1
|
Baker KR, Flentie K, Spears BR, Mozharov S, Roberts K, El ganbour A, Somers M, Calkwood J, Liu J, DaPonte K, Sam N, Kaur G, Chen F, Donato J, Chao A, Lewis A, Sherman J, Mortimer K, Harrington AT, Traczewski M, Carpenter D, Shortridge D, Lindley J, Diep A, Norton E, Green M, Gajewski J, Landrith R, Nalubega F, McCallum J, Beiswenger M, Dolan B, Brennan K, Carpenter A, Vacic A, Flyer AN, Pierce VM, Hooper DC, Lewis II JS, Stern E. Multicenter evaluation of the Selux Next-Generation Phenotyping antimicrobial susceptibility testing system. J Clin Microbiol 2024; 62:e0054623. [PMID: 38051069 PMCID: PMC10793272 DOI: 10.1128/jcm.00546-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 12/07/2023] Open
Abstract
The Selux Next-Generation Phenotyping (NGP) system (Charlestown, MA) is a new antimicrobial susceptibility testing system that utilizes two sequential assays performed on all wells of doubling dilution series to determine MICs. A multicenter evaluation of the performance of the Selux NGP system compared with reference broth microdilution was conducted following FDA recommendations and using FDA-defined breakpoints. A total of 2,488 clinical and challenge isolates were included; gram-negative isolates were tested against 24 antimicrobials, and gram-positive isolates were tested against 15 antimicrobials. Data is provided for all organism-antimicrobial combinations evaluated, including those that did and did not meet FDA performance requirements. Overall very major error and major error rates were less than 1% (31/3,805 and 107/15,606, respectively), essential agreement and categorical agreement were >95%, reproducibility was ≥95%, and the average time-to-result (from time of assay start to time of MIC result) was 5.65 hours.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mark Somers
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Jamie Liu
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Nikitha Sam
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Gurleen Kaur
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Felicia Chen
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Alan Chao
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Autumn Lewis
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | | | - Amanda T. Harrington
- Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, Illinois, USA
| | | | | | | | - Jill Lindley
- JMI Laboratories/Element, North Liberty, Iowa, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Virginia M. Pierce
- Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David C. Hooper
- Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James S. Lewis II
- Department of Pharmacy Services, Oregon Health and Science University Hospitals and Clinics, Portland, Oregon, USA
| | - Eric Stern
- Selux Diagnostics, Charlestown, Massachusetts, USA
| |
Collapse
|
2
|
Ren W, Mao Y, Li S, Gao B, Fu X, Liu X, Zhu P, Shang Y, Li Y, Ma B, Sun L, Xu J, Pang Y. Rapid Mycobacterium abscessus antimicrobial susceptibility testing based on antibiotic treatment response mapping via Raman Microspectroscopy. Ann Clin Microbiol Antimicrob 2023; 22:94. [PMID: 37904155 PMCID: PMC10617219 DOI: 10.1186/s12941-023-00644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
OBJECTIVES Antimicrobial susceptibility tests (ASTs) are pivotal tools for detecting and combating infections caused by multidrug-resistant rapidly growing mycobacteria (RGM) but are time-consuming and labor-intensive. DESIGN We used a Mycobacterium abscessus-based RGM model to develop a rapid (24-h) AST from the beginning of the strain culture, the Clinical Antimicrobials Susceptibility Test Ramanometry for RGM (CAST-R-RGM). The ASTs obtained for 21 clarithromycin (CLA)-treated and 18 linezolid (LZD)-treated RGM isolates. RESULTS CAST-R-RGM employs D2O-probed Raman microspectroscopy to monitor RGM metabolic activity, while also revealing bacterial antimicrobial drug resistance mechanisms. The results of clarithromycin (CLA)-treated and linezolid (LZD)-treated RGM isolates exhibited 90% and 83% categorical agreement, respectively, with conventional AST results of the same isolates. Furthermore, comparisons of time- and concentration-dependent Raman results between CLA- and LZD-treated RGM strains revealed distinct metabolic profiles after 48-h and 72-h drug treatments, despite similar profiles obtained for both drugs after 24-h treatments. CONCLUSIONS Ultimately, the rapid, accurate, and low-cost CAST-R-RGM assay offers advantages over conventional culture-based ASTs that warrant its use as a tool for improving patient treatment outcomes and revealing bacterial drug resistance mechanisms.
Collapse
Affiliation(s)
- Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuli Mao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Bo Gao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Liu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zhu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Single-Cell Biotech, Co. Ltd, Qingdao, Shandong, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuandong Li
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyang Sun
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jian Xu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
| |
Collapse
|
3
|
Del Rio A, Puci M, Muresu N, Sechi I, Saderi L, Cugia L, Sotgiu G, Piana A. Comparison of genotypic and phenotypic antimicrobial profile in carbapenemases producing Klebsiella pneumoniae. Acta Biomed 2023; 94:e2023201. [PMID: 37850773 PMCID: PMC10644917 DOI: 10.23750/abm.v94i5.14412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND AND AIM Prompt administration of appropriate antibiotic therapy is crucial in improving outcomes, particularly in cases sustained by multi-drug resistant strains. Although phenotypic antimicrobial susceptibility testing (AST) represents the gold standard to address antibiotics treatment, the long time required to obtained affordable results could negatively affect the prognosis. In contrast, rapid genotypic AST provide essential information for treatment and surveillance program. In order to evaluate the potential adoption of rapid AST in clinical routine, we compared the genotypic and phenotypic antimicrobial profiles of different K.pneumoniae strains, characterized by different expression of carbapenemases-encoding genes. METHODS A set of 109 strains of Cr-Kp were tested for the antimicrobial drugs by the automatized Vitek II system and, in parallel, to the new combination of β-lactams/β-lactamases inhibitors (BL/BLI) by Etest. An antimicrobial resistance index (ARI) was calculated for each strain, assigning each 1 or 0 points based on observed resistance/susceptibility, and dividing the total by the number of antibiotics tested. Kruskal-Wallis test, followed by Dunn's post hoc test (Bonferroni correction), were used to compare quantitative variables among resistance gene subgroups. RESULTS We observed a higher ARI score in KPC/OXA-48 strains, similar profile in KPC alone and KPC/CTX-M groups and a significant lower resistance in no-carbapenemases-producing group. Same trend was observed in AST for BL/BLI. CONCLUSIONS These preliminary results showed a close link between genotypic and phenotypic AST, supporting the adoption of rapid AST in cases of severe infections, ensuring to saving time and providing, the surveillance of MDR strains and improving stewardship programs.
