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Cooper L, Yu K, Van Benten K, Patkar A, Ye G, Gregory S, Ai C, Gupta V. Hospital mortality and length of stay associated with Enterobacterales positive blood cultures: a multicenter analysis. Microbiol Spectr 2024; 12:e0040224. [PMID: 38953323 PMCID: PMC11302144 DOI: 10.1128/spectrum.00402-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Delayed time to antimicrobial susceptibility results can impact patients' outcomes. Our study evaluated the impact of susceptibility turnaround time (TAT) and inadequate empiric antibacterial therapy (IET) in patients with bloodstream infections (BSI) caused by Enterobacterales (ENT) species on in-hospital mortality and length of stay (LOS). This retrospective, multicenter investigation which included 29,570 blood ENT-positive admissions across 161 US healthcare facilities evaluated the association between antimicrobial susceptibility testing (AST) TAT, carbapenem susceptibility, and empiric therapy on post-BSI in-hospital mortality and LOS following an ENT BSI event in adult patients. After adjusting for outcomes covariates, post-BSI in-hospital mortality was significantly higher for patients in the IET vs adequate empiric therapy (AET) group [odds ratio (OR): 1.61 (95% CI: 1.32, 1.98); P < 0.0001], and when AST TAT was >63 h [OR:1.48 (95% CI: 1.16, 1.90); P = 0.0017]. Patients with carbapenem non-susceptible (carb-NS) ENT BSI had significantly higher LOS (16.6 days, 95% CI: 15.6, 17.8) compared to carbapenem susceptible (carb-S, 12.2 days, 95% CI: 11.8, 12.6), (P < 0.0001). Extended AST TAT was significantly associated with longer LOS for TAT of 57-65 h and >65 h (P = 0.005 and P< 0.0001, respectively) compared to TAT ≤42 h (reference). Inadequate empiric therapy (IET), carb-NS, and delayed AST TAT are significantly associated with adverse hospital outcomes in ENT BSI. Workflows that accelerate AST TAT for ENT BSIs and facilitate timely and adequate therapy may reduce post-BSI in-hospital mortality rate and LOS.IMPORTANCEFor patients diagnosed with bloodstream infections (BSI) caused by Enterobacterales (ENT), delayed time to antimicrobial susceptibility (AST) results can significantly impact in-hospital mortality and hospital length of stay. However, this relationship between time elapsed from blood culture collection to AST results has only been assessed, to date, in a limited number of publications. Our study focuses on this important gap using retrospective data from 29,570 blood ENT-positive admissions across 161 healthcare facilities in the US as we believe that a thorough understanding of the dynamic between AST turnaround time, adequacy of empiric therapy, post-BSI event mortality, and hospital length of stay will help guide effective clinical management and optimize outcomes of patients with ENT infections.
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Affiliation(s)
- Lauren Cooper
- Becton, Dickinson and Company, Diagnostic Solutions, Sparks, Maryland, USA
| | - Kalvin Yu
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Kayla Van Benten
- Becton, Dickinson and Company, Diagnostic Solutions, Sparks, Maryland, USA
| | - Anuprita Patkar
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Gang Ye
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Sara Gregory
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - ChinEn Ai
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Vikas Gupta
- Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
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2
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Ioannou P, Baliou S, Kofteridis D. Robinsoniella peoriensis Infections in Humans-A Narrative Review. Antibiotics (Basel) 2024; 13:570. [PMID: 38927236 PMCID: PMC11200903 DOI: 10.3390/antibiotics13060570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped bacterium belonging to the phylum Firmicutes and the family Lachnospiraceae. Until now, R. peoriensis is the only species of its genus. It was first isolated in 2003 during a study into the flora of lagoons and manure pits. Given the rarity of this microorganism and the sparse information in the literature about its way of transmission, the way to diagnose its infections and identify it in the microbiology laboratory, and its public health relevance, the present study aimed to identify all the published cases of Robinsoniella, describe the epidemiological, clinical, and microbiological characteristics, and provide information about its antimicrobial resistance, treatment, and outcomes. A narrative review was performed based on a Pubmed/Medline and Scopus databases search. In total, 14 studies provided data on 17 patients with infections by Robinsoniella. The median age of patients was 63 years and 47% were male. The most common types of infection were bone and joint infections, bacteremia, infective endocarditis, and peritonitis. The only isolated species was R. peoriensis, and antimicrobial resistance to clindamycin was 50%, but was 0% to the combination of piperacillin with tazobactam, aminopenicillin with a beta-lactamase inhibitor, and metronidazole which were the most commonly used antimicrobials for the treatment of these infections. The overall mortality depends on the type of infection and is notable only for bacteremia, while all other infections had an optimal outcome. Future studies should better assess these infections' clinical and epidemiological characteristics and the mechanisms of the antimicrobial resistance of this microorganism from a mechanistic and genetic perspective.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
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3
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Watanabe N, Koyama S, Maeda T, Karaushi H, Taji Y, Kawasaki Y, Takahashi N, Mitsutake K, Ebihara Y. Direct Species Identification in Positive Blood Culture Bottles From Patients With Hematologic Malignancies. Cureus 2024; 16:e59043. [PMID: 38800333 PMCID: PMC11128060 DOI: 10.7759/cureus.59043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/29/2024] Open
Abstract
Background In patients with hematologic malignancies, faster species identification is particularly important in the management of bloodstream infection because of their immunocompromised and neutropenic status. In the present study, we analyzed direct species identification in patients with hematologic malignancies, and the factors that might influence the results of species identification. Methods We performed direct species identification using a Sepsityper® kit (Bruker Corporation, Billerica, Massachusetts, United States) and compared the results with a conventional method in patients with hematologic malignancies. Forty-five positive blood culture bottles containing single microorganisms from 37 patients were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). And patients' clinical data were compared between the groups with spectral scores at acceptable and unacceptable levels. Results Direct species identification correctly identified 42 of 45 isolates and three were misidentified. While 35 of 45 isolates showed a spectral score ≥1.7 (acceptable identification), 10 isolates had a spectral score <1.7 (unacceptable identification) including three misidentified isolates. The group with a spectral score ≥1.7 had significantly lower white blood cell (p<0.01), neutrophil (p<0.01), and platelet (p<0.01) counts in addition to more frequent central venous (CV) line insertion (p=0.01). Multivariate analysis revealed that pathogen type (gram-positive or negative) and CV line insertion were associated with spectral scores. Conclusion Direct species identification using the Sepsityper kit is an upcoming approach for blood culture bottles, which were flagged as positive even in patients with hematologic malignancies when the spectral score was ≥ 1.7. Our study also indicates that direct identification is more accurate in patients with CV lines, and may be less accurate when gram-positive bacteria are detected.
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Affiliation(s)
- Noriyuki Watanabe
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Sachie Koyama
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Tomoya Maeda
- Department of Hemato-Oncology, Saitama Medical University International Medical Center, Saitama, JPN
| | - Haruka Karaushi
- Department of Infectious Diseases and Infection Control, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yoshitada Taji
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yohei Kawasaki
- Department of Biostatistics, Graduate School of Medicine, Saitama Medical University, Saitama, JPN
| | - Naoki Takahashi
- Department of Hemato-Oncology, Saitama Medical University International Medical Center, Saitama, JPN
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, Saitama Medical University International Medical Center, Saitama, JPN
| | - Yasuhiro Ebihara
- Department of Laboratory Medicine, Saitama Medical University International Medical Center, Saitama, JPN
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4
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Kumar NR, Balraj TA, Kempegowda SN, Prashant A. Multidrug-Resistant Sepsis: A Critical Healthcare Challenge. Antibiotics (Basel) 2024; 13:46. [PMID: 38247605 PMCID: PMC10812490 DOI: 10.3390/antibiotics13010046] [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: 12/02/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Sepsis globally accounts for an alarming annual toll of 48.9 million cases, resulting in 11 million deaths, and inflicts an economic burden of approximately USD 38 billion on the United States healthcare system. The rise of multidrug-resistant organisms (MDROs) has elevated the urgency surrounding the management of multidrug-resistant (MDR) sepsis, evolving into a critical global health concern. This review aims to provide a comprehensive overview of the current epidemiology of (MDR) sepsis and its associated healthcare challenges, particularly in critically ill hospitalized patients. Highlighted findings demonstrated the complex nature of (MDR) sepsis pathophysiology and the resulting immune responses, which significantly hinder sepsis treatment. Studies also revealed that aging, antibiotic overuse or abuse, inadequate empiric antibiotic therapy, and underlying comorbidities contribute significantly to recurrent sepsis, thereby leading to septic shock, multi-organ failure, and ultimately immune paralysis, which all contribute to high mortality rates among sepsis patients. Moreover, studies confirmed a correlation between elevated readmission rates and an increased risk of cognitive and organ dysfunction among sepsis patients, amplifying hospital-associated costs. To mitigate the impact of sepsis burden, researchers have directed their efforts towards innovative diagnostic methods like point-of-care testing (POCT) devices for rapid, accurate, and particularly bedside detection of sepsis; however, these methods are currently limited to detecting only a few resistance biomarkers, thus warranting further exploration. Numerous interventions have also been introduced to treat MDR sepsis, including combination therapy with antibiotics from two different classes and precision therapy, which involves personalized treatment strategies tailored to individual needs. Finally, addressing MDR-associated healthcare challenges at regional levels based on local pathogen resistance patterns emerges as a critical strategy for effective sepsis treatment and minimizing adverse effects.
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Affiliation(s)
- Nishitha R. Kumar
- Department of Biochemistry, JSS Medical College and Hospital, JSS Academy of Higher Education & Research, Mysuru 570004, India; (N.R.K.); (S.N.K.)
| | - Tejashree A. Balraj
- Department of Microbiology, JSS Medical College and Hospital, JSS Academy of Higher Education & Research, Mysuru 570004, India;
| | - Swetha N. Kempegowda
- Department of Biochemistry, JSS Medical College and Hospital, JSS Academy of Higher Education & Research, Mysuru 570004, India; (N.R.K.); (S.N.K.)
| | - Akila Prashant
- Department of Biochemistry, JSS Medical College and Hospital, JSS Academy of Higher Education & Research, Mysuru 570004, India; (N.R.K.); (S.N.K.)
