was quantified with colorimetric, fluorescent, and chemiluminescent methods.
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Affiliation(s)
- S. D. Alcaine
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
| | - D. Pacitto
- Department of Microbiology
- University of Massachusetts
- Amherst
- USA
| | - D. A. Sela
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Department of Microbiology
| | - S. R. Nugen
- Department of Food Science
- University of Massachusetts
- Amherst
- USA
- Department of Microbiology
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Choi J, Yoo J, Lee M, Kim EG, Lee JS, Lee S, Joo S, Song SH, Kim EC, Lee JC, Kim HC, Jung YG, Kwon S. A rapid antimicrobial susceptibility test based on single-cell morphological analysis. Sci Transl Med 2014; 6:267ra174. [DOI: 10.1126/scitranslmed.3009650] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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134
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Using the number needed to treat to assess appropriate antimicrobial therapy as a determinant of outcome in severe sepsis and septic shock. Crit Care Med 2014; 42:2342-9. [PMID: 25072764 DOI: 10.1097/ccm.0000000000000516] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To assess appropriate antimicrobial therapy as an outcome determinant in severe sepsis and septic shock using the number needed to treat. DESIGN Single-center cohort study (January 2008 to December 2012). SETTING One thousand two hundred fifty-bed academic hospital. PATIENTS Two thousand five hundred ninety-four patients with positive blood culture. INTERVENTIONS We retrospectively identified patients with severe sepsis or septic shock. Inappropriate antimicrobial treatment was defined as an antimicrobial regimen that lacked in vitro activity against the isolated pathogen. Information regarding demographics, severity of illness, comorbidities, microbiology, and antimicrobial treatment was recorded. Logistic regression was used to identify risk factors for hospital mortality and inappropriate treatment. MEASUREMENTS AND MAIN RESULTS Seven hundred eighty-seven patients (30.3%) were nonsurvivors. Inappropriate antimicrobial treatment had the greatest adjusted odds ratio for hospital mortality (adjusted odds ratio, 3.4; 95% CI, 2.8-4.1; p < 0.001). Multivariate logistic regression analysis identified resistance to cefepime, resistance to meropenem, presence of multidrug resistance, nonabdominal surgery, and prior antibiotic use as being independently associated with the administration of inappropriate antimicrobial treatment. For the entire cohort, the number needed to treat with appropriate antimicrobial therapy to prevent one patient death was 4.0 (95% CI, 3.7-4.3). The prevalence-adjusted pathogen-specific number needed to treat (PNNT) with appropriate antimicrobial therapy to prevent one patient death was lowest for multidrug-resistant bacteria (PNNT = 20) followed by Candida species (PNNT = 34), methicillin-resistant Staphylococcus aureus (PNNT = 38), Pseudomonas aeruginosa (PNNT = 38), Escherichia coli (PNNT = 40), and methicillin-susceptible S. aureus (PNNT = 47). CONCLUSIONS Our results support the importance of appropriate antimicrobial treatment as a determinant of outcome in patients with severe sepsis and septic shock. Our analyses suggest that improved targeting of empiric antimicrobials for multidrug-resistant bacteria, Candida species, methicillin-resistant S. aureus, and P. aeruginosa would have the greatest impact in reducing mortality from inappropriate antimicrobial treatment in patients with severe sepsis and septic shock.
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135
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The resistome of Pseudomonas aeruginosa in relationship to phenotypic susceptibility. Antimicrob Agents Chemother 2014; 59:427-36. [PMID: 25367914 DOI: 10.1128/aac.03954-14] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many clinical isolates of Pseudomonas aeruginosa cause infections that are difficult to eradicate due to their resistance to a wide variety of antibiotics. Key genetic determinants of resistance were identified through genome sequences of 390 clinical isolates of P. aeruginosa, obtained from diverse geographic locations collected between 2003 and 2012 and were related to microbiological susceptibility data for meropenem, levofloxacin, and amikacin. β-Lactamases and integron cassette arrangements were enriched in the established multidrug-resistant lineages of sequence types ST111 (predominantly O12) and ST235 (O11). This study demonstrates the utility of next-generation sequencing (NGS) in defining relevant resistance elements and highlights the diversity of resistance determinants within P. aeruginosa. This information is valuable in furthering the design of diagnostics and therapeutics for the treatment of P. aeruginosa infections.