Collapse
|
4
|
Strubbe G, Messiaen AS, Vandendriessche S, Verhasselt B, Boelens J. EUCAST rapid antimicrobial susceptibility testing (RAST) compared to conventional susceptibility testing: implementation and potential added value in a tertiary hospital in Belgium. Acta Clin Belg 2023; 78:385-391. [PMID: 36999562 DOI: 10.1080/17843286.2023.2197314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/26/2023] [Indexed: 04/01/2023]
Abstract
OBJECTIVES EUCAST breakpoints for short incubation disk diffusion allow rapid antimicrobial susceptibility testing (RAST) directly from positive blood cultures. We evaluate the RAST methodology and assess its potential added value in a setting of low prevalence of multidrug-resistant (MDR) organisms. METHODS In our two-part study, we performed RAST on 127 clinical blood cultures at 6 and 8 h and determined categorical agreement with direct susceptibility testing. We also measure the impact of susceptibility results on antimicrobial therapy compared to empirical treatment. RESULTS Categorical agreement was 96.2% at 6 h (575/598 isolate-drug combinations) and 96.6% at 8 h (568/588 combinations). Major errors involved piperacillin/tazobactam in 16 of 31 cases. The second part of our study shows that AST reporting proved essential in correcting ineffective empirical therapy in 6.3% of the patients (8/126). CONCLUSION EUCAST RAST is an inexpensive and reliable method of susceptibility testing, although care must be taken with reporting piperacillin/tazobactam. In support of RAST implementation, we show that AST remains of great importance in providing effective therapy, even in a setting of low MDR prevalence and elaborate antibiotic guidelines.
Collapse
Affiliation(s)
- Gregory Strubbe
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | | | | | - Bruno Verhasselt
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| |
Collapse
|
5
|
Chen J, San SSS, Kung A, Tomasek M, Liu D, Rodgers W, Gau V. Direct-from-specimen microbial growth inhibition spectrums under antibiotic exposure and comparison to conventional antimicrobial susceptibility testing. PLoS One 2022; 17:e0263868. [PMID: 35171945 PMCID: PMC8849476 DOI: 10.1371/journal.pone.0263868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022] Open
Abstract
Increasing global travel and changes in the environment may escalate the frequency of contact with a natural host carrying an infection and, therefore, increase our chances of encountering microorganisms previously unknown to humans. During an emergency, the etiology of infection may be unknown at the time of patient treatment. The existing local or global Antimicrobial Stewardship Programs may not be fully prepared for emerging/re-emerging infectious disease outbreaks, especially if they are caused by an unknown organism, engineered bioterrorist attack, or rapidly evolving superbug. We demonstrate an antimicrobial efficacy profiling method that can be performed in hours directly from clinical urine specimens. The antimicrobial potency was determined by the level of microbial growth inhibition and compared to conventional antimicrobial susceptibility testing results. The oligonucleotide probe pairs on the sensors were designed to target Gram-negative bacteria, specifically Enterobacterales and Pseudomonas aeruginosa. A pilot study of 10 remnant clinical specimens from the Clinical Laboratory Improvement Amendments-certified labs of New York-Presbyterian Queens was conducted, and only one sample was not detected by the probes. The remaining nine samples agreed with reference AST methods (Vitek and broth microdilution), resulting in 100% categorical agreement. In a separate feasibility study, we evaluated a dual-kinetic response approach, in which we inoculated two antibiotic stripwells containing the same antimicrobial concentrations with clinical specimens at the original concentration (1x) and at a 10-fold dilution (0.1x) to cover a broader range of microbiological responses. The combined categorical susceptibility reporting of 12 contrived urine specimens was 100% for ciprofloxacin, gentamicin, and meropenem over a range of microbial loads from 105 to 108 CFU/mL.
Collapse
Affiliation(s)
- Jade Chen
- GeneFluidics, Los Angeles, California, United States of America
| | - Su Su Soe San
- GeneFluidics, Los Angeles, California, United States of America
| | - Amelia Kung
- GeneFluidics, Los Angeles, California, United States of America
| | - Michael Tomasek
- GeneFluidics, Los Angeles, California, United States of America
| | - Dakai Liu
- Department of Pathology and Clinical Laboratories, New York-Presbyterian Queens, Flushing, New York, United States of America
| | - William Rodgers
- Department of Pathology and Clinical Laboratories, New York-Presbyterian Queens, Flushing, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York City, New York, United States of America
| | - Vincent Gau
- GeneFluidics, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
6
|
Bellali S, Haddad G, Iwaza R, Fontanini A, Hisada A, Ominami Y, Raoult D, Khalil JB. Antimicrobial susceptibility testing for Gram positive cocci towards vancomycin using scanning electron microscopy. Current Research in Microbial Sciences 2022; 3:100154. [PMID: 35909629 PMCID: PMC9325908 DOI: 10.1016/j.crmicr.2022.100154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
SEM-based method can be applied for rapid phenotypic AST on Gram-positive cocci towards 2 vancomycin based on morphological changes 3. The ratio of septa as a marker of bacterial division and size of grape-like clusters enabled the 4 profiling of E. faecalis, E. faecium and S. aureus after brief incubation with vancomycin 5. SEM-AST strategy showed the feasibility of detecting antibiotic susceptibility or 6 resistance on Gram-positive cocci within one hour of exposition to vancomycin 7.
The rapid detection of resistant bacteria has become a challenge for microbiologists worldwide. Numerous pathogens that cause nosocomial infections are still being treated empirically and have developed resistance mechanisms against key antibiotics. Thus, one of the challenges for researchers has been to develop rapid antimicrobial susceptibility testing (AST) to detect resistant isolates, ensuring better antibiotic stewardship. In this study, we established a proof-of-concept for a new strategy of phenotypic AST on Gram-positive cocci towards vancomycin using scanning electron microscopy (SEM). Our study evaluated the profiling of Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus after brief incubation with vancomycin. Sixteen isolates were analysed aiming to detect ultrastructural modifications at set timepoints, comparing bacteria with and without vancomycin. After optimising slides preparation and micrographs acquisition, two analytical strategies were used. The high magnification micrographs served to analyse the division of cocci based on the ratio of septa, along with the bacterial size. Susceptible strains with vancomycin showed a reduced septa percentage and the average surface area was consequently double that of the controls. The resistant bacteria revealed multiple septa occurring at advanced timepoints. Low magnification micrographs made it possible to quantify the pixels at different timepoints, confirming the profiling of cocci towards vancomycin. This new phenotypic AST strategy proved to be a promising tool to discriminate between resistant and susceptible cocci within an hour of contact with vancomycin. The analysis strategies applied here would potentially allow the creation of artificial intelligence algorithms for septa detection and bacterial quantification, subsequently creating a rapid automated SEM-AST assay.