- Department of Medical Genetics, JSS Medical College and Hospital, JSS Academy of Higher Education & Research, Mysuru 570004, India
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5
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Uzuriaga M, Leiva J, Guillén-Grima F, Rua M, Yuste JR. Clinical Impact of Rapid Bacterial Microbiological Identification with the MALDI-TOF MS. Antibiotics (Basel) 2023; 12:1660. [PMID: 38136694 PMCID: PMC10740418 DOI: 10.3390/antibiotics12121660] [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: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Rapid microbiological reports to clinicians are related to improved clinical outcomes. We conducted a 3-year quasi-experimental design, specifically a pretest-posttest single group design in a university medical center, to evaluate the clinical impact of rapid microbiological identification information using MALDI-TOF MS on optimizing antibiotic prescription. A total of 363 consecutive hospitalized patients with bacterial infections were evaluated comparing a historical control group (CG) (n = 183), in which the microbiological information (bacterial identification and antibiotic susceptibility) was reported jointly to the clinician between 18:00 h and 22:00 h of the same day and a prospective intervention group (IG) (n = 180); the bacterial identification information was informed to the clinician as soon as it was available between 12:00 h and 14:00 h and the antibiotic susceptibility between 18:00 h and 22:00 h). We observed, in favor of IG, a statistically significant decrease in the information time (11.44 h CG vs. 4.48 h IG (p < 0.01)) from the detection of bacterial growth in the culture medium to the communication of identification. Consequently, the therapeutic optimization was improved by introducing new antibiotics in the 10-24 h time window (p = 0.05) and conversion to oral route (p = 0.01). Additionally, we observed a non-statistically significant decrease in inpatient mortality (global, p = 0.15; infection-related, p = 0.21) without impact on hospital length of stay. In conclusion, the rapid communication of microbiological identification to clinicians reduced reporting time and was associated with early optimization of antibiotic prescribing without worsening clinical outcomes.
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Affiliation(s)
- Miriam Uzuriaga
- Clinical Microbiology Service, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (M.U.); (M.R.)
| | - José Leiva
- Clinical Microbiology Service, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (M.U.); (M.R.)
- Healthcare Research Institute of Navarre (IdiSNA), 31008 Pamplona, Spain; (F.G.-G.); (J.R.Y.)
| | - Francisco Guillén-Grima
- Healthcare Research Institute of Navarre (IdiSNA), 31008 Pamplona, Spain; (F.G.-G.); (J.R.Y.)
- Department of Preventive Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Institute of Health Carlos III, 46980 Madrid, Spain
- Department of Health Sciences, Public University of Navarra, 31008 Pamplona, Spain
| | - Marta Rua
- Clinical Microbiology Service, Clínica Universidad de Navarra, 31008 Pamplona, Spain; (M.U.); (M.R.)
- Healthcare Research Institute of Navarre (IdiSNA), 31008 Pamplona, Spain; (F.G.-G.); (J.R.Y.)
| | - José R. Yuste
- Healthcare Research Institute of Navarre (IdiSNA), 31008 Pamplona, Spain; (F.G.-G.); (J.R.Y.)
- Service of Infectious Diseases, Clínica Universidad de Navarra, 31008 Pamplona, Spain
- Department of Internal Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
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6
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Kalın G, Alp E, Chouaikhi A, Roger C. Antimicrobial Multidrug Resistance: Clinical Implications for Infection Management in Critically Ill Patients. Microorganisms 2023; 11:2575. [PMID: 37894233 PMCID: PMC10609422 DOI: 10.3390/microorganisms11102575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing incidence of antimicrobial resistance (AMR) worldwide represents a serious threat in the management of sepsis. Due to resistance to the most common antimicrobials prescribed, multidrug-resistant (MDR) pathogens have been associated with delays in adequate antimicrobial therapy leading to significant increases in mortality, along with prolonged hospital length of stay (LOS) and increases in healthcare costs. In response to MDR infections and the delay of microbiological results, broad-spectrum antibiotics are frequently used in empirical antimicrobial therapy. This can contribute to the overuse and misuse of antibiotics, further promoting the development of resistance. Multiple measures have been suggested to combat AMR. This review will focus on describing the epidemiology and trends concerning MDR pathogens. Additionally, it will explore the crucial aspects of identifying patients susceptible to MDR infections and optimizing antimicrobial drug dosing, which are both pivotal considerations in the fight against AMR. Expert commentary: The increasing AMR in ICUs worldwide makes the empirical antibiotic therapy challenging in septic patients. An AMR surveillance program together with improvements in MDR identification based on patient risk stratification and molecular rapid diagnostic tools may further help tailoring antimicrobial therapies and avoid unnecessary broad-spectrum antibiotics. Continuous infusions of antibiotics, therapeutic drug monitoring (TDM)-based dosing regimens and combination therapy may contribute to optimizing antimicrobial therapy and limiting the emergence of resistance.
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Affiliation(s)
- Gamze Kalın
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38280, Türkiye
| | - Emine Alp
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University, Ankara 06760, Türkiye;
| | - Arthur Chouaikhi
- Department of Anesthesiology and Intensive Care, Pain and Emergency Medicine, Nîmes-Caremeau University Hospital, Place du Professeur Robert Debré, CEDEX 9, 30029 Nîmes, France;
| | - Claire Roger
- Department of Anesthesiology and Intensive Care, Pain and Emergency Medicine, Nîmes-Caremeau University Hospital, Place du Professeur Robert Debré, CEDEX 9, 30029 Nîmes, France;
- UR UM 103 IMAGINE, Faculty of Medicine, Montpellier University, Chemin du Carreau de Lanes, 30029 Nîmes, France
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7
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Lapin JS, Smith RD, Hornback KM, Johnson JK, Claeys KC. From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing. Pharmacotherapy 2023; 43:847-863. [PMID: 37158053 DOI: 10.1002/phar.2813] [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: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 05/10/2023]
Abstract
Antimicrobial stewardship (AMS) programs have been quick to adopt novel molecular rapid diagnostic technologies (mRDTs) for bloodstream infections (BSIs) to improve antimicrobial management. As such, most of the literature demonstrating the clinical and economic benefits of mRDTs for BSI is in the presence of active AMS intervention. Leveraging mRDTs to improve antimicrobial therapy for BSI is increasingly integral to AMS program activities. This narrative review discusses available and future mRDTs, the relationship between the clinical microbiology laboratory and AMS programs, and practical considerations for optimizing the use of these tools within a health system. Antimicrobial stewardship programs must work closely with their clinical microbiology laboratories to ensure that mRDTs are used to their fullest benefit while remaining cognizant of their limitations. As more mRDT instruments and panels become available and AMS programs continue to expand, future efforts must consider the expansion beyond traditional settings of large academic medical centers and how combinations of tools can further improve patient care.
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Affiliation(s)
- Jonathan S Lapin
- Department of Pharmacy Practice, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Richard D Smith
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Krutika M Hornback
- Department of Pharmacy Practice, Medical University of South Carolina (MUSC) Health, Charleston, South Carolina, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kimberly C Claeys
- Department of Pharmacy Science and Health Outcomes Research, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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8
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Moore LSP, Villegas MV, Wenzler E, Rawson TM, Oladele RO, Doi Y, Apisarnthanarak A. Rapid Diagnostic Test Value and Implementation in Antimicrobial Stewardship Across Low-to-Middle and High-Income Countries: A Mixed-Methods Review. Infect Dis Ther 2023:10.1007/s40121-023-00815-z. [PMID: 37261612 DOI: 10.1007/s40121-023-00815-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/20/2023] [Indexed: 06/02/2023] Open
Abstract
Despite technological advancements in infectious disease rapid diagnostic tests (RDTs) and use to direct therapy at the per-patient level, RDT utilisation in antimicrobial stewardship programmes (ASPs) is variable across low-to-middle income and high-income countries. Key insights from a panel of seven infectious disease experts from Colombia, Japan, Nigeria, Thailand, the UK, and the USA, combined with evidence from a literature review, were used to assess the value of RDTs in ASPs. From this, a value framework is proposed which aims to define the benefits of RDT use in ASPs, separate from per-patient benefits. Expert insights highlight that, to realise the value of RDTs within ASPs, effective implementation is key; actionable advice for choosing an RDT is proposed. Experts advocate the inclusion of RDTs in the World Health Organization Model List of essential in vitro diagnostics and in iterative development of national action plans.
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Affiliation(s)
- Luke S P Moore
- Clinical Infection Department, Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.
- Imperial College Healthcare NHS Trust, North West London Pathology, London, UK.
- NIHR Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Imperial College London, London, UK.
| | - Maria Virginia Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque, Bogotá, Colombia
- Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia
| | - Eric Wenzler
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Timothy M Rawson
- NIHR Health Protection Research Unit in Healthcare Associated Infections & Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Antimicrobial Optimisation, Imperial College London, London, UK
| | - Rita O Oladele
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Yohei Doi
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anucha Apisarnthanarak
- Research Group in Infectious Diseases Epidemiology and Prevention, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Thammasat University, Pathum Thani, Thailand
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9
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Kraus CK, Nguyen HB, Jacobsen RC, Ledeboer NA, May LS, O'Neal HR, Puskarich MA, Rice TW, Self WH, Rothman RE. Rapid identification of sepsis in the emergency department. J Am Coll Emerg Physicians Open 2023; 4:e12984. [PMID: 37284425 PMCID: PMC10239543 DOI: 10.1002/emp2.12984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Objectives Recent research has helped define the complex pathways in sepsis, affording new opportunities for advancing diagnostics tests. Given significant advances in the field, a group of academic investigators from emergency medicine, intensive care, pathology, and pharmacology assembled to develop consensus around key gaps and potential future use for emerging rapid host response diagnostics assays in the emergency department (ED) setting. Methods A modified Delphi study was conducted that included 26 panelists (expert consensus panel) from multiple specialties. A smaller steering committee first defined a list of Delphi statements related to the need for and future potential use of a hypothetical sepsis diagnostic test in the ED. Likert scoring was used to assess panelists agreement or disagreement with statements. Two successive rounds of surveys were conducted and consensus for statements was operationally defined as achieving agreement or disagreement of 75% or greater. Results Significant gaps were identified related to current tools for assessing risk of sepsis in the ED. Strong consensus indicated the need for a test providing an indication of the severity of dysregulated host immune response, which would be helpful even if it did not identify the specific pathogen. Although there was a relatively high degree of uncertainty regarding which patients would most benefit from the test, the panel agreed that an ideal host response sepsis test should aim to be integrated into ED triage and thus should produce results in less than 30 minutes. The panel also agreed that such a test would be most valuable for improving sepsis outcomes and reducing rates of unnecessary antibiotic use. Conclusion The expert consensus panel expressed strong consensus regarding gaps in sepsis diagnostics in the ED and the potential for new rapid host response tests to help fill these gaps. These finding provide a baseline framework for assessing key attributes of evolving host response diagnostic tests for sepsis in the ED.