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136
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Number Needed to Treat—To Get Clinicians’ Attention*. Crit Care Med 2014; 42:2444-5. [DOI: 10.1097/ccm.0000000000000578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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137
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Fleurbaaij F, Heemskerk AAM, Russcher A, Klychnikov OI, Deelder AM, Mayboroda OA, Kuijper EJ, van Leeuwen HC, Hensbergen PJ. Capillary-electrophoresis mass spectrometry for the detection of carbapenemases in (multi-)drug-resistant Gram-negative bacteria. Anal Chem 2014; 86:9154-61. [PMID: 25155175 DOI: 10.1021/ac502049p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In a time in which the spread of multidrug resistant microorganisms is ever increasing, there is a need for fast and unequivocal identification of suspect organisms to supplement existing techniques in the clinical laboratory, especially in single bacterial colonies. Mass-spectrometry coupled with efficient peptide separation techniques offer great potential for identification of resistant-related proteins in complex microbiological samples in an unbiased manner. Here, we developed a capillary electrophoresis-electrospray ionization-tandem mass spectrometry CE-ESI-MS/MS bottom-up proteomics workflow for sensitive and specific peptide analysis with the emphasis on the identification of β-lactamases (carbapenemases OXA-48 and KPC in particular) in bacterial species. For this purpose, tryptic peptides from whole cell lysates were analyzed by sheathless CE-ESI-MS/MS and proteins were identified after searching of the spectral data against bacterial protein databases. The CE-ESI-MS/MS workflow was first evaluated using a recombinant TEM-1 β-lactamase, resulting in 68% of the amino acid sequence being covered by 20 different unique peptides. Subsequently, a resistant and susceptible Escherichia coli lab strain were analyzed and based on the observed β-lactamase peptides, the two strains could easily be discriminated. Finally, the method was tested in an unbiased setup using a collection of in-house characterized OXA-48 (n = 17) and KPC (n = 10) clinical isolates. The developed CE-ESI-MS/MS method was able to identify the presence of OXA-48 and KPC in all of the carbapenemase positive samples, independent of species and degree of susceptibility. Four negative controls were tested and classified as negative by this method. Furthermore, a number of extended-spectrum beta-lactamases (ESBL) were identified in the same analyses, confirming the multiresistant character in 19 out of 27 clinical isolates. Importantly, the method performed equally well on protein lysates from single colonies. As such, it demonstrates CE-ESI-MS/MS as a potential next generation mass spectrometry platform within the clinical microbiology laboratory.
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Affiliation(s)
- Frank Fleurbaaij
- Department of Medical Microbiology, Section Experimental Microbiology, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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WEN XX, XU BL, WANG WX, LIANG GT, CHEN B, YANG YM, LIU DY. Rapid Identification of Multiple Bacteria on a Microfluidic Chip. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60737-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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140
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Tuite N, Reddington K, Barry T, Zumla A, Enne V. Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? J Antimicrob Chemother 2014; 69:1729-33. [PMID: 24677160 DOI: 10.1093/jac/dku083] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A key component for tackling the ever more serious antimicrobial resistance problem in Gram-negative bacteria is the introduction of rapid nucleic acid diagnostics. Successful incorporation of new diagnostic technologies has the potential benefit of improving not only patient treatment but also infection control and antimicrobial stewardship. However, there are still many hurdles to overcome, such as the complexity of resistance mechanisms in Gram-negative bacteria, the discrepancy between phenotype and genotype and the difficulty in distinguishing pathogens from background commensals. A small number of manufacturers have introduced tests to the market that concentrate partly or specifically on resistance determinants in Gram-negative bacteria. These are currently predominantly based on different types of PCR technology. The development of new technologies, such as whole-genome sequencing and the combination of MALDI-TOF with PCR, holds much promise for the introduction of improved diagnostics for the future.
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Affiliation(s)
- Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Alimuddin Zumla
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
| | - Virve Enne
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
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141
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Machen A, Drake T, Wang YF(W. Same day identification and full panel antimicrobial susceptibility testing of bacteria from positive blood culture bottles made possible by a combined lysis-filtration method with MALDI-TOF VITEK mass spectrometry and the VITEK2 system. PLoS One 2014; 9:e87870. [PMID: 24551067 PMCID: PMC3925102 DOI: 10.1371/journal.pone.0087870] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 12/31/2013] [Indexed: 12/03/2022] Open
Abstract
Rapid identification and antimicrobial susceptibility testing of microorganisms causing bloodstream infections or sepsis have the potential to improve patient care. This proof-of-principle study evaluates the Lysis-Filtration Method for identification as well as antimicrobial susceptibility testing of bacteria directly from positive blood culture bottles in a clinical setting. A total of 100 non-duplicated positive blood cultures were tested and 1012 microorganism-antimicrobial combinations were assessed. An aliquot of non-charcoal blood culture broth was incubated with lysis buffer briefly before being filtered and washed. Microorganisms recovered from the filter membrane were first identified by using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight VITEK® Mass Spectrometry (VITEK MS). After quick identification from VITEK MS, filtered microorganisms were inoculated to VITEK®2 system for full panel antimicrobial susceptibility testing analysis. Of 100 bottles tested, the VITEK MS resulted in 94.0% correct organism identification to the species level. Compared to the conventional antimicrobial susceptibility testing methods, direct antimicrobial susceptibility testing from VITEK®2 resulted in 93.5% (946/1012) category agreement of antimicrobials tested, with 3.6% (36/1012) minor error, 1.7% (7/1012) major error, and 1.3% (13/1012) very major error of antimicrobials. The average time to identification and antimicrobial susceptibility testing was 11.4 hours by using the Lysis-Filtration method for both VITEK MS and VITEK®2 compared to 56.3 hours by using conventional methods (p<0.00001). Thus, the same-day results of microorganism identification and antimicrobial susceptibility testing directly from positive blood culture can be achieved and can be used for appropriate antibiotic therapy and antibiotic stewardship.