Collapse
|
7
|
Heuer C, Bahnemann J, Scheper T, Segal E. Paving the Way to Overcome Antifungal Drug Resistance: Current Practices and Novel Developments for Rapid and Reliable Antifungal Susceptibility Testing. Small Methods 2021; 5:e2100713. [PMID: 34927979 DOI: 10.1002/smtd.202100713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/05/2021] [Indexed: 06/14/2023]
Abstract
The past year has established the link between the COVID-19 pandemic and the global spread of severe fungal infections; thus, underscoring the critical need for rapid and realizable fungal disease diagnostics. While in recent years, health authorities, such as the Centers for Disease Control and Prevention, have reported the alarming emergence and spread of drug-resistant pathogenic fungi and warned against the devastating consequences, progress in the diagnosis and treatment of fungal infections is limited. Early diagnosis and patient-tailored therapy are established to be key in reducing morbidity and mortality associated with fungal (and cofungal) infections. As such, antifungal susceptibility testing (AFST) is crucial in revealing susceptibility or resistance of these pathogens and initiating correct antifungal therapy. Today, gold standard AFST methods require several days for completion, and thus this much delayed time for answer limits their clinical application. This review focuses on the advancements made in developing novel AFST techniques and discusses their implications in the context of the practiced clinical workflow. The aim of this work is to highlight the advantages and drawbacks of currently available methods and identify the main gaps hindering their progress toward clinical application.
Collapse
Affiliation(s)
- Christopher Heuer
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| |
Collapse
|
8
|
Michael CA, Gillings MR, Blaskovich MAT, Franks AE. The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.692674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The global rise of antimicrobial resistance (AMR) phenotypes is an exemplar for rapid evolutionary response. Resistance arises as a consequence of humanity’s widespread and largely indiscriminate use of antimicrobial compounds. However, some features of this crisis remain perplexing. The remarkably widespread and rapid rise of diverse, novel and effective resistance phenotypes is in stark contrast to the apparent paucity of antimicrobial producers in the global microbiota. From the viewpoint of evolutionary theory, it should be possible to use selection coefficients to examine these phenomena. In this work we introduce an elaboration on the selection coefficient s termed selective efficiency, considering the genetic, metabolic, ecological and evolutionary impacts that accompany selective phenotypes. We then demonstrate the utility of the selective efficiency concept using AMR and antimicrobial production phenotypes as ‘worked examples’ of the concept. In accomplishing this objective, we also put forward cogent hypotheses to explain currently puzzling aspects of the AMR crisis. Finally, we extend the selective efficiency concept into a consideration of the ongoing management of the AMR crisis.
Collapse
|
9
|
Wang G, Song G, Xu Y. A Rapid Antimicrobial Susceptibility Test for Klebsiella pneumoniae Using a Broth Micro-Dilution Combined with MALDI TOF MS. Infect Drug Resist 2021; 14:1823-1831. [PMID: 34025124 PMCID: PMC8132464 DOI: 10.2147/idr.s305280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Background Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a novel method that can be used to identify pathogens and has potential applications in the detection of drug-resistant bacteria. Purpose To evaluate the ability of a MALDI-TOF MS-based broth micro-dilution method in detecting the minimum inhibitory concentration (MIC) values of Klebsiella pneumoniae to ceftriaxone and imipenem. Materials and Methods Sixty strains of K. pneumoniae with different levels of resistance to carbapenems and cephalosporins were randomly collected. The 0.5 McFarland (Mc) concentration of the bacterial suspension was inoculated in cation-adjusted Mueller-Hinton broth (CAMHB) with a final cell turbidity of 5×105 CFU/mL. The broth was incubated with serial concentrations of antibiotics. After centrifuging the bacterial suspensions, the lysed cells were analyzed by MALDI-TOF MS to identify the growth-promoting or inhibitory effects on K. pneumoniae. The molecular mechanisms of resistance were investigated by PCR and DNA sequencing analysis. Results The expression of known resistance genes (blaKPC, blaFOX, blaDHA, blaCTX-M and blaTEM) was detected in the 30 carbapenems-resistant strains. The agreement between the MIC values derived from the MALDI-TOF MS analysis and from the broth micro-dilution method was 61.7% for ceftriaxone and 71.7% for imipenem. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoint of resistance to ceftriaxone and imipenem, the 60 isolates were accurately classified as resistant or susceptible isolates with 100% sensitivity and 100% specificity. Conclusion The transmission and infection of multidrug-resistant bacteria could be better managed and treated with the rapid identification of strains and antimicrobial susceptibility. A MALDI-TOF MS-based susceptibility test could be used to identify resistance of K. pneumoniae within a short time-frame. This approach could potentially be used as a supplementary antimicrobial susceptibility test that could be investigated on more bacterial species combined with different antibiotics.
Collapse
Affiliation(s)
- Gang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| | - Guobin Song
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China.,Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| |
Collapse
|
10
|
Abstract
BACKGROUND Rapid antimicrobial susceptibility tests are expected to reduce the time to clinically important results of a blood culture. This might enable clinicians to better target therapy to a person's needs, and thereby, improve health outcomes (mortality, length of hospital stay), and reduce unnecessary prescribing of broad-spectrum antibiotics; thereby reducing antimicrobial resistance rates. OBJECTIVES To assess the effects of rapid susceptibility testing versus standard susceptibility testing for bloodstream infections (BSIs). SEARCH METHODS To identify studies with selected outcomes, we searched the Cochrane Infectious Diseases Group Specialised Register, CENTRAL, MEDLINE, LILACS, and two trials registries, between 1987 and October 2020. We used 'bloodstream infection' and 'antimicrobial susceptibility tests' as search terms. We had no language or publication status limitations. SELECTION CRITERIA Randomized controlled trials (RCTs) comparing rapid antimicrobial susceptibility testing (with a time-to-result of ≤ 8 hours) versus conventional antimicrobial susceptibility testing in people with a BSI caused by any bacteria, as identified by a positive blood culture. DATA COLLECTION AND ANALYSIS Two review authors independently screened references, full-text reports of potentially relevant studies, extracted data from the studies, and assessed risk of bias. Any disagreement was discussed and resolved with a third review author. For mortality, a dichotomous outcome, we extracted the number of events in each arm, and presented a risk ratio (RR) with 95% confidence interval (CI) to compare rapid susceptibility testing to conventional methods. We used Review Manager 5.4 to meta-analyse the data. For other outcomes, which are time-to-event outcomes (time-to-discharge from hospital, time-to-first appropriate antibiotic change), we conducted qualitative narrative synthesis, due to heterogeneity of outcome measures. MAIN RESULTS: We included six trials, with 1638 participants. For rapid antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.10, 95% CI 0.82 to 1.46; 6 RCTs, 1638 participants; low-certainty evidence). In subgroup analysis, for rapid genotypic or molecular antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.02, 95% CI 0.69 to 1.49; 4 RCTs, 1074 participants; low-certainty evidence). For phenotypic rapid susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.37, 95% CI 0.80 to 2.35; 2 RCTs, 564 participants; low-certainty evidence). In qualitative analysis, rapid susceptibility testing may make little or no difference in time-to-discharge (4 RCTs, 1165 participants; low-certainty evidence). In qualitative analysis, rapid genotypic susceptibility testing compared to conventional testing may make little or no difference in time-to-appropriate antibiotic (3 RCTs, 929 participants; low-certainty evidence). In subgroup analysis, rapid phenotypic susceptibility testing compared to conventional testing may improve time-to-appropriate antibiotic (RR -17.29, CI -45.05 to 10.47; 2 RCTs, 564 participants; low-certainty evidence). AUTHORS' CONCLUSIONS: The theoretical benefits of rapid susceptibility testing have not been demonstrated to directly improve mortality, time-to-discharge, or time-to-appropriate antibiotic in these randomized studies. Future large prospective studies should be designed to focus on the most clinically meaningful outcomes, and aim to optimize blood culture pathways.