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Affiliation(s)
- Chadd K. Kraus
- Department of Emergency MedicineGeisinger Medical CenterDanvillePennsylvaniaUSA
| | - H. Bryant Nguyen
- Department of MedicinePulmonary and Critical Care DivisionLoma Linda UniversityLoma LindaCaliforniaUSA
| | - Ryan C. Jacobsen
- Department of Emergency MedicineUniversity of Kansas HospitalKansas CityKansasUSA
| | - Nathan A. Ledeboer
- Department of Pathology & Laboratory MedicineMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Larissa S. May
- Department of Emergency MedicineUC Davis HealthDavisCaliforniaUSA
| | - Hollis R. O'Neal
- Department of Critical Care MedicineLouisiana State UniversityBaton RougeLouisianaUSA
| | - Michael A. Puskarich
- Department of Emergency MedicineHennepin County Medical CenterUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Todd W. Rice
- Vanderbilt Institute for Clinical and Translational Sciences and Division of AllergyPulmonary and Critical Care MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Wesley H. Self
- Vanderbilt Institute for Clinical and Translational Sciences and Department of Emergency MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Richard E. Rothman
- Department of Emergency MedicineJohns Hopkins UniversityBaltimoreMarylandUSA
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Reiber C, Bodendoerfer E, Brugger SD, Eberhard N, Hitz E, Hofmaenner DA, Herren S, Kolesnik-Goldmann N, Manicini S, Zbinden R, Zinkernagel AS, Hasse B. Rapid antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales: an implementation study. Swiss Med Wkly 2023; 153:40066. [PMID: 37190876 DOI: 10.57187/smw.2023.40066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
AIMS OF THE STUDY The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed to analyse how rapid automated antimicrobial susceptibility testing influences clinical decision-making. METHODS This single-centre study conducted at the University Hospital of Zurich included data from all consecutive patients with Enterobacterales bacteraemia from November 2019 to October 2020. There was no control group. The primary outcome was the effect of rapid automated antimicrobial susceptibility testing on antibiotic therapy (no adjustment, escalation to a broader-spectrum antibiotic or de-escalation to a narrower-spectrum antibiotic). Rapid automated antimicrobial susceptibility testing results were further compared to susceptibility tests using European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard methods and erroneous results were noted. Additionally, we investigated turnaround times for rapid automated antimicrobial susceptibility testing and routine diagnostic testing. RESULTS We analysed 106 patients with 116 episodes of bacteraemia due to Enterobacterales, with Escherichia coli and Klebsiella pneumoniae being the most frequent isolates. Almost 8% of pathogens were multidrug resistant. Rapid automated antimicrobial susceptibility testing showed category agreement in 98.4% of all interpretable cases. A significant reduction of more than 20 h in turnaround times could be achieved with rapid automated antimicrobial susceptibility testing compared to the routine diagnostic workflow. In the majority of cases, rapid automated antimicrobial susceptibility testing had no effect, given that the empirical therapy was already correct or circumstances did not allow for de-escalation. In 38.8% of cases, antimicrobial therapy was adjusted, whereas eight cases were de-escalated based on rapid automated antimicrobial susceptibility testing alone. CONCLUSIONS Rapid automated antimicrobial susceptibility testing may be a valuable and safe way to accelerate diagnosis. In particular, time to suitable therapy can be shortened in cases of incorrect therapy. However, physicians are reluctant to de-escalate antibiotic therapy based on rapid automated antimicrobial susceptibility testing alone, limiting its impact in everyday clinics. To further explore the potential of rapid automated antimicrobial susceptibility testing, a stringent/compulsory antibiotic stewardship programme would be a valuable next step.
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Affiliation(s)
- Claudine Reiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Elias Bodendoerfer
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadia Eberhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Eva Hitz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sebastian Herren
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | | | - Stefano Manicini
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Potvin M, Larranaga Lapique E, Hites M, Martiny D. Implementing Alfred60 AST in a clinical lab: Clinical impact on the management of septic patients and financial analysis. ANNALES PHARMACEUTIQUES FRANÇAISES 2023; 81:466-474. [PMID: 36402206 DOI: 10.1016/j.pharma.2022.11.009] [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: 05/17/2022] [Revised: 07/22/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Sepsis is an important cause of morbidity and mortality. An accelerated microbiology diagnosis is crucial in order to reduce the time to initiate targeted antibiotic therapy. The Alfred60AST system is able to provide phenotypic Antimicrobial Susceptibility Testing (AST) results within hours. This study has two objectives: assess the clinical impact of this technology and determine its cost-effectiveness. METHODS During a ten-week period, all new enterobacterial or enterococcal bloodstream infection was analyzed with the Alfred60AST system, in parallel with routine methods. Its impact on the clinician's therapeutic strategy was studied. In order to assess the financial and practical aspects of the method, an analysis of the extracosts and a survey of the technical staff were conducted. RESULTS Fifty-three cases of bacteriemia were included. For the Enterobacteriaceae bacteriemias, a clinical impact was shown in 18.9% of the cases (e.g, treatment modification). The financial analysis highlighted an increase in costs (+38% for Enterobacteriaceae, +50% for Enterococci), compared to the theoretical costs reported by the firm, due to the workflow and the volumes of samples used. Finally, results of the technical staff survey were favorable in terms of ease of use of the system. CONCLUSION In addition to its ease of use, the Alfred60AST system is able to provide an AST in a record time. This study shows a real interest of the technique in the therapeutic management of patients with enterobacterial sepsis. However, its routine implementation requires an increase of the analyzed volumes as well as a 24/7 organization of the laboratory in order to be profitable.
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Affiliation(s)
- M Potvin
- Microbiology Department, LHUB-ULB, rue haute, 322, 1000 Brussels, Belgium.
| | - E Larranaga Lapique
- Department of Infectious Disease, Erasme Hospital, route de Lennik, 808, 1070 Brussels, Belgium
| | - M Hites
- Department of Infectious Disease, Erasme Hospital, route de Lennik, 808, 1070 Brussels, Belgium
| | - D Martiny
- Microbiology Department, LHUB-ULB, rue haute, 322, 1000 Brussels, Belgium
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Zhang YM, Tsao MF, Chang CY, Lin KT, Keller JJ, Lin HC. Rapid identification of carbapenem-resistant Klebsiella pneumoniae based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry and an artificial neural network model. J Biomed Sci 2023; 30:25. [PMID: 37069555 PMCID: PMC10108464 DOI: 10.1186/s12929-023-00918-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a clinically critical pathogen that causes severe infection. Due to improper antibiotic administration, the prevalence of CRKP infection has been increasing considerably. In recent years, the utilization of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has enabled the identification of bacterial isolates at the families and species level. Moreover, machine learning (ML) classifiers based on MALDI-TOF MS have been recently considered a novel method to detect clinical antimicrobial-resistant pathogens. METHODS A total of 2683 isolates (369 CRKP cases and 2314 carbapenem-susceptible Klebsiella pneumoniae [CSKP]) collected in the clinical laboratories of Taipei Medical University Hospital (TMUH) were included in this study, and 80% of data was split into the training data set that were submitted for the ML model. The remaining 20% of data was used as the independent data set for external validation. In this study, we established an artificial neural network (ANN) model to analyze all potential peaks on mass spectrum simultaneously. RESULTS Our artificial neural network model for detecting CRKP isolates showed the best performance of area under the receiver operating characteristic curve (AUROC = 0.91) and of area under precision-recall curve (AUPRC = 0.90). Furthermore, we proposed the top 15 potential biomarkers in probable CRKP isolates at 2480, 4967, 12,362, 12,506, 12,855, 14,790, 15,730, 16,176, 16,218, 16,758, 16,919, 17,091, 18,142, 18,998, and 19,095 Da. CONCLUSIONS Compared with the prior MALDI-TOF and machine learning studies of CRKP, the amount of data in our study was more sufficient and allowing us to conduct external validation. With better generalization abilities, our artificial neural network model can serve as a reliable screening tool for CRKP isolates in clinical practice. Integrating our model into the current workflow of clinical laboratories can assist the rapid identification of CRKP before the completion of traditional antimicrobial susceptibility testing. The combination of MADLI-TOF MS and machine learning techniques can support physicians in selecting suitable antibiotics, which has the potential to enhance the patients' outcomes and lower the prevalence of antimicrobial resistance.
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Affiliation(s)
- Yu-Ming Zhang
- School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Mei-Fen Tsao
- Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ching-Yu Chang
- Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Kuan-Ting Lin
- Department of Business Administration, National Taiwan University, Taipei, Taiwan
| | - Joseph Jordan Keller
- Western Michigan University Homer Stryker M.D. School of Medicine, Department of Psychiatry, Kalamazoo, MI, USA
| | - Hsiu-Chen Lin
- Department of Clinical Pathology, Taipei Medical University Hospital, Taipei, Taiwan.
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wu-Hsing St, Taipei, 11031, Taiwan.
