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Tomazin R, Pliberšek T, Oštrbenk Valenčak A, Matos T. Different BD BACTEC ™ Blood Culture Bottle Types for the Detection of Fungi in Simulated Sterile Body Fluid Samples. Diagnostics (Basel) 2023; 13:diagnostics13101699. [PMID: 37238183 DOI: 10.3390/diagnostics13101699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Blood culture systems are a potential alternative to classical cultivation of fungi on mycological media, but there are limited data on the suitability of these systems for culturing other sample types (e.g., sterile body fluids). We conducted a prospective study to evaluate different types of blood culture (BC) bottles for the detection of different fungal species in non-blood samples. A total of 43 fungal isolates were tested for their ability to grow in BD BACTEC Mycosis-IC/F (Mycosis bottles), BD BACTEC Plus Aerobic/F (Aerobic bottles) and BD BACTEC Plus Anaerobic/F (Anaerobic bottles) (Becton Dickinson, East Rutherford, NJ, USA) BC bottles inoculated with spiked samples without the addition of blood or fastidious organism supplement. Time to detection (TTD) was determined for all BC types tested and compared between groups. In general, Mycosis and Aerobic bottles were similar (p > 0.05). The Anaerobic bottles failed to support growth in >86% of cases. The Mycosis bottles were superior in detecting Candida glabrata, Cryptococcus spp. and Aspergillus spp. (p < 0.05). The performance of Mycosis and Aerobic bottles was similar, but if cryptococcosis or aspergillosis is suspected, the use of Mycosis bottles is recommended. Anaerobic bottles are not recommended for fungal detection.
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Affiliation(s)
- Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
| | | | - Anja Oštrbenk Valenčak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
| | - Tadeja Matos
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
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Ahlström MG, Antsupova VS, Pedersen M, Johansen HK, Hansen DS, Knudsen IJD. A Dedicated Mycosis Flask Increases the Likelihood of Identifying Candidemia Sepsis. J Fungi (Basel) 2023; 9:jof9040441. [PMID: 37108896 PMCID: PMC10146598 DOI: 10.3390/jof9040441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/09/2023] Open
Abstract
Introduction: Candidemia is a severe condition associated with high mortality, and fungi are often not covered by empiric antimicrobial regimes for sepsis. Therefore, the shortest possible time to detection of yeast in the blood is of the essence. Materials and methods: We performed a cohort study of blood culture flasks drawn from patients aged 18 or older in the capital region of Denmark. In 2018 a blood cultures set consisted of two aerobic and two anaerobic flasks. This was changed in 2020 to two aerobic, one anaerobic, and one mycosis flask. We used time-to-event statistics to model time to positivity and compared 2018 with 2020; further, we stratified analyses on the blood culture system used (BacTAlert™ vs. BACTEC™) and high-risk vs. low-risk departments. Results: We included 175,416 blood culture sets and 107,077 unique patients. We found an absolute difference in the likelihood of identifying fungi in a blood culture set of 1.2 (95% CI: 0.72; 1.6) pr. 1.000 blood culture sets corresponding to the number needed to treat 853 (617; 1382). In high-risk departments, the absolute difference was profound, whereas it was negligible and statistically non-significant in low-risk departments 5.2 (95% CI: 3.4; 7.1) vs. 0.16 (−0.17; 0.48) pr. 1.000 blood culture sets. Conclusions: We found that including a mycosis flask in a blood culture set increases the likelihood of identifying candidemia. The effect was mainly seen in high-risk departments.
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Affiliation(s)
- Magnus G. Ahlström
- Department of Clinical Microbiology, Herlev & Gentofte Hospital, 2730 Herlev, Denmark
| | - Valeria S. Antsupova
- Department of Clinical Microbiology, Herlev & Gentofte Hospital, 2730 Herlev, Denmark
| | - Michael Pedersen
- Department of Clinical Microbiology, Amager & Hvidovre Hospital, 2650 Hvidovre, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
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Xu L, Mo YJ, Weng XB. False-negative cerebral spinal fluid cryptococcal antigen lateral flow assay due to postzone phenomenon in a patient with disseminated cryptococcal disease: a case report. J Int Med Res 2023; 51:3000605231156767. [PMID: 36883444 PMCID: PMC9998416 DOI: 10.1177/03000605231156767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
This report presents the case of false-negative cerebral spinal fluid (CSF) cryptococcal antigen (CrAg) lateral flow assay (LFA) in a HIV-positive 25-year-old male. The patient presented with headache, nausea and vomiting for 5 days and syncope for 1 day. An initial CSF CrAg LFA test was negative, but a 1:4 dilution of the CSF was weakly positive and a 1:8 dilution was positive. A serum cryptococcal antigen test was weakly positive. Cultures of blood and CSF were all positive for Cryptococcus neoformans. The explanation for the false-negative CSF CrAg LFA test is that the antigen concentration was too high causing the postzone phenomenon.