Collapse
Affiliation(s)
- Vanesa Anton-Vazquez
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Paul Hine
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sanjeev Krishna
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Marty Chaplin
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Timothy Planche
- Medical Microbiology Department, SouthWest London Pathology, Jenner Wing St George's Hospital, London, UK
| |
Collapse
|
11
|
Basbas C, Byrne BA, Chigerwe M, Escobar ED, Hodzic E, Pires AFA, Pereira RV. Detection of Cephalosporin and Fluoroquinolone Resistance Genes via Novel Multiplex qPCR in Fecal Salmonella Isolates From Northern Californian Dairy Cattle, 2002-2016. Front Microbiol 2021; 12:601924. [PMID: 33658984 PMCID: PMC7917062 DOI: 10.3389/fmicb.2021.601924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023] Open
Abstract
The objectives of this study were to evaluate the prevalence of extended spectrum β-lactamase (ESBL) genes, AmpC-type β-lactamase (ACBL) genes, and plasmid mediated quinolone resistance (PMQR) genes in Salmonella isolated at a Veterinary Medical Teaching Hospital microbiology laboratory, examine trends in presence of these resistance genes, and to explore the correlation between phenotypic resistance and presence of specific genes. The presence of ESBL, ACBL, and PMQR genes were detected using a single, novel multiplex qPCR. Only the genes blaCMY–2 and blaTEM were detected in the 110 Salmonella isolates tested. PMQR genes were not detected in isolates screened. Of 94 third-generation cephalosporin resistant isolates, representing eight serotypes, 48% (n = 45) were positive for blaCMY–2 only and 50% (n = 47) were simultaneously positive for blaCMY–2 and blaTEM. Two third-generation cephalosporin resistant isolates were tested negative for all β-lactamase genes in our qPCR assay and likely house ESBL genes not screened for by our qPCR assay. A logistic regression model revealed that for serotype Dublin isolates (n = 38) the odds ratio for testing positive for blaTEM when compared to all other serotypes was 51.6 (95% CI: 4.01–664.03, p = 0.0029). For serotype Typhimurium (n = 9) the odds ratio for testing positive for blaTEM when compared to all other serotypes was 43.3 (95% CI: 1.76–1000, p = 0.0216). Overall, our results suggest that the prevalence of resistance to cephalosporins and fluoroquinolones due to ESBLs, ACBLs, and PMQR genes present in bovine nontyphoidal Salmonella enterica isolates has remained relatively constant in the isolates screened over a 14-year period.
Collapse
Affiliation(s)
- Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Barbara A Byrne
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Munashe Chigerwe
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Edlin D Escobar
- Real-Time PCR Research and Diagnostics Core Facility, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Emir Hodzic
- Real-Time PCR Research and Diagnostics Core Facility, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Alda F A Pires
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Richard V Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| |
Collapse
|
12
|
Ehren K, Meißner A, Jazmati N, Wille J, Jung N, Vehreschild JJ, Hellmich M, Seifert H. Clinical Impact of Rapid Species Identification From Positive Blood Cultures With Same-day Phenotypic Antimicrobial Susceptibility Testing on the Management and Outcome of Bloodstream Infections. Clin Infect Dis 2021; 70:1285-1293. [PMID: 31094414 DOI: 10.1093/cid/ciz406] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Timely availability of microbiological results from positive blood cultures is essential to enable early pathogen-directed therapy. The Accelerate Pheno system (ADX) is a novel technology using fluorescence in situ hybridization for rapid species identification (ID) and morphokinetic bacterial analysis for phenotypic antimicrobial susceptibility testing (AST), with promising results. Yet the impact of this technology on clinical management and patient outcome remains unclear. METHODS We conducted a quasiexperimental before-and-after observational study and analyzed 3 groups with different diagnostic and therapeutic pathways following recent integration of ADX: conventional microbiological diagnostics with and without antimicrobial stewardship program (ASP) intervention, and rapid diagnostics (ADX in addition to conventional standard) with ASP intervention. Primary endpoints were time to adequate, to optimal and to step-down antimicrobial therapy. Secondary endpoints were antimicrobial consumption, in-hospital mortality, length of stay (LOS), and the incidence of Clostridioidesdifficile infection (CDI). RESULTS Two hundred four patients (conventional diagnostics, n = 64; conventional diagnostics + ASP, n = 68; rapid diagnostics + ASP; n = 72) were evaluated. The use of ADX significantly decreased time from Gram stain to ID (median, 23 vs 2.2 hours, P < .001) and AST (median, 23 vs 7.4 hours, P < .001), from Gram stain to optimal therapy (median, 11 vs 7 hours, P = .024) and to step-down antimicrobial therapy (median, 27.8 vs 12 hours, P = .019). However, groups did not differ in antimicrobial consumption, duration of antimicrobial therapy, mortality, LOS, or incidence of CDI. CONCLUSIONS Use of ADX significantly reduced time to ID and AST as well as time to optimal antimicrobial therapy but did not affect antimicrobial consumption and clinical outcome.