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Affiliation(s)
- Alexandra Machen
- Department of Pathology and laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Tim Drake
- Department of Pathology and Laboratory Medicine, Grady Health System, Atlanta, Georgia, United States of America
| | - Yun F. (Wayne) Wang
- Department of Pathology and laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Grady Health System, Atlanta, Georgia, United States of America
- * E-mail:
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142
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Sin MLY, Mach KE, Wong PK, Liao JC. Advances and challenges in biosensor-based diagnosis of infectious diseases. Expert Rev Mol Diagn 2014; 14:225-44. [PMID: 24524681 DOI: 10.1586/14737159.2014.888313] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rapid diagnosis of infectious diseases and timely initiation of appropriate treatment are critical determinants that promote optimal clinical outcomes and general public health. Conventional in vitro diagnostics for infectious diseases are time-consuming and require centralized laboratories, experienced personnel and bulky equipment. Recent advances in biosensor technologies have potential to deliver point-of-care diagnostics that match or surpass conventional standards in regards to time, accuracy and cost. Broadly classified as either label-free or labeled, modern biosensors exploit micro- and nanofabrication technologies and diverse sensing strategies including optical, electrical and mechanical transducers. Despite clinical need, translation of biosensors from research laboratories to clinical applications has remained limited to a few notable examples, such as the glucose sensor. Challenges to be overcome include sample preparation, matrix effects and system integration. We review the advances of biosensors for infectious disease diagnostics and discuss the critical challenges that need to be overcome in order to implement integrated diagnostic biosensors in real world settings.
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Affiliation(s)
- Mandy L Y Sin
- Department of Urology, Stanford University School of Medicine , Stanford, CA 94305-5118 , USA
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143
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Rapid resistome fingerprinting and clonal lineage profiling of carbapenem-resistant Klebsiella pneumoniae isolates by targeted next-generation sequencing. J Clin Microbiol 2014; 52:987-90. [PMID: 24403299 DOI: 10.1128/jcm.03247-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thirty-two carbapenem-resistant Klebsiella pneumoniae isolates, representative of different resistance mechanisms and clonal lineages, were analyzed with the Pathogenica HAI BioDetection system, based on targeted next-generation sequencing (NGS) technology. With most strains, the system simultaneously yielded comprehensive information on relevant β-lactam resistance determinants and accurate discrimination of clonal lineages, in a shorter time frame and in a less labor-intensive manner than currently available methods for molecular epidemiology analysis. Results supported the usefulness of targeted NGS-based technologies for similar applications.
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144
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Kollef MH. What can be expected from antimicrobial de-escalation in the critically ill? Intensive Care Med 2013; 40:92-5. [PMID: 24248604 DOI: 10.1007/s00134-013-3154-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8052, St. Louis, MO, 63110, USA,
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145
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Strategies to minimize antibiotic resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4274-305. [PMID: 24036486 PMCID: PMC3799537 DOI: 10.3390/ijerph10094274] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 02/07/2023]
Abstract
Antibiotic resistance can be reduced by using antibiotics prudently based on guidelines of antimicrobial stewardship programs (ASPs) and various data such as pharmacokinetic (PK) and pharmacodynamic (PD) properties of antibiotics, diagnostic testing, antimicrobial susceptibility testing (AST), clinical response, and effects on the microbiota, as well as by new antibiotic developments. The controlled use of antibiotics in food animals is another cornerstone among efforts to reduce antibiotic resistance. All major resistance-control strategies recommend education for patients, children (e.g., through schools and day care), the public, and relevant healthcare professionals (e.g., primary-care physicians, pharmacists, and medical students) regarding unique features of bacterial infections and antibiotics, prudent antibiotic prescribing as a positive construct, and personal hygiene (e.g., handwashing). The problem of antibiotic resistance can be minimized only by concerted efforts of all members of society for ensuring the continued efficiency of antibiotics.
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