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Affiliation(s)
- Lu Xu
- Department of Laboratory Medicine, The Affiliated People's Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Yi-Jun Mo
- Department of Laboratory Medicine, Ningbo City First Hospital, Ningbo, Zhejiang Province, China
| | - Xing-Bei Weng
- Department of Laboratory Medicine, Ningbo City First Hospital, Ningbo, Zhejiang Province, China
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Laroche L, Mercier V, Sasso M. BD BACTEC™ Mycosis IC/F culture vials for fungemia diagnosis and follow-up: a retrospective study from 2013 to 2020. Diagn Microbiol Infect Dis 2023; 105:115863. [PMID: 36463694 DOI: 10.1016/j.diagmicrobio.2022.115863] [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: 06/10/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
This retrospective study compared the BD BACTEC™ Mycosis IC/F with the BD BACTEC™ Plus Aerobic/F and BD BACTEC™ Lytic Anaerobic/F culture vials (i.e., standard vials) for fungemia diagnosis at Nîmes University Hospital, France. From 2013 to 2020, 57 blood samples were concomitantly collected in the 3 culture vial types. For 43.8% of these samples, all vials were positive for yeast. The mean time to positivity was shorter (32.0 hours vs 44.2 hours; -12.2 hours) and longer (89.4 hours vs 33.7 hours; +55.7 hours) with the BD BACTEC™ Mycosis IC/F culture vials than with the other culture vials in patients without and with antifungal treatment, respectively. Moreover 31.6% and 24.6% of samples were positive only with the standard vials and with the BD BACTEC™ Mycosis IC/F culture vials, respectively. The BD BACTEC™ Mycosis IC/F culture vials are useful for the initial fungemia diagnosis (before any treatment) because they provide faster results.
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Affiliation(s)
- Laëtitia Laroche
- Laboratoire de Parasitologie-Mycologie, CHU Nîmes, Nîmes, France
| | - Victor Mercier
- Laboratoire de Parasitologie-Mycologie, CHU Nîmes, Université de Montpellier, CNRS, IRD, MiVEGEC, Montpellier, France
| | - Milène Sasso
- Laboratoire de Parasitologie-Mycologie, CHU Nîmes, Université de Montpellier, CNRS, IRD, MiVEGEC, Montpellier, France.
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A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc Natl Acad Sci U S A 2022; 119:e2209607119. [PMID: 36161889 DOI: 10.1073/pnas.2209607119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.
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Govindaraju VK, Chao JT, Duvall ER, Baker NS, Fahey KM, Lee R, Williams GA, Stec LA. Incidence of Endogenous Fungal Endophthalmitis in Screening Dilated Exams in Patients with Elevated Beta-D-Glucan Levels versus Positive Fungal Blood Cultures. Clin Ophthalmol 2022; 16:2743-2750. [PMID: 36035241 PMCID: PMC9416315 DOI: 10.2147/opth.s362888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Endogenous endophthalmitis is a severe intraocular infectious condition requiring rapid diagnosis and treatment. This study examines the incidence of fungal endophthalmitis in patients with elevated beta-D-glucan (BG) levels and those with positive blood culture and the utility of ophthalmology consultation in these patients. Methods Single center retrospective consecutive cohort study was conducted on patients at Beaumont Health from 2016–2021 who either had positive fungal blood cultures or an elevated BG level. Results A total of 147 patients were examined by the ophthalmology department where 30 patients had an elevated BG level and 100 patients had a positive fungal blood culture. Incidence of fungal endophthalmitis was 0% in the elevated BG group and 1.5% in the positive fungal culture group, corresponding to a relative risk ratio of 0.0 (p = 0.31). Conclusion BG testing may be useful in diagnosing isolated cases outside the standard screening paradigm, however the data within this study support the conclusion that there is no compelling evidence at this time to add or use BG as a surrogate for endophthalmitis screening. Further studies are required to further elucidate the role of BG in the care of critically ill patients.