Collapse
Affiliation(s)
- Kathrin Ehren
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Germany
| | - Arne Meißner
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Germany.,Department of Hospital Hygiene and Infection Control, University Hospital of Cologne, Germany
| | - Nathalie Jazmati
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, University Hospital of Cologne, Germany
| | - Norma Jung
- Department I for Internal Medicine, University Hospital of Cologne, Germany
| | - Jörg Janne Vehreschild
- German Center for Infection Research, Partner Site Bonn-Cologne, University Hospital of Cologne, Germany.,Department I for Internal Medicine, University Hospital of Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics and Computational Biology, University Hospital of Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, University Hospital of Cologne, Germany
| |
Collapse
|
13
|
Åkerlund A, Jonasson E, Matuschek E, Serrander L, Sundqvist M, Kahlmeter G. EUCAST rapid antimicrobial susceptibility testing (RAST) in blood cultures: validation in 55 European laboratories. J Antimicrob Chemother 2020; 75:3230-3238. [PMID: 32789506 PMCID: PMC7566356 DOI: 10.1093/jac/dkaa333] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES When bloodstream infections are caused by resistant bacteria, rapid antimicrobial susceptibility testing (RAST) is important for adjustment of therapy. The EUCAST RAST method, directly from positive blood cultures, was validated in a multi-laboratory study in Europe. METHODS RAST was performed in 40 laboratories in northern Europe (NE) and 15 in southern Europe (SE) from clinical blood cultures positive for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus or Streptococcus pneumoniae. Categorical results at 4, 6 and 8 h of incubation were compared with results for EUCAST standard 16-20 h disc diffusion. The method, preliminary breakpoints and the performance of the laboratories were evaluated. RESULTS The total number of isolates was 833/318 in NE/SE. The number of zone diameters that could be read (88%, 96% and 99%) and interpreted (70%, 81% and 85%) increased with incubation time (4, 6 and 8 h). The categorical agreement was acceptable, with total error rates in NE/SE of 2.4%/4.9% at 4 h, 1.1%/3.5% at 6 h and 1.1%/3.3% at 8 h. False susceptibility at 4, 6 and 8 h of incubation was below 0.3% and 1.1% in NE and SE, respectively, and the corresponding percentages for false resistance were below 1.9% and 2.8%. After fine-tuning breakpoints, more zones could be interpreted (73%, 89% and 93%), with only marginally affected error rates. CONCLUSIONS The EUCAST RAST method can be implemented in routine laboratories without major investments. It provides reliable antimicrobial susceptibility testing results for relevant bloodstream infection pathogens after 4-6 h of incubation.
Collapse
Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, County Hospital Ryhov, Jönköping, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Linköping University Hospital, Linköping, Sweden
| | - Emma Jonasson
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
- EUCAST Development Laboratory, Växjö, Sweden
| | | | - Lena Serrander
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Linköping University Hospital, Linköping, Sweden
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
- EUCAST Development Laboratory, Växjö, Sweden
| |
Collapse
|
14
|
Abstract
![]()
Growing
antimicrobial resistance (AMR) is a serious global threat to human
health. Current methods to detect resistance include phenotypic antibiotic
sensitivity testing (AST), which measures bacterial growth and is
therefore hampered by a slow time to obtain results (∼12–24
h). Therefore, new rapid phenotypic methods for AST are urgently needed.
Nanomechanical cantilever sensors have recently shown promise for
rapid AST but challenges of bacterial immobilization can lead to variable
results. Herein, a novel cantilever-based method is described for
detecting phenotypic antibiotic resistance within ∼45 min,
capable of detecting single bacteria. This method does not require
complex, variable bacterial immobilization and instead uses a laser
and detector system to detect single bacterial cells in media as they
pass through the laser focus. This provides a simple readout of bacterial
antibiotic resistance by detecting growth (resistant) or death (sensitive),
much faster than the current methods. The potential of this technique
is demonstrated by determining the resistance in both laboratory and
clinical strains of Escherichia coli (E. coli), a key species responsible
for clinically burdensome urinary tract infections. This work provides
the basis for a simple and fast diagnostic tool to detect antibiotic
resistance in bacteria, reducing the health and economic burdens of
AMR.
Collapse
Affiliation(s)
- Isabel Bennett
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Alice L. B. Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Materials Science and Engineering, Sir Robert Hadfield Building, University of Sheffield, Sheffield S1 3JD, United Kingdom
| | - Rachel A. McKendry
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| |
Collapse
|
15
|
MacVane SH, Oppermann N, Humphries RM. Time to Result for Pathogen Identification and Antimicrobial Susceptibility Testing of Bronchoalveolar Lavage and Endotracheal Aspirate Specimens in U.S. Acute Care Hospitals. J Clin Microbiol 2020; 58:e01468-20. [PMID: 32878953 DOI: 10.1128/JCM.01468-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/30/2020] [Indexed: 01/16/2023] Open
Abstract
Identification (ID) and antimicrobial susceptibility testing (AST) of respiratory pathogens are critical to the management of patients with pneumonia to facilitate optimal antibiotic therapy selection. Few studies have examined the time to results (TTR) for this critical specimen, and such data can be valuable for benchmarking the current paradigm of diagnostic approaches. TTR for bronchoalveolar lavage (BAL) and endotracheal aspirate (ETA) specimens from hospitalized patients was evaluated using the Premier Healthcare Database, a comprehensive database of 194 U.S. hospitals. Times from specimen collection to reporting of organism ID/AST were evaluated and compared by specimen types and characteristics. A total of 79,662 (43,129 BAL; 36,533 ETA) specimens were included, of which 19.3% harbored no growth, 47.1% contained normal respiratory flora alone (including yeast), and 0.6% contained mycobacteria/molds. Potential bacterial pathogens (PBP) were recovered from 33.0%. ETA specimens had a higher proportion of specimens with isolation of PBP (39.2% versus 27.7%) and with normal respiratory flora (52.0% versus 43.0%) and were less likely to be negative (8.2% versus 28.6%) than BAL specimens (all P < 0.0001). Staphylococcus aureus and Pseudomonas aeruginosa were isolated in 10.5 and 6.4% of the specimens, respectively, and were the most common organisms identified. Median (interquartile range) TTR were 37.0 h (21.8 to 51.7 h) and 60.5 h (46.6 to 72.4 h) for ID and AST, respectively. Median TTR for major respiratory pathogens by organism ranged from 29.2 to 43.9 h for ID and from 47.9 to 73.9 h for AST. Organism type, specimen collection time, and hospital teaching status influenced TTR. Mechanically vented patients and ETA specimens were more likely to recover PBP.
Collapse
|
16
|
Infante A, Ortiz de la Tabla V, Martín C, Gázquez G, Buñuel F. Rapid identification and antimicrobial susceptibility testing of Gram-negative rod on positive blood cultures using MicroScan panels. Eur J Clin Microbiol Infect Dis 2020; 40:151-157. [PMID: 32860091 DOI: 10.1007/s10096-020-04014-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022]
Abstract
Shortening the turnaround time of antimicrobial susceptibility testing (AST) of bacteria permits a significant reduction of patient morbidity, mortality, and cost. Conventional blood culture methods are the gold standard diagnostic test to guide management of patient with sepsis, but the conventional process requires at least 12 to 24 h after the blood culture has been flagged as positive due to requirement for pure colonies. We describe a simple and inexpensive method to obtain faster AST with MicroScan system (Beckman Coulter) directly from positive blood cultures. Conventional and direct identification and AST were performed simultaneously by both methods in 1070 blood cultures, and 9106 MICs were determinated. About 96.5% were correctly identified with the direct method. Overall, categorical agreement was 92.86%. We found 46 very major errors, but globally the results showed a good correlation with the standard method, particularly favorable for E. coli and K. pneumoniae, except amoxicillin-clavulanate and piperacillin-tazobactam. For P. mirabilis, betalactams antibiotics (except second- and third-generation cephalosporines) showed a good correlation, and also a good correlation was found for ciprofloxacine and gentamicine in P. aeruginosa and amoxicillin-clavulanate, ciprofloxacine, gentamicine, and cotrimoxazole in E. cloacae. This method has the main advantage of providing reliable results 1 day earlier, being a simple, fast, and cheap method for identification and antimicrobial susceptibility testing results from positive blood cultures.