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Clinical impact of a multiplex rapid diagnostic pneumonia panel in critically ill patients. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e5. [PMID: 36714280 PMCID: PMC9879924 DOI: 10.1017/ash.2022.358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Objective To evaluate the clinical impact of the BioFire FilmArray Pneumonia Panel (PNA panel) in critically ill patients. Design Single-center, preintervention and postintervention retrospective cohort study. Setting Tertiary-care academic medical center. Patients Adult ICU patients. Methods Patients with quantitative bacterial cultures obtained by bronchoalveolar lavage or tracheal aspirate either before (January-March 2021, preintervention period) or after (January-March 2022, postintervention period) implementation of the PNA panel were randomly screened until 25 patients per study month (75 in each cohort) who met the study criteria were included. Antibiotic use from the day of culture collection through day 5 was compared. Results The primary outcome of median time to first antibiotic change based on microbiologic data was 50 hours before the intervention versus 21 hours after the intervention (P = .0006). Also, 56 postintervention regimens (75%) were eligible for change based on PNA panel results; actual change occurred in 30 regimens (54%). Median antibiotic days of therapy (DOTs) were 8 before the intervention versus 6 after the intervention (P = .07). For the patients with antibiotic changes made based on PNA panel results, the median time to first antibiotic change was 10 hours. For patients who were initially on inadequate therapy, time to adequate therapy was 67 hours before the intervention versus 37 hours after the intervention (P = .27). Conclusions The PNA panel was associated with decreased time to first antibiotic change and fewer antibiotic DOTs. Its impact may have been larger if a higher percentage of potential antibiotic changes had been implemented. The PNA panel is a promising tool to enhance antibiotic stewardship.
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Selvam K, Ganapathy T, Najib MA, Khalid MF, Abdullah NA, Harun A, Wan Mohammad WMZ, Aziah I. Burden and Risk Factors of Melioidosis in Southeast Asia: A Scoping Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:15475. [PMID: 36497549 PMCID: PMC9741171 DOI: 10.3390/ijerph192315475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
This scoping review aims to provide a comprehensive overview of human melioidosis in Southeast Asia as well as to highlight knowledge gaps in the prevalence and risk factors of this life-threatening disease using available evidence-based data for better diagnosis and treatment. Preferred Reporting Items for Systematic Review and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) was used as the guideline for this review. The literature search was conducted on 23 March 2022 through two electronic databases (PubMed and Scopus) using lists of keywords referring to the Medical Subject Headings (MeSH) thesaurus. A total of 38 articles related to human melioidosis were included from 645 screened articles. These studies were carried out between 1986 and 2019 in six Southeast Asian countries: Thailand, Cambodia, Malaysia, Myanmar, Singapore, and Vietnam. Melioidosis has been reported with a high disease prevalence among high-risk populations. Studies in Thailand (48.0%) and Cambodia (74.4%) revealed disease prevalence in patients with septic arthritis and children with suppurative parotitis, respectively. Other studies in Thailand (63.5%) and Malaysia (54.4% and 65.7%) showed a high seroprevalence of melioidosis among Tsunami survivors and military personnel, respectively. Additionally, this review documented soil and water exposure, diabetes mellitus, chronic renal failure, thalassemia, and children under the age of 15 as the main risk factors for melioidosis. Human melioidosis is currently under-reported in Southeast Asia and its true prevalence is unknown.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Thanasree Ganapathy
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nor Azlina Abdullah
- Department of Community Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Jalan Raja Perempuan Zainab 2, Kubang Kerian 16150, Kelantan, Malaysia
| | - Wan Mohd Zahiruddin Wan Mohammad
- Department of Community Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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Shi L, Habib A, Bi L, Hong H, Begum R, Wen L. Ambient Ionization Mass Spectrometry: Application and Prospective. Crit Rev Anal Chem 2022:1-50. [PMID: 36206159 DOI: 10.1080/10408347.2022.2124840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Mass spectrometry (MS) is a formidable analytical tool for the analysis of non-polar to polar compounds individually and/or from mixtures, providing information on the molecular weights and chemical structures of the analytes. During the last more than one-decade, ambient ionization mass spectrometry (AIMS) has developed quickly, producing a wide range of platforms and proving scientific improvements in a variety of domains, from biological imaging to quick quality control. These methods have made it possible to detect target analytes in real time without sample preparation in an open environment, and they can be connected to any MS system with an atmospheric pressure interface. They also have the ability to analyze explosives, illicit drugs, disease diagnostics, drugs in biological samples, adulterants in food and agricultural products, reaction progress, and environmental monitoring. The development of novel ambient ionization techniques, such as probe electrospray ionization, paper spray ionization, and fiber spray ionization, employed even at picolitre to femtolitre solution levels to provide femtogram to attogram levels of the target analytes. The special characteristic of this ambient ion source, which has been extensively used, is the noninvasive property of PESI of examination of biological real samples. The results in the current review supports the idea that AIMS has emerged as a pioneer in MS-based approaches and that methods will continue to be developed along with improvements to existing ones in the near future.
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Affiliation(s)
- Lulu Shi
- Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Lei Bi
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Huanhuan Hong
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Rockshana Begum
- Department of Chemistry, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Luhong Wen
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
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Bassetti M, Kanj SS, Kiratisin P, Rodrigues C, Van Duin D, Villegas MV, Yu Y. Early appropriate diagnostics and treatment of MDR Gram-negative infections. JAC Antimicrob Resist 2022; 4:dlac089. [PMID: 36111208 PMCID: PMC9469888 DOI: 10.1093/jacamr/dlac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.
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Affiliation(s)
- Matteo Bassetti
- Department of Health Science, University of Genoa , Italy
- Infectious Diseases Clinic, Ospedale Policlinico San Martino Hospital – IRCCS , Genoa , Italy
| | - Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center , Beirut , Lebanon
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre , Mumbai, Maharashtra , India
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine , Chapel Hill, NC , USA
| | - María Virginia Villegas
- Grupo de Investigaciones en Resistencia Antimicrobiana y Epidemiología Hospitalaria (RAEH), Universidad El Bosque , Bogotá DC , Colombia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang , China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province , Hangzhou, Zhejiang , China
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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Watanabe N, Koyama S, Taji Y, Mitsutake K, Ebihara Y. Direct microorganism species identification and antimicrobial susceptibility tests from positive blood culture bottles using rapid Sepsityper Kit. J Infect Chemother 2022; 28:563-568. [PMID: 35027301 DOI: 10.1016/j.jiac.2021.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION We evaluated the performance of Rapid Sepsityper Kit in species identification (ID) and antimicrobial susceptibility testing (AST). METHODS Positive blood culture bottles (n = 227) containing single microorganisms were enrolled. We compared the direct method using Rapid Sepsityper Kit for ID and AST with the conventional method. The analyses of ID and AST were performed using MALDI Biotyper and BD Phoenix platform, respectively. RESULTS The direct ID method correctly identified 89.4% (203/227) of samples, and Gram-negative bacilli (95.2%) had a higher ID rate than Gram-positive cocci (84.4%). Five cases were misidentified, and non-acceptable identification was high among Streptococcus species. Direct AST results were obtained from 168 isolates. Non-acceptable ID occurred among 24 isolates; 4 Streptococcus species, and 31 isolates, which did not grow in the direct AST method, were excluded. A total of 1714 antibiotic susceptibility tests (625 from 69 Gram-positive cocci and 1089 from 99 Gram-negative bacilli) were performed. The direct AST methods showed 98.3% (1685/1714) of categorical agreement (CA), 0.7% (12/1714) of very major errors, 0.2% (4/1714) of major errors, and 0.8% (13/1714) of minor errors. Complete CA was obtained for methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Escherichia coli. CONCLUSIONS The direct ID method using Rapid Sepsityper Kit and the direct AST method in combination with the BD Phoenix platform, which was associated with a reduction of turnaround time, may be a reliable approach for blood culture bottles. However, additional validation and further improvements, especially for Gram-positive cocci, would have an impact on microbiological diagnoses.
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Affiliation(s)
- Noriyuki Watanabe
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, Japan
| | - Sachie Koyama
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, Japan
| | - Yoshitada Taji
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, Japan
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, Saitama Medical University International Medical Center, Saitama, Japan
| | - Yasuhiro Ebihara
- Clinical Laboratory, Saitama Medical University International Medical Center, Saitama, Japan; Department of Laboratory Medicine, Saitama Medical University International Medical Center, Saitama, Japan.
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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Puckett LM, Rajkotia P, Coppola L, Baumgartner L, Roberts AL, Maldonado Y, Girotto JE. Impact of Direct From Blood Culture Identification of Pathogens Paired With Antimicrobial Stewardship Interventions in a Pediatric Hospital. J Pediatr Pharmacol Ther 2021; 26:802-808. [PMID: 34790069 DOI: 10.5863/1551-6776-26.8.802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/17/2021] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Identification of organisms directly from positive blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has the potential for improved clinical outcomes through earlier organism identification and shorter time to appropriate clinical intervention. The uses of this technology in pediatric patients and its impact in this patient population have not been well described. METHODS Direct from positive blood culture organism identification via MALDI-TOF was implemented in September 2019. A quality improvement project was performed to assess its impact on admissions for contaminant blood cultures and time to effective and optimal antimicrobials and clinical decision-making. A pre- and post-implementation retrospective review for consecutive September through February time periods, was conducted on patients with positive monomicrobial blood cultures. Statistics were evaluated using Mann-Whitney U and χ2 tests. RESULTS One hundred nineteen patients with 131 unique blood cultures (65 in pre- and 66 in post-implementation) were identified. Time to identification was shorter, median 35.4 hours (IQR, 22.7-54.3) versus 42.3 hours (IQR, 36.5-49) in post- and pre-groups, respectively (p = 0.02). Patients were less likely to be admitted for a contaminated blood culture in the post-implementation, 26% versus 11% in the pre-implementation (p = 0.03) group. In patients treated for bacteremia, there was a shorter time to optimal therapy from Gram stain reporting in the post-implementation (median 42.7 hours [IQR, 27.2-72]) versus pre-implementation (median 60.8 hours [IQR, 42.9-80.6]) (p = 0.03). CONCLUSIONS Direct from positive blood culture identification by MALDI-TOF decreased time to effective and optimal antimicrobials and decreased unnecessary admission in pediatric patients for contaminated blood cultures.
