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López-Cortés XA, Manríquez-Troncoso JM, Kandalaft-Letelier J, Cuadros-Orellana S. Machine learning and matrix-assisted laser desorption/ionization time-of-flight mass spectra for antimicrobial resistance prediction: A systematic review of recent advancements and future development. J Chromatogr A 2024; 1734:465262. [PMID: 39197363 DOI: 10.1016/j.chroma.2024.465262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND The use of matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF MS) combined with machine learning techniques has recently emerged as a method to address the public health crisis of antimicrobial resistance. This systematic review, conducted following Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, aims to evaluate the current state of the art in using machine learning for the detection and classification of antimicrobial resistance from MALDI-TOF mass spectrometry data. METHODS A comprehensive review of the literature on machine learning applications for antimicrobial resistance detection was performed using databases such as Web Of Science, Scopus, ScienceDirect, IEEE Xplore, and PubMed. Only original articles in English were included. Studies applying machine learning without using MALDI-TOF mass spectra were excluded. RESULTS Forty studies met the inclusion criteria. Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli were the most frequently cited bacteria. The antibiotics resistance most studied corresponds to methicillin for S. aureus, cephalosporins for K. pneumoniae, and aminoglycosides for E. coli. Random forest, support vector machine and logistic regression were the most employed algorithms to predict antimicrobial resistance. Additionally, seven studies reported using artificial neural networks. Most studies reported metrics such as accuracy, sensitivity, specificity, and the area under the receiver operating characteristic (AUROC) above 0.80. CONCLUSIONS Our study indicates that random forest, support vector machine, and logistic regression are effective for predicting antimicrobial resistance using MALDI-TOF MS data. Recent studies also highlight the potential of deep learning techniques in this area. We recommend further exploration of deep learning and multi-label supervised learning for comprehensive antibiotic resistance prediction in clinical practice.
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Affiliation(s)
- Xaviera A López-Cortés
- Department of Computer Sciences and Industries, Universidad Católica del Maule, Talca, 3480112, Chile; Centro de Innovación en Ingeniería Aplicada (CIIA), Universidad Católica del Maule, Talca, 3480112, Chile.
| | - José M Manríquez-Troncoso
- Department of Computer Sciences and Industries, Universidad Católica del Maule, Talca, 3480112, Chile
| | - John Kandalaft-Letelier
- Department of Computer Sciences and Industries, Universidad Católica del Maule, Talca, 3480112, Chile
| | - Sara Cuadros-Orellana
- Centro de Biotecnología de los Recursos Naturales, Universidad Católica del Maule, Talca, 3480112, Chile
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2
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Pickens CI, Wunderink RG. Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient. Infect Dis Clin North Am 2024; 38:51-63. [PMID: 38280767 DOI: 10.1016/j.idc.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.
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Affiliation(s)
- Chiagozie I Pickens
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA.
| | - Richard G Wunderink
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA
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3
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Brosh-Nissimov T, Tzur A, Grupel D, Cahan A, Ma'aravi N, Heled-Akiva M, Jawamis H, Leskes H, Barenboim E, Sorek N. Clinical impact of the accelerate PhenoTest® BC system on patients with gram-negative bacteremia and high risk of antimicrobial resistance: a prospective before-after implementation study. Ann Clin Microbiol Antimicrob 2023; 22:62. [PMID: 37516885 PMCID: PMC10387206 DOI: 10.1186/s12941-023-00619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND The Accelerate PhenoTest® BC system (AXDX) is a novel assay for rapid bacterial identification and antimicrobial susceptibility (AST). We report an evaluation of its impact on treatment of patients with Gram-negative bacteremia (GNB) with a high risk of antimicrobial resistance (AMR). METHODS A prospective single-center evaluation before and after implementation of AXDX in addition to standard-of-care (SOC) microbiology and antimicrobial stewardship program (ASP). Patients with GNB reported during laboratory working hours and prespecified risk factors for AMR were included. The primary outcome was an ASP-oriented beneficial antimicrobial change, defined as either an escalation of an inappropriate empiric treatment or de-escalation of a broad-spectrum treatment of a susceptible organism. Main secondary outcomes were time to an appropriate treatment, antimicrobial treatment duration, length of stay (LOS) and mortality. RESULTS Included were 46 and 57 patients in the pre- and post-intervention periods, respectively. The median time to an AST-oriented beneficial change was 29.2 h vs. 49.6 h, respectively (p < 0.0001). There were no significant differences in the time to appropriate treatment, LOS or mortality. Antimicrobial treatment duration was longer during the intervention period (10 vs. 8 days, p = 0.007). AXDX failed to correctly identify pathogens in all 6 cases of polymicrobial bacteremia. In two cases patient care was potentially compromised due to inappropriate de-escalation. CONCLUSIONS AXDX implementation resulted in a 20.4-hour shorter time to an ASP-oriented beneficial antimicrobial change. This should be weighed against the higher costs, the lack of other proven clinical benefits and the potential harm from mis-identification of polymicrobial bacteremias.