Collapse
Affiliation(s)
- A Infante
- Servicio de Microbiología, Hospital Universitario San Juan de Alicante, Alicante, Spain.
| | - V Ortiz de la Tabla
- Servicio de Microbiología, Hospital Universitario San Juan de Alicante, Alicante, Spain
| | - C Martín
- Servicio de Microbiología, Hospital Universitario San Juan de Alicante, Alicante, Spain
| | - G Gázquez
- Servicio de Microbiología, Hospital Universitario San Juan de Alicante, Alicante, Spain
| | - F Buñuel
- Servicio de Microbiología, Hospital Universitario San Juan de Alicante, Alicante, Spain
| |
Collapse
|
17
|
Abstract
Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.
Collapse
Affiliation(s)
- Antti Vasala
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P. Hytönen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Olli H. Laitinen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| |
Collapse
|
18
|
De Angelis G, Posteraro B, Menchinelli G, Liotti FM, Spanu T, Sanguinetti M. Antimicrobial susceptibility testing of pathogens isolated from blood culture: a performance comparison of Accelerate Pheno™ and VITEK® 2 systems with the broth microdilution method. J Antimicrob Chemother 2020; 74:i24-i31. [PMID: 30690539 PMCID: PMC6382034 DOI: 10.1093/jac/dky532] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Objectives To compare the performance of the Accelerate Pheno™ system with that of the conventional phenotypic VITEK® 2 system for rapid antimicrobial susceptibility testing (AST) of bacterial pathogens from positive blood culture (PBC) samples, based on the reference broth microdilution (BMD) method. Methods Prospectively collected PBCs that represented patient-unique bloodstream infection episodes were included. For PBC samples showing monomicrobial growth (n = 86), AST was performed using both Accelerate Pheno™ and VITEK® 2 systems directly from PBC broth. Colony isolates derived from subculture of PBC broth were then used for BMD testing. AST results were interpreted according to 2017 EUCAST breakpoints. Results The overall categorical agreement between Accelerate Pheno™ system and BMD was 92.7% (467/504) for Gram-negative organisms and 99.0% (95/96) for Gram-positive organisms, with rates for very major errors of 3.6% (6/166), major errors 2.2% (9/416) and minor errors 3.8% (23/600). The overall categorical agreement between the VITEK® 2 system and BMD was 91.7% (463/505) for Gram-negative organisms and 99.0% (97/98) for Gram-positive organisms, with rates of very major errors of 2.4% (4/169), major errors 1.0% (4/416) and minor errors 5.8% (35/603). Importantly, unlike the VITEK® 2 system, no false-susceptible results occurred with two colistin-resistant organism-growing PBCs tested using the Accelerate Pheno™ system. Conclusions Based on these findings, the Accelerate Pheno™ system can be a valid alternative for the rapid AST of Gram-negative and Gram-positive bacteria in bloodstream infections.
Collapse
Affiliation(s)
- Giulia De Angelis
- Istituto di Microbiologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Istituto di Patologia Speciale Medica e Semeiotica Medica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giulia Menchinelli
- Istituto di Microbiologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Flora Marzia Liotti
- Istituto di Microbiologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Teresa Spanu
- Istituto di Microbiologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Istituto di Microbiologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| |
Collapse
|
19
|
Pilmis B, Jiang O, Thy M, Defarge S, Mizrahi A, Couzigou C, Vidal B, Le Monnier A, Nguyen Van JC. Clinical impact of rapid susceptibility testing on Mueller-Hinton Rapid-SIR directly from urine specimens. Eur J Clin Microbiol Infect Dis 2020; 39:1373-7. [PMID: 32090300 DOI: 10.1007/s10096-020-03855-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/17/2020] [Indexed: 10/23/2022]
Abstract
Urinary tract infection diagnosis and management generally involves a 48-h microbiological delay to obtain the antibiotic susceptibility test (AST) results. In the context of multidrug resistance, reducing the time to obtain AST results is an essential factor, allowing for more timely appropriate treatment. We conducted a single-centre prospective study on urinary samples meeting two criteria: significant leukocyturia > 50/mm3 and exclusive presence of Gram-negative bacilli on direct examination. AST were performed by direct inoculation on Mueller-Hinton Rapid-SIR (MHR-SIR) agar. We evaluated the time to antibiotic adaptation by the antimicrobial stewardship team according to rapid AST results. Patients were subsequently excluded from the study if asymptomatic bacteria were confirmed, or in the absence of clinical data. Seventy patients were included. Mean age of patients was 68.8 years (± 21.3). Empirical antibiotic treatment were mainly based on third generation cephalosporins (n = 33), fluoroquinolones (n = 15), beta-lactamin/beta-lactamase inhibitors (n = 7), fosfomycin and nitrofurantoin (n = 5, each). The average time to obtain results was 7.2 h (± 1.6 h). Adaptation of therapy following MHR-SIR was performed for 29 patients (41%) with early switch to oral antibiotics, de-escalation or escalation in respectively 72.3%, 30%, and 11% of cases. Time saving of MHR-SIR compared with the standard technique was 42.6 (± 16.7) h. This study showed that rapid antibiotic susceptibility test results, using MHR-SIR method directly from urine, can be obtained 40 h earlier than conventional AST. The study also demonstrated significant clinical impact on the selection and reduction of the antibiotic therapy spectrum.