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Abstract
Purpose of Review Sepsis is a leading cause of death worldwide. Groundbreaking international collaborative efforts have culminated in the widely accepted surviving sepsis guidelines, with iterative improvements in management strategies and definitions providing important advances in care for patients. Key to the diagnosis of sepsis is identification of infection, and whilst the diagnostic criteria for sepsis is now clear, the diagnosis of infection remains a challenge and there is often discordance between clinician assessments for infection. Recent Findings We review the utility of common biochemical, microbiological and radiological tools employed by clinicians to diagnose infection and explore the difficulty of making a diagnosis of infection in severe inflammatory states through illustrative case reports. Finally, we discuss some of the novel and emerging approaches in diagnosis of infection and sepsis. Summary While prompt diagnosis and treatment of sepsis is essential to improve outcomes in sepsis, there remains no single tool to reliably identify or exclude infection. This contributes to unnecessary antimicrobial use that is harmful to individuals and populations. There is therefore a pressing need for novel solutions. Machine learning approaches using multiple diagnostic and clinical inputs may offer a potential solution but as yet these approaches remain experimental.
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Åkerlund A, Petropoulos A, Malmros K, Tängdén T, Giske CG. Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories. Clin Microbiol Infect 2021; 28:731.e1-731.e7. [PMID: 34537364 DOI: 10.1016/j.cmi.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/17/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Accurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013. METHODS An online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018. RESULTS The response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60-70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common. CONCLUSIONS CMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.
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Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, Laboratory Medicine, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Sweden; Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University Hospital, Linköping, Sweden.
| | - Alexandros Petropoulos
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Malmros
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
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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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24
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Samuel LP, Hansen GT, Kraft CS, Pritt BS. The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory. J Clin Microbiol 2021; 59:e0154919. [PMID: 33597258 PMCID: PMC8288296 DOI: 10.1128/jcm.01549-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.
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Affiliation(s)
- Linoj P. Samuel
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
| | - Glen T. Hansen
- Department of Pathology and Laboratory Medicine, Hennepin County Medical Center, Minneapolis, Minnesota, USA
- Department of Pathology and Laboratory Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Medicine, Division of Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Colleen S. Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
| | - Bobbi S. Pritt
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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25
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Rapid diagnostic testing for antimicrobial stewardship: Utility in Asia Pacific. Infect Control Hosp Epidemiol 2021; 42:864-868. [PMID: 34128462 DOI: 10.1017/ice.2021.149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rapid diagnostic testing (RDT) can provide prompt, accurate identification of infectious organisms and be a key component of antimicrobial stewardship (AMS) programs. However, their use is less widespread in Asia Pacific than western countries. Cost can be prohibitive, particularly in less resource-replete settings. A selective approach is required, possibly focusing on the initiation of antimicrobials, for differentiating bacterial versus viral infections and identifying locally relevant tropical diseases. Across Asia Pacific, more data are needed on RDT use within AMS, focusing on the impact on antimicrobial usage, patient morbidity and mortality, and cost effectiveness. Moreover, in the absence of formal guidelines, regional consensus statements to guide clinical practice are warranted. These will provide a regionally relevant definition for RDT; greater consensus on its role in managing infections; advice on implementation and overcoming barriers; and guidance on optimizing human resource capacity. By addressing these issues, the outcomes of AMS programs should improve.
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Abstract
Over the past decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry has revolutionized the practice of clinical microbiology and infectious disease diagnostics. Rapid advancement has occurred through the development and implementation of mass spectrometric protein profiling technologies that are widely available. Ease of sample preparation, rapid turnaround times, and high throughput accuracy have accelerated acceptance within the clinical laboratory. New mass spectrometric technologies centered on multiple microbial diagnostic markers are in development. Such new applications, reviewed in this article and on the near horizon, stand to greatly enhance the capabilities and utility for improved mass spectrometric microbial identification and patient care.
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27
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Jain D, Torres R, Celli R, Koelmel J, Charkoftaki G, Vasiliou V. Evolution of the liver biopsy and its future. Transl Gastroenterol Hepatol 2021; 6:20. [PMID: 33824924 PMCID: PMC7829074 DOI: 10.21037/tgh.2020.04.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
Liver biopsies are commonly used to evaluate a wide variety of medical disorders, including neoplasms and post-transplant complications. However, its use is being impacted by improved clinical diagnosis of disorders, and non-invasive methods for evaluating liver tissue and as a result the indications of a liver biopsy have undergone major changes in the last decade. The evolution of highly effective treatments for some of the common indications for liver biopsy in the last decade (e.g., viral hepatitis B and C) has led to a decline in the number of liver biopsies in recent years. At the same time, the emergence of better technologies for histologic evaluation, tissue content analysis and genomics are among the many new and exciting developments in the field that hold great promise for the future and are going to shape the indications for a liver biopsy in the future. Recent advances in slide scanners now allow creation of "digital/virtual" slides that have image of the entire tissue section present in a slide [whole slide imaging (WSI)]. WSI can now be done very rapidly and at very high resolution, allowing its use in routine clinical practice. In addition, a variety of technologies have been developed in recent years that use different light sources and/or microscopes allowing visualization of tissues in a completely different way. One such technique that is applicable to liver specimens combines multiphoton microscopy (MPM) with advanced clearing and fluorescent stains known as Clearing Histology with MultiPhoton Microscopy (CHiMP). Although it has not yet been extensively validated, the technique has the potential to decrease inefficiency, reduce artifacts, and increase data while being readily integrable into clinical workflows. Another technology that can provide rapid and in-depth characterization of thousands of molecules in a tissue sample, including liver tissues, is matrix assisted laser desorption/ionization (MALDI) mass spectrometry. MALDI has already been applied in a clinical research setting with promising diagnostic and prognostic capabilities, as well as being able to elucidate mechanisms of liver diseases that may be targeted for the development of new therapies. The logical next step in huge data sets obtained from such advanced analysis of liver tissues is the application of machine learning (ML) algorithms and application of artificial intelligence (AI), for automated generation of diagnoses and prognoses. This review discusses the evolving role of liver biopsies in clinical practice over the decades, and describes newer technologies that are likely to have a significant impact on how they will be used in the future.
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Affiliation(s)
- Dhanpat Jain
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Torres
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Romulo Celli
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeremy Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
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28
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Point-of-care and Near Real-time Testing for Antiretroviral Adherence Monitoring to HIV Treatment and Prevention. Curr HIV/AIDS Rep 2021; 17:487-498. [PMID: 32627120 DOI: 10.1007/s11904-020-00512-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE OF REVIEW In this report, we review the need for point-of-care (POC) or near real-time testing for antiretrovirals, progress in the field, evidence for guiding implementation of these tests globally, and future directions in objective antiretroviral therapy (ART) or pre-exposure prophylaxis (PrEP) adherence monitoring. RECENT FINDINGS Two cornerstones to end the HIV/AIDS pandemic are ART, which provides individual clinical benefits and eliminates forward transmission, and PrEP, which prevents HIV acquisition with high effectiveness. Maximizing the individual and public health benefits of these powerful biomedical tools requires high and sustained antiretroviral adherence. Routine monitoring of medication adherence in individuals receiving ART and PrEP may be an important component in interpreting outcomes and supporting optimal adherence. Existing practices and subjective metrics for adherence monitoring are often inaccurate or unreliable and, therefore, are generally ineffective for improving adherence. Laboratory measures of antiretroviral concentrations using liquid chromatography tandem mass spectrometry have been utilized in research settings to assess medication adherence, although these are too costly and resource-intensive for routine use. Newer, less costly technologies such as antibody-based methods can provide objective drug-level measurement and may allow for POC or near-patient adherence monitoring in clinical settings. When coupled with timely and targeted counseling, POC drug-level measures can support adherence clinic-based interventions to ART or PrEP in near real time.
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29
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Sweileh WM. Bibliometric analysis of peer-reviewed literature on antimicrobial stewardship from 1990 to 2019. Global Health 2021; 17:1. [PMID: 33397377 PMCID: PMC7780390 DOI: 10.1186/s12992-020-00651-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The World Health Organization recommended the implementation of antimicrobial stewardship (AMS) in the clinical settings to minimize the development and spread of antimicrobial resistance (AMR). The current study aimed to assess global research activity on AMS as one measure for efforts dedicated to contain AMR. METHOD A bibliometric method was applied using Scopus. A validated search query was implemented. Bibliometric indicators and mapping were generated. The study period was from 1990 to 2019. The search query utilized the keywords "antimicrobial stewardship" or "antibiotic stewardship" in the titles or abstracts. In addition, documents with the term "restrict" or "restriction" if used with the terms "antimicrobial" or "antibiotic" were retrieved. RESULTS The search query returned 4402 documents. The keyword "antimicrobial stewardship" returned 2849 documents while the keyword "antibiotic stewardship" returned 1718 documents. The terms restrict/restriction and antimicrobial/antibiotics returned 209 documents. The number of publications and cumulative citations showed a steep and parallel increase in the last decade. The region of the Americas returned the most while the Eastern Mediterranean region returned the least. The United States (n = 1834, 41.7%) ranked first. Main research themes in the retrieved literature were the (1) impact of AMS on hospital length stay, (2) role of pharmacists, and (3) development of resistance of various pathogens. Clostridium difficile (n = 94) and Staphylococcus aureus (n = 76) were among the most frequently encountered author keywords. The Infection Control and Hospital Epidemiology journal ranked first (n = 245, 5.6%, h-index = 134) while documents published in the Clinical Infectious Diseases journal (h-index = 321) received the highest number of citations per document (70.7). At the institutional level, the US Centers for Disease Prevention and Control (n = 93, 2.1%) ranked first followed by the Imperial College London (n = 86, 2.0%). The main funding sponsors were the National Institute of Health. Pfizer, Merck, and Bayer pharmaceutical companies played a key role in funding AMS research. International research collaboration between developed (n = 3693, 83.9%) and developing countries (n = 759, 17.2%). CONCLUSION The fight against AMR is a global responsibility and implementation of AMS need to be carried out across the globe. International research collaboration between developing and developed countries should be encouraged.