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Affiliation(s)
- Tal Brosh-Nissimov
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel.
- Faculty of Health Sciences, Ben Gurion University in the Negev, Be'er Sheva, Israel.
| | - Anka Tzur
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Daniel Grupel
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
- Faculty of Health Sciences, Ben Gurion University in the Negev, Be'er Sheva, Israel
| | - Amos Cahan
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Nir Ma'aravi
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Maya Heled-Akiva
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Hasan Jawamis
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Hanna Leskes
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Erez Barenboim
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
| | - Nadav Sorek
- Samson Assuta Ashdod University Hospital, Harefua st. 7, Ashdod, 7747629, Israel
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4
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Humphries RM, Miller L, Zimmer B, Matuschek E, Hindler JA. Contemporary Considerations for Establishing Reference Methods for Antibacterial Susceptibility Testing. J Clin Microbiol 2023; 61:e0188622. [PMID: 36971571 PMCID: PMC10281161 DOI: 10.1128/jcm.01886-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Antibacterial susceptibility testing (AST) is performed to guide therapy, perform resistance surveillance studies, and support development of new antibacterial agents. For 5 decades, broth microdilution (BMD) has served as the reference method to assess in vitro activity of antibacterial agents against which both novel agents and diagnostic tests have been measured. BMD relies on in vitro inhibition or killing of bacteria. It is associated with several limitations: it is a poor mimic of the in vivo milieu of bacterial infections, requires multiple days to perform, and is associated with subtle, difficult to control variability. In addition, new reference methods will soon be needed for novel agents whose activity cannot be evaluated by BMD (e.g., those that target virulence). Any new reference methods must be standardized, correlated with clinical efficacy and be recognized internationally by researchers, industry, and regulators. Herein, we describe current reference methods for in vitro assessment of antibacterial activity and highlight key considerations for the generation of novel reference methods.
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Affiliation(s)
- Romney M. Humphries
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Linda Miller
- CMID Pharma Consulting, LLC, Dresher, Pennsylvania, USA
| | - Barbara Zimmer
- Beckman Coulter Microbiology, Sacramento, California, USA
| | | | - Janet A. Hindler
- Los Angeles County Department of Public Health, Public Health Laboratory, Los Angeles, California, USA
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Donnars A, Mahieu R, Declerck C, Chenouard R, Lemarié C, Pailhoriès H, Requin J, Kempf M, Eveillard M. BIOFIRE® Blood Culture IDentification 2 (BCID2) panel for early adaptation of antimicrobial therapy in adult patients with bloodstream infections: a real-life experience. Diagn Microbiol Infect Dis 2023; 105:115858. [PMID: 36442386 DOI: 10.1016/j.diagmicrobio.2022.115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Our objective was to assess the effectiveness of a multiplex PCR panel for blood culture identification (BCID2) on the implementation of appropriate antimicrobial therapy. We conducted a monocentric pre/post study comparing the time to result from direct microscopic examination (DE) to bacterial identification (BI) in positive blood cultures between 2 different periods: P1 without BCID2 and P2 with BCID2. Appropriate treatments prescribed before DE and after DE / BCID2 and after BI / BCID2 were compared using direct proportion comparison and survival analysis. For mono-microbial bloodstream infections, the proportion of appropriate antimicrobial treatment after DE was 50% in P1 vs. 87.5% after BCID2 in P2 (P < 0.001) for Gram-negative bacteria and 33.0% in P1 vs. 64.4% in P2 (P < 0.01) for Gram-positive bacteria. A significant difference (P = 0.04) was recorded with survival curves for Gram positive bacteria. BCID2 seems effective in reducing the time for prescribing appropriate antimicrobials.
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Affiliation(s)
- Anne Donnars
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Rafael Mahieu
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Charles Declerck
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Jim Requin
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Marie Kempf
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Matthieu Eveillard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France.