Collapse
|
20
|
Nix ID, Idelevich EA, Storck LM, Sparbier K, Drews O, Kostrzewa M, Becker K. Detection of Methicillin Resistance in Staphylococcus aureus From Agar Cultures and Directly From Positive Blood Cultures Using MALDI-TOF Mass Spectrometry-Based Direct-on-Target Microdroplet Growth Assay. Front Microbiol 2020; 11:232. [PMID: 32117194 PMCID: PMC7033577 DOI: 10.3389/fmicb.2020.00232] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 11/26/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS)-based direct-on-target microdroplet growth assay (DOT-MGA) was recently described as a novel method of phenotypic antimicrobial susceptibility testing (AST). Here, we developed the application of MALDI-TOF MS-based DOT-MGA for Gram-positive bacteria including AST from agar cultures and directly from positive blood cultures (BCs) using the detection of methicillin resistance as example. Consecutively collected, a total of 14 methicillin-resistant Staphylococcus aureus (MRSA) and 14 methicillin-susceptible S. aureus (MSSA) clinical isolates were included. Furthermore, a collection of MRSA challenge strains comprising different SCCmec types, mec genes, and spa types was tested. Blood samples were spiked with MRSA and MSSA and positive BC broth processed by three different methods: serial dilution of BC broth, lysis/centrifugation, and differential centrifugation. Processed BC broth was directly used for rapid AST using DOT-MGA. Droplets of 6 μl with and without cefoxitin at the EUCAST breakpoint concentration were spotted in triplicates onto the surface of a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard as a quality control (QC). Spectra were acquired and evaluated using MALDI Biotyper software. First, tests were considered as valid, if the growth control achieved an identification score of ≥1.7. For valid tests, same score criterion was used for resistant isolates when incubated with cefoxitin. An identification score <1.7 after incubation with cefoxitin defined susceptible isolates. On-target protein extraction using formic acid considerably improved detection of methicillin resistance in S. aureus and DOT-MGA showed feasible results for AST from agar cultures after 4 h incubation time. Comparing the different processing methods of positive BC broth, lysis/centrifugation method with a final dilution step 10–1 of the 0.5 McFarland suspension resulted in best test performance after 4 h incubation time. Overall, 96.4% test validity, 100% sensitivity, and 100% specificity were achieved for detection of methicillin resistance in clinical isolates. All strains of the MRSA challenge collection were successfully tested as methicillin-resistant. This first study on Gram-positive organisms showed feasibility and accuracy of MALDI-TOF MS-based DOT-MGA for rapid AST of S. aureus from agar cultures and directly from positive BCs.
Collapse
Affiliation(s)
- Ilka D Nix
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Evgeny A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Luise M Storck
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | | | | | | | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.,Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
21
|
Wang R, Vemulapati S, Westblade LF, Glesby MJ, Mehta S, Erickson D. cAST: Capillary-Based Platform for Real-Time Phenotypic Antimicrobial Susceptibility Testing. Anal Chem 2020; 92:2731-2738. [PMID: 31944675 DOI: 10.1021/acs.analchem.9b04991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance is recognized as one of the greatest emerging threats to public health. Antimicrobial resistant (AMR) microorganisms affect nearly 2 million people a year in the United States alone and place an estimated $20 billion burden on the healthcare system. The rise of AMR microorganisms can be attributed to a combination of overprescription of antimicrobials and a lack of accessible diagnostic methods. Delayed diagnosis is one of the primary reasons for empiric therapy, and diagnostic methods that enable rapid and accurate results are highly desirable to facilitate evidence-based treatment. This is particularly true for clinical situations at the point-of-care where access to state-of-the-art diagnostic equipment is scarce. Here, we present a capillary-based antimicrobial susceptibility testing platform (cAST), a unique approach that offers accelerated assessment of antimicrobial susceptibility in a low-cost and simple testing format. cAST delivers an expedited time-to-readout by means of optical assessment of bacteria incubated in a small capillary form factor along with a resazurin dye. cAST was designed using a combination of off-the-shelf and custom 3D-printed parts, making it extremely suitable for use in resource-limited settings. We demonstrate that growth of bacteria in cAST is approximately 25% faster than in a conventional microplate, further validate the diagnostic performance with clinical isolates, and show that cAST can deliver accurate antimicrobial susceptibility test results within 4-8 h.
Collapse
Affiliation(s)
- Ruisheng Wang
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Sasank Vemulapati
- Sibley School of Mechanical and Aerospace Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine , Weill Cornell Medicine , New York , New York 10065 , United States.,Division of Infectious Diseases, Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Marshall J Glesby
- Division of Infectious Diseases, Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Saurabh Mehta
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14853 , United States
| | - David Erickson
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States.,Division of Nutritional Sciences , Cornell University , Ithaca , New York 14853 , United States
| |
Collapse
|
22
|
Toosky MN, Grunwald JT, Pala D, Shen B, Zhao W, D’Agostini C, Coghe F, Angioni G, Motolese G, Abram TJ, Nicolai E. A rapid, point-of-care antibiotic susceptibility test for urinary tract infections. J Med Microbiol 2020; 69:52-62. [PMID: 31846419 PMCID: PMC7440674 DOI: 10.1099/jmm.0.001119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/12/2019] [Indexed: 11/18/2022] Open
Abstract
Introduction. The alarming rise in urinary tract infection (UTI) antimicrobial resistance has resulted from a combination of high prevalence, low specificity and the lack of a rapid, point-of-care (POC) antibiotic susceptibility test (AST), which has led to the overuse/inappropriate use of antibiotics.Aim. This study aimed to evaluate the performance of a rapid POC phenotypic AST device in reporting susceptibility information within 2 h.Methodology. Instrument calibration was performed with model bacteria and fluorescent microbeads to determine the dynamic range and limit of detection for quantifying concentrations of bacteria and demonstrate the ability to rapidly differentiate susceptible and resistant model bacteria. We then evaluated 30 presumptive UTI-positive patient urine samples in a clinical pilot study using a panel of 5 common UTI antibiotics plus a growth control and compared our results to the hospital standard of care AST.Results. Our device was able to robustly detect and quantify bacteria concentrations from 50 to 105 colony-forming units (c.f.u.) ml-1. The high sensitivity of this measurement technique enabled the device to differentiate between susceptible and resistant model bacteria with 100 % specificity over a 2 h growth period. In the clinical pilot study, an overall categorical agreement (CA) of 90.7 % was observed (sensitivity=91.4 %, specificity=88.9 %, n=97) with performance for individual drugs ranging from 85 % CA (ceftazidime) to 100 % (nitrofurantoin).Conclusions. By reducing the typical timeframe for susceptibility testing from 2-3 days to 2 h, our POC phenotypic AST can provide critical information to clinicians prior to the administration of antibiotic therapy.