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Affiliation(s)
- Waleed M Sweileh
- Department of Physiology, Pharmacology/Toxicology, Division of Biomedical Sciences, College of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
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30
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Bryant S, Almahmoud I, Pierre I, Bardet J, Touati S, Maubon D, Cornet M, Richarme C, Maurin M, Pavese P, Caspar Y. Evaluation of Microbiological Performance and the Potential Clinical Impact of the ePlex ® Blood Culture Identification Panels for the Rapid Diagnosis of Bacteremia and Fungemia. Front Cell Infect Microbiol 2020; 10:594951. [PMID: 33324578 PMCID: PMC7726344 DOI: 10.3389/fcimb.2020.594951] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular rapid diagnostic assays associated with antimicrobial stewardship have proven effective for the early adaptation of empiric therapy in bloodstream infections. The ePlex® BCID (GenMark Diagnostics) Panels allow identification of 56 bacteria and fungi and 10 resistance genes in 90 min directly from positive blood cultures. We prospectively evaluated 187 sepsis episodes at Grenoble University Hospital and retrospectively analyzed the cases to measure the potential clinical impact of the ePlex BCID results. Identification of all pathogens was obtained for 164/187 (88%) bloodstream infections with 100% detection of antimicrobial resistance genes (17 blaCTX-M , 1 vanA, and 17 mecA genes). Only 15/209 (7%) strains were not covered by the panels. Sensitivity for detection of micro-organisms targeted by the RUO BCID-GP, BCID-GN, and BCID-FP Panels was respectively 84/84 (100%), 103/107 (96%), and 14/14 (100%). Interestingly, accurate identification of all pathogens was achieved in 15/17 (88%) polymicrobial samples. Retrospective analysis of medical records showed that a modification of antimicrobial treatment would have been done in 45% of the patients. Treatment modifications would have been an optimization of empiric therapy, a de-escalation or an escalation in respectively 16, 17, and 11% of the patients. Moreover, 11% of the samples were classified as contaminants or not clinically relevant and would have led to early de-escalation or withdrawal of any antibiotic. Detection of resistance genes in addition to identification alone increased escalation rate from 4 to 11% of the patients. Absence of the ePlex result was considered a lost opportunity for therapy modification in 28% of patients.
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Affiliation(s)
- Sabrina Bryant
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Iyad Almahmoud
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Isabelle Pierre
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Julie Bardet
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Saber Touati
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Daniele Maubon
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Muriel Cornet
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Patricia Pavese
- Service des maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Yvan Caspar
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
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31
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Abstract
Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.
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Affiliation(s)
- Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Boulevard MS#32, Los Angeles, CA 90027, USA; University of Southern California, Keck School of Medicine.
| | - Erin McElvania
- Department of Pathology and Laboratory Medicine, Evanston Hospital, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201, USA; University of Chicago Pritzker School of Medicine. https://twitter.com/e_mcelvania
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32
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Uchida-Fujii E, Niwa H, Kinoshita Y, Nukada T. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for Identification of Bacterial Isolates From Horses. J Equine Vet Sci 2020; 95:103276. [PMID: 33276932 DOI: 10.1016/j.jevs.2020.103276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is used for bacterial identification by analyzing the spectra of isolates and comparing them against a database of reference spectra; it is known for its rapidity and accuracy. Although MALDI-TOF MS is used for identification of bacterial isolates from animals, not all animal pathogens are identified correctly. In this study, we used a commercial MALDI-TOF MS identification system to examine 3724 bacterial isolates from horses and their environments. Isolates that could not be identified with MALDI-TOF MS were identified by 16S rRNA gene sequence taxonomic analysis. MALDI-TOF MS could identify 86.2% of the isolates from horses to the species level, showing that this method could be successfully applied for bacterial identification in horses. However, some species known to be equine pathogenic agents including Taylorella equigenitalis and Rhodococcus equi were difficult to identify with MALDI-TOF MS, which might be the result of an inadequate reference database. Some Prevotella, Staphylococcus, and Streptococcus isolates, which could not be identified with either MALDI-TOF MS or 16S rRNA gene sequencing analysis, formed clusters in the 16S rRNA phylogenic tree, and might be unknown species isolated from horses. Adding the spectra of isolates identified in this study to an in-house database might make MALDI-TOF MS a more useful tool for identifying equine isolates.
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Affiliation(s)
- Eri Uchida-Fujii
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
| | - Hidekazu Niwa
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Yuta Kinoshita
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Toshio Nukada
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
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Nitrosetein T, Wongwattanakul M, Chonanant C, Leelayuwat C, Charoensri N, Jearanaikoon P, Lulitanond A, Wood BR, Tippayawat P, Heraud P. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy combined with chemometric modelling for the classification of clinically relevant Enterococci. J Appl Microbiol 2020; 130:982-993. [PMID: 32780423 DOI: 10.1111/jam.14820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 01/03/2023]
Abstract
AIMS Attenuated Total Reflection Fourier Transform Infrared (ATR-FT-IR) Spectroscopy and chemometric modelling, including soft independent modelling by class analogy (SIMCA), partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM), were applied to attempt to discriminate 60 clinical isolates of Enterococcus faecium and Enterococcus faecalis and hence evaluate the performance of the spectroscopic approach in identifying enterococci infections. METHODS AND RESULTS The bacterial samples were identified by polymerize chain reaction (PCR) amplification and their ATR-FT-IR spectra acquired. Spectra were processed to the second derivative using the Savitzky-Golay algorithm and normalized using extended multiplicative signal correction employing the UnscramblerX (CAMO, Norway) software package. Multivariate classification models and their performance were evaluated using Cohen's Kappa coefficient. Principal component analysis (PCA) score plots showed separate clusters of spectra related to membership to E. faecium and E. faecalis, with this explained by bands assigned to PO2 (1230 cm-1 ), P-O-C (1114 cm-1 ), monosubstituted alkene (997, 987 cm-1 ) and C-O (1070, 1055, 1036 cm-1 ) corresponding to teichoic acids, polysaccharides and peptidoglycan from the cell wall in PCA and PLS-DA loading plots. The best classification model for E. faecium and E. faecalis is SVM, indicating via highest Kappa score. The classification coefficient between SIMCA, PLS-DA, SVM and PCR as reference method were 0·59, 0·9 and 1, respectively, shown as the Kappa scores. CONCLUSIONS The main spectral differences observed between the two clinically relevant enterococci species were associated with changes in the teichoic acid content of cell walls. With regard to the binary classification method, SVM was found to be the best performing classification model, providing the highest correlation with the PCR results. SIGNIFICANCE AND IMPACT OF THE STUDY The study shows that ATR-FT-IR spectroscopy in combination with chemometric modelling can be applied for the phenotypic identification and discrimination of clinically relevant and similar enterococcal species.
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Affiliation(s)
- T Nitrosetein
- Biomedical Science Program, Graduate School, Khon Kaen University, Khon Kaen, Thailand.,Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - M Wongwattanakul
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - C Chonanant
- Faculty of Allied Health Sciences, Burapha University, Chonburi, Thailand
| | - C Leelayuwat
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - N Charoensri
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - P Jearanaikoon
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - A Lulitanond
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - B R Wood
- Centre for Biospectroscopy, School of Chemistry, Faculty of Science, Monash University, Victoria, Australia
| | - P Tippayawat
- Centre for Research and Development of Medical Diagnostic Laboratories (CDML), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - P Heraud
- Centre for Biospectroscopy, School of Chemistry, Faculty of Science, Monash University, Victoria, Australia.,Department of Microbiology and the Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Australia
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34
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Vasala A, Hytönen VP, Laitinen OH. Modern Tools for Rapid Diagnostics of Antimicrobial Resistance. Front Cell Infect Microbiol 2020; 10:308. [PMID: 32760676 PMCID: PMC7373752 DOI: 10.3389/fcimb.2020.00308] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022] Open
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.
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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
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Frühe Optimierung der Antibiotikatherapie durch den schnellen Nachweis von Erregern und Empfindlichkeit. Med Klin Intensivmed Notfmed 2020; 115:420-427. [DOI: 10.1007/s00063-020-00680-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/06/2019] [Accepted: 03/08/2020] [Indexed: 11/25/2022]
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Dare RK, Lusardi K, Pearson C, McCain KD, Daniels B, Van S, Rico JC, Painter J, Lakkad M, Rosenbaum ER, Bariola JR. Clinical Impact of Accelerate PhenoTM Rapid Blood Culture Detection System in Bacteremic Patients. Clin Infect Dis 2020; 73:e4616-e4626. [PMID: 32463864 DOI: 10.1093/cid/ciaa649] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/22/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Accelerate Pheno blood culture detection system (AXDX) provides identification (ID) and antimicrobial susceptibility testing (AST) results within 8h of blood culture growth. Limited data exists regarding its clinical impact. Other rapid platforms coupled with antimicrobial stewardship program (ASP) real-time notification (RTN) have shown improved length of stay (LOS) in bacteremia. METHODS A single-center, quasi-experimental study of adult bacteremic inpatients before/after AXDX implementation was conducted comparing clinical outcomes from 1 historical and 2 intervention cohorts (AXDX and AXDX+RTN). Primary outcome was LOS. RESULTS Of 830 bacteremic episodes, 188 (77%) of 245 historical and 308 (155 AXDX, 153 AXDX+RTN; 65%) of 585 intervention episodes were included. Median LOS was shorter with AXDX (6.3d) and AXDX+RTN (6.7d) compared to historical (8.1d; P=0.001). Achievement of optimal therapy (AOT) was more frequent (93.6% and 95.4%) and median time to optimal therapy (TTOT) was faster (1.3d and 1.4d) in AXDX and AXDX+RTN compared to historical (84.6%, P≤0.001 and 2.4d; P≤0.001) respectively. Median antimicrobial days of therapy (DOT) was shorter in both intervention arms compared to historical (6d each vs 7d; P=0.011). Median LOS benefit was most pronounced in patients with coagulase negative Staphylococcus bacteremia (5.5d and 4.5d vs 7.2d; P=0.003) in AXDX, AXDX+RTN, and historical cohorts respectively. CONCLUSIONS LOS, AOT, TTOT, and total DOT significantly improved after AXDX implementation. Addition of RTN did not show further improvement over AXDX and an already active ASP. These results suggest AXDX can be integrated into healthcare systems with an active ASP even without the resources to include RTN.