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6
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Donnars A, Eveillard M. [Rapid diagnosis of bacteremia by genomic identification]. ANNALES PHARMACEUTIQUES FRANÇAISES 2022; 81:425-432. [PMID: 36464071 DOI: 10.1016/j.pharma.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Our objective was to make a focus on the methods for rapid diagnosis of bacteremia by genomic identification. We also aimed to evaluate the interest of using them in the laboratory practice. The different methods currently available have been presented according to their technologic approach. It is also possible to classify these methods according to the data provided, only bacterial and/or resistance gene identification or also bacterial susceptibility to antibiotics. In case of mono-microbial blood cultures, the performances recorded with these methods are very good as compared to the subcultures on agar media. Nevertheless, they are better for identifications (>90%) than for susceptibility to antibiotics (>80%). Numerous studies demonstrated the positive impact of these methods for decreasing the time necessary to the prescription of an appropriate antimicrobial treatment. However, it is noteworthy that an appropriate organization of the laboratory and a strategy of antimicrobial stewardship in the hospital are necessary. Concurrently, the impact on the patient outcome has not been clearly demonstrated. Lastly, few medico-economic studies have been reported. However, as these methods have a substantial cost, their utilization strategy must be economically viable.
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Affiliation(s)
- A Donnars
- Laboratoire de bactériologie, département de biologie des agents infectieux, centre hospitalier universitaire d'Angers, Angers, France
| | - M Eveillard
- Laboratoire de bactériologie, département de biologie des agents infectieux, centre hospitalier universitaire d'Angers, Angers, France.
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Pickens CI, Wunderink RG. Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient. Clin Chest Med 2022; 43:401-410. [PMID: 36116810 DOI: 10.1016/j.ccm.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.
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Affiliation(s)
- Chiagozie I Pickens
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA.
| | - Richard G Wunderink
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA
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8
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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] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
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.
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Affiliation(s)
- Sara Bellali
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
| | - Gabriel Haddad
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille 13385, France
| | - Rim Iwaza
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille 13385, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
| | - Akiko Hisada
- Hitachi, Ltd., Research & Development Group, 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Yusuke Ominami
- Hitachi High-Tech Corporation, 882 Ichige, Hitachinaka-shi, Ibaraki-ken 312-8504, Japan
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille 13385, France
| | - Jacques Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille 13385, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille 13385, France
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Lephart P, LeBar W, Newton D. Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership. Infect Dis Clin North Am 2021; 35:789-802. [PMID: 34362544 DOI: 10.1016/j.idc.2021.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.
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Affiliation(s)
- Paul Lephart
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA.
| | - William LeBar
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
| | - Duane Newton
- NaviDx Consulting, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
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10
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Rotem S, Shifman O, Aftalion M, Gur D, Aminov T, Aloni-Grinstein R. Rapid Antibiotic Susceptibility Testing of Tier-1 Agents Bacillus anthracis, Yersinia pestis, and Francisella tularensis Directly From Whole Blood Samples. Front Microbiol 2021; 12:664041. [PMID: 34305832 PMCID: PMC8299750 DOI: 10.3389/fmicb.2021.664041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
Rapid antibiotic susceptibility tests, performed directly on whole blood samples, will offer great clinical advantages. This issue is of considerable importance when it comes to bioterror pathogens where prompt antibiotic treatment should be offered to infected patients as well as prophylaxis to suspected exposed individuals. Herein, we describe a novel and rapid method, named MAPt, that is based on the direct application of a blood sample onto solid agar that has been embedded with different concentrations of the tested antibiotic. Following a short incubation, bacterial growth is monitored by qPCR. The method was applied on blood cultures and whole blood samples inoculated with the Tier-1 pathogens Bacillus anthracis, Yersinia pestis, and Francisella tularensis. The use of agar medium, which better supports the growth of bacteria at low concentrations, together with the use of qPCR, which provides sensitivity and specificity, allowed minimal inhibitory concentration (MIC) determination to a wide range of bacterial concentrations, ranging from ∼5 × 102 cfu/ml up to 108 cfu/ml. The omission of the enrichment procedure in blood culture and the isolation step, both required in standard antibiotic susceptibility tests (ASTs), allowed a dramatic reduction in time to answer, from a few days to a few hours. The total time required for MIC determination was ∼6 h for fast-growing bacteria, such as B. anthracis, and 12-16 h for slow-growing bacteria, represented by Y. pestis and F. tularensis. Accordingly, MAPt may offer health authorities means for public preparedness in the case of a bioterror attack as well as prompt clinical treatment options in common blood stream infections.