Collapse
Affiliation(s)
| | | | - Daniela Pala
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
| | | | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Cartesio D’Agostini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Ferdinando Coghe
- Laboratory Clinical Chemical Analysis and Microbiology, University Hospital of Cagliari, Cagliari, Italy
| | - Giancarlo Angioni
- Laboratory Clinical Chemical Analysis and Microbiology, AOBrotzu, Cagliari, Italy
| | - Guido Motolese
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
| | | | - Eleonora Nicolai
- Apparecchiature Scientifiche Innovative, S.r.l., Milan, Italy
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| |
Collapse
|
23
|
Dewachter L, Fauvart M, Michiels J. Bacterial Heterogeneity and Antibiotic Survival: Understanding and Combatting Persistence and Heteroresistance. Mol Cell 2019; 76:255-67. [DOI: 10.1016/j.molcel.2019.09.028] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022]
|
24
|
Hogan CA, Watz N, Budvytiene I, Banaei N. Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia. Diagn Microbiol Infect Dis 2019; 94:116-121. [PMID: 30711413 DOI: 10.1016/j.diagmicrobio.2019.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/28/2018] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Optimizing therapy for bacteremia is currently limited by the 1-2-day turnaround time required for antimicrobial susceptibility testing (AST). Here, we assess a rapid AST method with VITEK®2 (bioMérieux, France) directly from positive blood cultures. METHODS Patient-derived positive blood cultures with Gram-negative rods identified as Enterobacteriaceae and Pseudomonas aeruginosa were prospectively tested, and other blood culture bottles were spiked with carbapenem-resistant Enterobacteriaceae (CRE). Positive cultures were subjected to red blood cell lysis and centrifugation, and setup on VITEK®2. RESULTS A total of 109 patient blood cultures and 52 spiked blood cultures were tested. Overall, essential agreement was 97.7% [95% confidence interval (CI) 96.4-99.0], and categorical agreement was 96.8% (95% CI 95.0-98.6). Mean turnaround time from setup to susceptibility results for Enterobacteriaceae in the clinical cultures was 9.0 (±1.3) h. CONCLUSIONS Direct susceptibility testing of blood cultures by VITEK®2 for Enterobacteriaceae is an accurate, practical, and inexpensive diagnostic strategy for rapid automated AST.
Collapse
Affiliation(s)
- C A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Watz
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - I Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - N Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
25
|
Anton-Vazquez V, Hine P, Krishna S, Richardson M, Planche T. Rapid versus standard antibiotic susceptibility testing for treating bloodstream infections. Hippokratia 2018. [DOI: 10.1002/14651858.cd013235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vanesa Anton-Vazquez
- St Georges University of London, Institute of Infection and Immunity; Medical Microbiology Department; Cranmer Terrace London UK SW17 ORE
| | - Paul Hine
- Liverpool School of Tropical Medicine; Department of Clinical Sciences; Pembroke Place Liverpool UK L3 5QA
| | - Sanjeev Krishna
- St George's, University of London; Institute for Infection and Immunity; London UK
| | - Marty Richardson
- Liverpool School of Tropical Medicine; Department of Clinical Sciences; Pembroke Place Liverpool UK L3 5QA
| | - Timothy Planche
- SouthWest London Pathology, Jenner Wing St George’s Hospital; Medical Microbiology Department; Cranmer Terrace London UK SW17 ORE
| |
Collapse
|
26
|
Li M, Liu M, Song Q, Xiong L, Chen Z, Kang M, Xie Y. Rapid antimicrobial susceptibility testing by matrix-assisted laser desorption ionization–time of flight mass spectrometry using a qualitative method in Acinetobacter baumannii complex. J Microbiol Methods 2018; 153:60-5. [DOI: 10.1016/j.mimet.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 11/24/2022]
|
27
|
Idelevich EA, Storck LM, Sparbier K, Drews O, Kostrzewa M, Becker K. Rapid Direct Susceptibility Testing from Positive Blood Cultures by the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Direct-on-Target Microdroplet Growth Assay. J Clin Microbiol 2018; 56:e00913-18. [PMID: 30093392 DOI: 10.1128/JCM.00913-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022] Open
Abstract
The recently developed direct-on-target microdroplet growth assay (DOT-MGA) allows rapid universal antimicrobial susceptibility testing (AST) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Here, we investigated a direct application of this method on positive blood cultures (BCs) for the acceleration of sepsis diagnostics. Blood samples spiked with meropenem-nonsusceptible and meropenem-susceptible Enterobacterales isolates were inoculated into Bactec Plus Aerobic/F bottles and incubated in the Bactec automated system. Positive-BC broth was processed using four different methods, filtration/dilution, dilution, lysis/centrifugation, and differential centrifugation. For both dilution-based methods, AST was performed from 1:100, 1:1,000, and 1:10,000 dilutions of positive-BC broth in cation-adjusted Mueller-Hinton broth (CA-MHB). For both centrifugation-based methods, a 0.5 McFarland standard turbidity suspension was prepared from a bacterial pellet and adjusted to a final inoculum of 5 × 105 CFU/ml in CA-MHB. Six-microliter microdroplets with or without meropenem at the breakpoint concentration were spotted in triplicate onto a MALDI-TOF MS target, followed by incubation in a humidity chamber for 3 or 4 h and subsequent broth removal. Spectra were evaluated by MALDI Biotyper software. The test was considered valid if the growth control without antibiotic achieved an identification score of ≥1.7. For samples with meropenem, successful identification (score, ≥1.7) was interpreted as a nonsusceptible result, whereas failed identification (score, <1.7) defined susceptibility. The best test performance was achieved with the lysis/centrifugation method after a 4-h incubation. At this time point, 96.3% validity, 91.7% sensitivity, and 100% specificity were reached. This study demonstrated the feasibility and accuracy of a rapid DOT-MGA from positive BCs. Parallel to susceptibility determination, this method provides simultaneous species identification.
Collapse
|
28
|
Sanguinetti M, Posteraro B. Susceptibility Testing of Fungi to Antifungal Drugs. J Fungi (Basel) 2018; 4:jof4030110. [PMID: 30223554 PMCID: PMC6162686 DOI: 10.3390/jof4030110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 01/05/2023] Open
Abstract
Susceptibility testing of fungi against antifungal drugs commonly used for therapy is a key component of the care of patients with invasive fungal infections. Antifungal susceptibility testing (AFST) has progressed in recent decades to finally become standardized and available as both Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference methods and in commercial manual/automated phenotypic methods. In clinical practice, the Sensititre YeastOne and Etest methods are widely used for AFST, particularly for sterile site isolates of Candida. Nevertheless, AFST is moving toward new phenotypic methods, such as matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), that are capable of providing rapid, and potentially more actionable, results for the treating clinician. Our objective is to summarize updated data on phenotypic methods for AFST of Candida and Aspergillus species and to assess their significance in view of opposing, but emerging, molecular genotypic methods.
Collapse
Affiliation(s)
- Maurizio Sanguinetti
- Insititute of Micorbiology, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
| | - Brunella Posteraro
- Insitutue of Public Health (Section of Hygiene), Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
| |
Collapse
|
29
|
Pereckaite L, Tatarunas V, Giedraitiene A. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings. J Microbiol Methods 2018; 152:154-164. [PMID: 30063958 DOI: 10.1016/j.mimet.2018.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 11/17/2022]
Abstract
The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.
Collapse
Affiliation(s)
- Laura Pereckaite
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vacis Tatarunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Agne Giedraitiene
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
| |
Collapse
|