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Affiliation(s)
- R K Dare
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - K Lusardi
- Hospital Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Pearson
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - K D McCain
- Hospital Pharmacy, Wadley Regional Medical Center, Texarkana, TX, USA
| | - B Daniels
- College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S Van
- College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J C Rico
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J Painter
- Division of Pharmaceutical Evaluation and Policy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - M Lakkad
- Division of Pharmaceutical Evaluation and Policy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - E R Rosenbaum
- Department of Pathology and Laboratory Services, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J R Bariola
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Nomura F, Tsuchida S, Murata S, Satoh M, Matsushita K. Mass spectrometry-based microbiological testing for blood stream infection. Clin Proteomics 2020; 17:14. [PMID: 32435163 PMCID: PMC7222329 DOI: 10.1186/s12014-020-09278-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive blood culture bottles with MALDI-TOF MS including our own protocols. We touch upon the increasing roles of Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) as well. MAIN BODY Because blood culture bottles contain a variety of nonbacterial proteins that may interfere with analysis and interpretation, appropriate pretreatments are prerequisites for successful ID. Pretreatments include purification of bacterial pellets and short-term subcultures to form microcolonies prior to MALDI-TOF MS analysis. Three commercial protocols are currently available: the Sepsityper® kit (Bruker Daltonics), the Vitek MS blood culture kit (bioMerieux, Inc.), and the rapid BACpro® II kit (Nittobo Medical Co., Tokyo). Because these commercially available kits are costly and bacterial ID rates using these kits are not satisfactory, particularly for Gram-positive bacteria, various home-brew protocols have been developed: 1. Stepwise differential sedimentation of blood cells and microorganisms, 2. Combination of centrifugation and lysis procedures, 3. Lysis-vacuum filtration, and 4. Centrifugation and membrane filtration technique (CMFT). We prospectively evaluated the performance of this CMFT protocol compared with that of Sepsityper® using 170 monomicrobial positive blood cultures. Although preliminary, the performance of the CMFT was significantly better than that of Sepsityper®, particularly for Gram-positive isolates. MALDI-TOF MS-based testing of polymicrobial blood specimens, however, is still challenging. Also, its contribution to assessment of susceptibility and resistance to antibiotics is still limited. For this purpose, liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) should be more useful because this approach can identify as many as several thousand peptide sequences. CONCLUSION MALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future.
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Affiliation(s)
- Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Syota Murata
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677 Japan
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Ushering in Diagnostic Stewardship: a Step Towards Antibiotic Stewardship. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2020. [DOI: 10.1007/s40506-020-00224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Araújo TMC, Pereira RDCL, Freitag IGR, Rusak LA, Botelho LAB, Hofer E, Hofer CB, Vallim DC. Evaluation of MALDI-TOF MS as a tool for detection of Listeria spp. directly from selective enrichment broth from food and stool samples. J Microbiol Methods 2020; 173:105936. [PMID: 32360382 DOI: 10.1016/j.mimet.2020.105936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/29/2022]
Abstract
We evaluated the detection of Listeria spp. using MALDI-TOF MS directly in enrichment broths, without isolated colonies, with naturally contaminated food and stool samples. The success rate was 77%. Considering the reduced time for diagnosis and the success rate, this is a promising screening tool, but more tests are needed to determine its viability.
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Affiliation(s)
- Thais Martins Campos Araújo
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil
| | | | | | - Leonardo Alves Rusak
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Fisiologia Bacteriana, Rio de Janeiro/RJ, Brazil
| | - Larissa Alvarenga Batista Botelho
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Prof. Paulo de Góes, Laboratório de Investigação em Microbiologia Médica, Rio de Janeiro/RJ, Brazil
| | - Ernesto Hofer
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil
| | - Cristina Barroso Hofer
- Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Rio de Janeiro/RJ, Brazil
| | - Deyse Christina Vallim
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Zoonoses Bacterianas/Setor Listeria, Rio de Janeiro/RJ, Brazil.
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Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A. Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies. Clin Microbiol Rev 2020; 33:e00057-19. [PMID: 32102900 PMCID: PMC7048017 DOI: 10.1128/cmr.00057-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Géraldine Durand
- bioMérieux, Microbiology Research and Development, La Balme Les Grottes, France
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Patrick Murray
- BD Life Sciences Integrated Diagnostic Solutions, Scientific Affairs, Sparks, Maryland, USA
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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Lellman SE, Cramer R. Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. ACTA ACUST UNITED AC 2019; 58:930-938. [DOI: 10.1515/cclm-2019-0908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/25/2019] [Indexed: 12/16/2022]
Abstract
Abstract
Background
In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.
Methods
Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.
Results
Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.
Conclusions
Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.
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Affiliation(s)
- Sophie E. Lellman
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
| | - Rainer Cramer
- Department of Chemistry , University of Reading , Whiteknights, Reading , UK
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Shemanski S, Bennett N, Essmyer C, Kennedy K, Buchanan DM, Warnes A, Boyd S. Centralized Communication of Blood Culture Results Leveraging Antimicrobial Stewardship and Rapid Diagnostics. Open Forum Infect Dis 2019; 6:ofz321. [PMID: 31660401 PMCID: PMC6736069 DOI: 10.1093/ofid/ofz321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/03/2019] [Indexed: 12/26/2022] Open
Abstract
Objective This study aimed to determine if integrating antimicrobial stewardship program (ASP) personnel with rapid diagnostic testing resulted in improved outcomes for patients with positive blood cultures. Method Beginning in 2016, Saint Luke’s Health System (SLHS) implemented a new process where all positive blood cultures were communicated to ASP personnel or SLHS pharmacy staff. Pharmacists then became responsible for interpreting results, assessing patient specific information, and subsequently relaying culture and treatment information to providers. This was a multisite, pre-post, quasi-experimental study (Pre: August to December 2014; Post: August to December 2016). Patients 18 years of age and older with a positive blood culture during admission were included (2014, n = 218; 2016, n = 286). Coprimary outcomes of time to optimal and appropriate therapy were determined from time of culture positivity via gram stain. Secondary outcomes focused on clinical, process, and fiscal endpoints. A pre-post intervention physician survey was conducted to assess the impact on antimicrobial decision making and perceived effect on patient outcomes. Results There was no difference in time to appropriate therapy groups (P = .079). Time to optimal therapy was 9.2 hours shorter in 2016 (P = .004). Provider surveys indicated the process improved communication among clinicians and facilitated a shared decision-making process with a perceived improvement in patient care. Conclusions An ASP-led blood culture communication process for patients with positive blood cultures was shown to improve time to optimal therapy, support physicians in their decision making on critical lab data, and improve the care for hospitalized patients.
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Affiliation(s)
- Shelby Shemanski
- Saint Luke's Pharmacy, Saint Luke's Health System, Kansas City, Missouri
| | - Nicholas Bennett
- Antimicrobial Stewardship Program, Saint Luke's Health System, Kansas City, Missouri
| | - Cynthia Essmyer
- Department of Microbiology, Saint Luke's Health System, Kansas City, Missouri
| | - Kevin Kennedy
- Department of Research, Saint Luke's Health System, Kansas City, Missouri
| | - Donna M Buchanan
- Research Administration, Department of Biomedical and Health Informatics, University of Missouri-Kansas City School of Medicine, Saint Luke's Health System, Kansas City, Missouri
| | - Andrew Warnes
- Infectious Diseases, Saint Luke's Health System, Kansas City, Missouri
| | - Sarah Boyd
- Infectious Diseases, Saint Luke's Health System, Kansas City, Missouri
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Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges. J Clin Microbiol 2019; 57:JCM.00425-19. [PMID: 31043466 DOI: 10.1128/jcm.00425-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sepsis is a major source of mortality and morbidity globally. Accurately diagnosing sepsis remains challenging due to the heterogeneous nature of the disease, and delays in diagnosis and intervention contribute to high mortality rates. Measuring the host response to infection enables more rapid diagnosis of sepsis than is possible through direct detection of the causative pathogen, and recent advances in host response diagnostics and prognostics hold promise for improving outcomes. The current review discusses recent advances in the technologies used to probe the host response to infection, particularly those based on transcriptomics. These are discussed in the context of contemporary approaches to diagnosing and prognosing sepsis, and recommendations are made for successful development and validation of host response technologies.
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Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry and real-time PCR in a combined protocol for diagnosis of bloodstream infections: a turnaround time approach. Braz J Infect Dis 2019; 23:164-172. [PMID: 31175842 PMCID: PMC9428233 DOI: 10.1016/j.bjid.2019.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/25/2022] Open
Abstract
Bloodstream infections (BSIs) are serious infections associated with high rates of morbidity and mortality. Every hour delay in initiation of an effective antibiotic increases mortality due to sepsis by 7%. Turnaround time (TAT) for conventional blood cultures takes 48 h, forcing physicians to streamline therapy by exposing patients to broad-spectrum antimicrobials. Our objective was (1) to evaluate the accuracy and TAT of an optimized workflow combining direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and in-house real-time polymerase chain reaction (PCR) for bacterial identification and antimicrobial resistance profiling directly from positive blood bottles for diagnosing bloodstream infections and (2) to verify the effect of reporting results to medical staff. A total of 103 BSI episodes from 91 patients admitted to three hospitals in São Paulo, Brazil were included. TAT from molecular versus conventional methods was measured and compared. Our protocol showed an overall agreement of 93.5% for genus and 78.5% for species identification; 74.2% for methicillin resistance detection, 89.2% for extended-spectrum β-lactamase profiling, 77.8% for metallo-β-lactamase profiling, and 100% for carbapenemase profile and vancomycin-resistance detection when compared with conventional testing. TAT of molecular sample processing according to our protocol was 38 h shorter than conventional methods. Antimicrobial interventions were possible in 27 BSI episodes. Antimicrobial discontinuation was achieved in 12 BSI episodes while escalation of therapy occurred in 15 episodes. Antimicrobial therapy was inadequate in three (12%) BSI episodes diagnosed using results of molecular testing. Our in-house rapid protocol for identifying both bacteria and antimicrobial resistance provided rapid and accurate results, having good agreement with conventional testing results. These results could contribute to faster antimicrobial therapy interventions in BSI episodes.