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Affiliation(s)
- Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | | | | | | | - Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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11
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Walsh TL, Bremmer DN, Moffa MA, Trienski TL, Buchanan C, Stefano K, Hand C, Taylor T, Kasarda K, Shively NR, Bhanot N, Cheronis N, DiSilvio BE, Cho CY, Carr DR. Impact of an Antimicrobial Stewardship Program-bundled initiative utilizing Accelerate Pheno™ system in the management of patients with aerobic Gram-negative bacilli bacteremia. Infection 2021; 49:511-519. [PMID: 33528813 PMCID: PMC8159835 DOI: 10.1007/s15010-021-01581-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/18/2021] [Indexed: 12/01/2022]
Abstract
PURPOSE Gram-negative bacteria (GNB) are a leading cause of bloodstream infections (BSI) and management is complicated by antibiotic resistance. The Accelerate Pheno™ system (ACC) can provide rapid organism identification and antimicrobial susceptibility testing (AST). METHODS A retrospective, pre-intervention/post-intervention study was conducted to compare management of non-critically ill patients with GNB BSI before and after implementation of a bundled initiative. This bundled initiative included dissemination of a clinical decision algorithm, ACC testing on all GNB isolated from blood cultures, real-time communication of results to the Antimicrobial Stewardship Program (ASP), and prospective audit with feedback by the ASP. The pre-intervention period was January 2018 through December 2018, and the post-intervention period was May 2019 through February 2020. RESULTS Seventy-seven and 129 patients were included in the pre-intervention and post-intervention cohorts, respectively. When compared with the pre-intervention group, the time from Gram stain to AST decreased from 46.1 to 6.9 h (p < 0.001), and the time to definitive therapy (TTDT) improved from 32.6 to 10.5 h (p < 0.001). Implementation led to shorter median total duration of antibiotic therapy (14.2 vs 9.5 days; p < 0.001) and mean hospital length of stay (7.9 vs 5.3 days; p = 0.047) without an increase in 30-day readmissions (22.1% vs 14%; p = 0.13). CONCLUSION Implementation of an ASP-bundled approach incorporating the ACC aimed at optimizing antibiotic therapy in the management GNB BSI in non-critically ill patients led to reduced TTDT, shorter duration of antibiotic therapy, and shorter hospital length of stay without adversely affecting readmission rates.
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Affiliation(s)
- Thomas L Walsh
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA.
| | - Derek N Bremmer
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Matthew A Moffa
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA.
| | - Tamara L Trienski
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Carley Buchanan
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Kelly Stefano
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Catharine Hand
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Tricia Taylor
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Karen Kasarda
- Department of Microbiology, Allegheny Health Network, Pittsburgh, PA, USA
| | - Nathan R Shively
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA
| | - Nitin Bhanot
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA
| | - Nicholas Cheronis
- Medicine Institute and Division of Infectious Diseases, Allegheny Health Network, Allegheny General Hospital, 320 East North Ave. East Wing Office Building, Suite 406, Pittsburgh, PA, 15212, USA
- Medicine Institute and Division of Pulmonary and Critical Care Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Briana E DiSilvio
- Medicine Institute and Division of Pulmonary and Critical Care Medicine, Allegheny Health Network, Pittsburgh, PA, USA
| | - Christian Y Cho
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
| | - Dustin R Carr
- Department of Pharmacy, Allegheny Health Network, Pittsburgh, PA, USA
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12
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Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021; 10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.
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Affiliation(s)
- Georgia D. Kaprou
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Ieva Bergšpica
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia
| | - Elena A. Alexa
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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Abstract
Prompt and effective antimicrobial therapy is crucial for the management of patients with severe bacterial infections but is becoming increasingly difficult to provide due to emerging antibiotic resistance. The traditional methods for antibiotic susceptibility testing (AST) used in most clinical laboratories are reliable but slow with turnaround times of 2 to 3 days, which necessitates the use of empirical therapy with broad-spectrum antibiotics. There is a great need for fast and reliable AST methods that enable starting targeted treatment within a few hours to improve patient outcome and reduce the overuse of broad-spectrum antibiotics. The multiplex fluidic chip for phenotypic AST described in the present study may enable data on antimicrobial resistance within 2 to 4 h, allowing for an early initiation of appropriate antibiotic therapy. Many patients with severe infections receive inappropriate empirical treatment, and rapid detection of bacterial antibiotic susceptibility can improve clinical outcome and reduce mortality. To this end, we have developed a multiplex fluidic chip for rapid phenotypic antibiotic susceptibility testing of bacteria. A total of 21 clinical isolates of Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus were acquired from the EUCAST Development Laboratory and tested against amikacin, ceftazidime, and meropenem (Gram-negative bacteria) or gentamicin, ofloxacin, and tetracycline (Gram-positive bacteria). The bacterial samples were mixed with agarose and loaded in an array of growth chambers in the chip where bacterial microcolony growth was monitored over time using automated image analysis. MIC values were automatically obtained by tracking the growth rates of individual microcolonies in different regions of antibiotic gradients. Stable MIC values were obtained within 2 to 4 h, and the results showed categorical agreement with reference MIC values as determined by broth microdilution in 86% of the cases.
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