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Niwa T, Yonetamari J, Hayama N, Fujibayashi A, Ito-Takeichi S, Suzuki K, Ohta H, Niwa A, Tsuchiya M, Yamamoto M, Hatakeyama D, Hayashi H, Obara M, Sugiyama T, Baba H, Suzuki A, Murakami N. Clinical impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry combined with antimicrobial stewardship interventions in patients with bloodstream infections in a Japanese tertiary hospital. Int J Clin Pract 2019; 73:e13332. [PMID: 30810264 DOI: 10.1111/ijcp.13332] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/19/2018] [Accepted: 02/24/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has the potential to permit early organism identification and optimization of antibiotic therapy. However, MALDI-TOF MS combined with antimicrobial stewardship is available at only a limited number of institutions. Here, we evaluated the clinical impact of implementing MALDI-TOF MS combined with antimicrobial stewardship intervention in patients with bloodstream infections. METHODS We conducted a single-centre, prospective cohort study to evaluate the clinical impact of implementing MALDI-TOF MS combined with antimicrobial stewardship intervention in patients with bloodstream infections. Processes and clinical outcomes in patients with bloodstream infections were compared before and after implementation of MALDI-TOF MS. RESULTS Compared with the conventional identification method, MALDI-TOF MS combined with antimicrobial stewardship intervention significantly decreased the time to organism identification (48.6 ± 46.0 hours vs 78.1 ± 38.9 hours, P < 0.001), effective antimicrobial therapy (12.9 ± 19.0 hours vs 26.2 ± 44.8 hours, P < 0.001) and optimal antimicrobial therapy (53.3 ± 55.0 hours vs 91.7 ± 88.7 hours, P < 0.001. Moreover, the rate of clinical failure (14.0% vs 33.3%, P < 0.001) and incidence of adverse events (7.5% vs 23.9%, P < 0.001) was lower in the MALDI-TOF MS group than in the conventional identification group. A multivariate Cox proportional hazard analysis indicated that implementation of MALDI-TOF MS was a protective factor against clinical failure in patients with bloodstream infections (hazard ratio, 0.61; 95% confidence interval, 0.38-0.99; P = 0.047). CONCLUSIONS Implementation of the MALDI-TOF MS combined with antimicrobial stewardship intervention facilitated early optimization of antimicrobial therapy with a remarkable concomitant reduction in clinical failure and adverse events in patients with bloodstream infections.
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Affiliation(s)
- Takashi Niwa
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Jun Yonetamari
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Nozomi Hayama
- Laboratory of Community Healthcare Pharmacy, Gifu Pharmaceutical University, Gifu, Japan
| | - Ayasa Fujibayashi
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Syuri Ito-Takeichi
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Keiko Suzuki
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Hirotoshi Ohta
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Ayumi Niwa
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Mayumi Tsuchiya
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Masayo Yamamoto
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Daijiro Hatakeyama
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Hideki Hayashi
- Laboratory of Community Healthcare Pharmacy, Gifu Pharmaceutical University, Gifu, Japan
- Laboratory of Pharmacy Practice and Social Science, Gifu Pharmaceutical University, Gifu, Japan
| | - Michiko Obara
- Laboratory of Community Healthcare Pharmacy, Gifu Pharmaceutical University, Gifu, Japan
| | - Tadashi Sugiyama
- Laboratory of Community Healthcare Pharmacy, Gifu Pharmaceutical University, Gifu, Japan
- Laboratory of Pharmacy Practice and Social Science, Gifu Pharmaceutical University, Gifu, Japan
| | - Hisashi Baba
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
| | - Akio Suzuki
- Department of Pharmacy, Gifu University Hospital, Gifu, Japan
| | - Nobuo Murakami
- Center for Nutrition Support & Infection Control, Gifu University Hospital, Gifu, Japan
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Identification of Burkholderia pseudomallei by Use of the Vitek Mass Spectrometer. J Clin Microbiol 2019; 57:JCM.00081-19. [PMID: 30842230 DOI: 10.1128/jcm.00081-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis. This condition most often presents as pneumonia and bacteremia, with mortality rates of 9% to 70%. Therefore, early identification of this organism may aid in directing appropriate management. This study aimed to use the Vitek matrix-assisted laser desorption ionization-time of flight mass spectrometer to create a spectrum for the rapid identification of B. pseudomallei Spectra from 85 isolate cultures were acquired using the Vitek mass spectrometer research mode. A SuperSpectrum was created using peak matching and subsequently activated for analysis of organism identification. All 85 isolates were correctly identified as B. pseudomallei A total of 899 spectra were analyzed and demonstrated a specificity of 99.8%. Eighty-one clinical isolates were used, of which 10 were neuromelioidosis, and no discernible spectrum difference was appreciated. Spectrum acquisition from a single spot was only successful in 374/899 (41%) of isolates. This increased to 100% when 3 spots of the same extract were analyzed. The Vitek mass spectrometer can be used for the rapid identification of B. pseudomallei with a high level of specificity.
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Bradley N, Lee Y. Practical Implications of New Antibiotic Agents for the Treatment of Carbapenem-Resistant Enterobacteriaceae. Microbiol Insights 2019; 12:1178636119840367. [PMID: 30992668 PMCID: PMC6449805 DOI: 10.1177/1178636119840367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/09/2019] [Indexed: 11/29/2022] Open
Abstract
Objective: To provide insight into the practical implications of the use of
ceftazidime/avibactam and meropenem/vaborbactam for the management of
carbapenem-resistant Enterobacteriaceae (CRE) and to identify strategies for
overcoming barriers to the use of these agents in clinical practice. Data sources: A literature search of PubMed was conducted using the following search terms:
ceftazidime/avibactam, meropenem/vaborbactam, carbapenem-resistant
Enterobacteriaceae, antimicrobial stewardship, and clinical laboratory
standards institute. Abstracts from infectious diseases conferences, article
bibliographies, and relevant drug monographs were also reviewed. Study selection/data extraction: Relevant English-language studies were considered. Data synthesis: Studies demonstrating the clinical utility of ceftazidime/avibactam and
meropenem/vaborbactam over older agents for CRE were summarized. Laboratory
challenges, including lack of widespread technology and delays in usable
information, and formulary considerations were discussed. Insight was
provided into overcoming these challenges and minimizing barriers using
infectious diseases pharmacists, antimicrobial stewardship teams, and
infection control teams. Relevance to patient care and clinical practice: This review informs clinicians of the potential difficulties of the use of
ceftazidime/avibactam and meropenem/vaborbactam in clinical practice and
provides tools to overcome these difficulties, thus allowing clinicians to
stay at the forefront of CRE treatment. Conclusions: Clinicians treating patients with CRE infections need to be aware of
challenges they may face when using ceftazidime/avibactam and
meropenem/vaborbactam. Infectious disease (ID) pharmacists and antimicrobial
stewardship teams play an important role in minimizing barriers and ensuring
appropriate use of these antibiotics.
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Affiliation(s)
- Nicole Bradley
- Department of Clinical Health Professions, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA
| | - Yuman Lee
- Department of Clinical Health Professions, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, USA
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48
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Abstract
Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.
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Affiliation(s)
- Donna M Wolk
- Clinical Microbiology, Department of Laboratory Medicine, Diagnostic Medicine Institute, Geisinger Health, 100 North Academy Avenue, Danville, PA 17822-1930, USA.
| | - Andrew E Clark
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA
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49
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Nathwani D, Varghese D, Stephens J, Ansari W, Martin S, Charbonneau C. Value of hospital antimicrobial stewardship programs [ASPs]: a systematic review. Antimicrob Resist Infect Control 2019; 8:35. [PMID: 30805182 PMCID: PMC6373132 DOI: 10.1186/s13756-019-0471-0] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 12/21/2022] Open
Abstract
Background Hospital antimicrobial stewardship programs (ASPs) aim to promote judicious use of antimicrobials to combat antimicrobial resistance. For ASPs to be developed, adopted, and implemented, an economic value assessment is essential. Few studies demonstrate the cost-effectiveness of ASPs. This systematic review aimed to evaluate the economic and clinical impact of ASPs. Methods An update to the Dik et al. systematic review (2000–2014) was conducted on EMBASE and Medline using PRISMA guidelines. The updated search was limited to primary research studies in English (30 September 2014–31 December 2017) that evaluated patient and/or economic outcomes after implementation of hospital ASPs including length of stay (LOS), antimicrobial use, and total (including operational and implementation) costs. Results One hundred forty-six studies meeting inclusion criteria were included. The majority of these studies were conducted within the last 5 years in North America (49%), Europe (25%), and Asia (14%), with few studies conducted in Africa (3%), South America (3%), and Australia (3%). Most studies were conducted in hospitals with 500–1000 beds and evaluated LOS and change in antibiotic expenditure, the majority of which showed a decrease in LOS (85%) and antibiotic expenditure (92%). The mean cost-savings varied by hospital size and region after implementation of ASPs. Average cost savings in US studies were $732 per patient (range: $2.50 to $2640), with similar trends exhibited in European studies. The key driver of cost savings was from reduction in LOS. Savings were higher among hospitals with comprehensive ASPs which included therapy review and antibiotic restrictions. Conclusions Our data indicates that hospital ASPs have significant value with beneficial clinical and economic impacts. More robust published data is required in terms of implementation, LOS, and overall costs so that decision-makers can make a stronger case for investing in ASPs, considering competing priorities. Such data on ASPs in lower- and middle-income countries is limited and requires urgent attention.
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Affiliation(s)
- Dilip Nathwani
- 1Ninewells Hospital and Medical School, Dundee, DD19SY UK
| | - Della Varghese
- 2Pharmerit International, 4350 East West Highway, Suite 1100, Bethesda, MD 20184 USA
| | - Jennifer Stephens
- 2Pharmerit International, 4350 East West Highway, Suite 1100, Bethesda, MD 20184 USA
| | | | - Stephan Martin
- 2Pharmerit International, 4350 East West Highway, Suite 1100, Bethesda, MD 20184 USA
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50
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Dubourg G, Raoult D, Fenollar F. Emerging methodologies for pathogen identification in bloodstream infections: an update. Expert Rev Mol Diagn 2019; 19:161-173. [DOI: 10.1080/14737159.2019.1568241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
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