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Affiliation(s)
- Viren K Govindaraju
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Jonathan T Chao
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Elizabeth R Duvall
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Nicolas S Baker
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Kelly M Fahey
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Ramon Lee
- Department of Vitreoretinal Surgery, Associated Retinal Consultants, Royal Oak, MI, USA
- Department of Vitreoretinal Surgery, Illinois Retina Associates, Rush University Medical Center, Chicago, IL, USA
| | - George A Williams
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
- Department of Vitreoretinal Surgery, Associated Retinal Consultants, Royal Oak, MI, USA
| | - Lori A Stec
- Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
- Department of Vitreoretinal Surgery, Associated Retinal Consultants, Royal Oak, MI, USA
- Correspondence: Lori A Stec, Email
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Comparison of Simulated Candidemia Detection During Prophylactic Antifungal Therapy. Diagn Microbiol Infect Dis 2022; 104:115768. [DOI: 10.1016/j.diagmicrobio.2022.115768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022]
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Ombelet S, Natale A, Ronat JB, Vandenberg O, Jacobs J, Hardy L. Considerations in evaluating equipment-free blood culture bottles: A short protocol for use in low-resource settings. PLoS One 2022; 17:e0267491. [PMID: 35468169 PMCID: PMC9037908 DOI: 10.1371/journal.pone.0267491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/07/2022] [Indexed: 12/21/2022] Open
Abstract
Use of equipment-free, “manual” blood cultures is still widespread in low-resource settings, as requirements for implementation of automated systems are often not met. Quality of manual blood culture bottles currently on the market, however, is usually unknown. An acceptable quality in terms of yield and speed of growth can be ensured by evaluating the bottles using simulated blood cultures. In these experiments, bottles from different systems are inoculated in parallel with blood and a known quantity of bacteria. Based on literature review and personal experiences, we propose a short and practical protocol for an efficient evaluation of manual blood culture bottles, aimed at research or reference laboratories in low-resource settings. Recommendations include: (1) practical equivalence of horse blood and human blood; (2) a diverse selection of 10 to 20 micro-organisms to be tested (both slow- and fast-growing reference organisms); (3) evaluation of both adult and pediatric bottle formulations and blood volumes; (4) a minimum sample size of 120 bottles per bottle type; (5) a formal assessment of usability. Different testing scenarios for increasing levels of reliability are provided, along with practical tools such as worksheets and surveys that can be used by laboratories wishing to evaluate manual blood culture bottles.
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Affiliation(s)
- Sien Ombelet
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Immunology & Microbiology Department, KU Leuven, Leuven, Belgium
| | | | - Jean-Baptiste Ronat
- Médecins Sans Frontières, Paris, France
- Team ReSIST, INSERM U1184, School of Medicine University Paris-Saclay, Paris, France
- Bacteriology-Hygiene Unit, Assistance Publique – Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Olivier Vandenberg
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), ULB, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Immunology & Microbiology Department, KU Leuven, Leuven, Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
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Farfour E, Le Brun C, Mizrahi A, Bargain P, Durieux MF, Boquel F, Corvec S, Jeddi F, Muggeo A, Huguenin A, Barraud O, Amara M, Fihman V, Bailly E, Botterel F, Guillard T, Vasse M. Contribution of the anaerobic blood culture vial for the recovery of Candida glabrata: a retrospective multicentric study. Med Mycol 2022; 60:6566345. [DOI: 10.1093/mmy/myac021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/01/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Although Candida spp are aerobic microorganisms, some Candida strains, mainly Candida glabrata, can be recovered from anaerobic blood culture vials. We assessed the contribution of the anaerobic vials for the diagnosis of candidemia, especially for C. glabrata. We conducted a multicenter retrospective study including eight University or regional hospitals. A single episode of monomicrobial candidemia per patient was included from September 1st, 2016, to August 31st, 2019. The characteristics of all aerobic and anaerobic blood culture vials sampled within 2 hours before and after the first positive blood culture vials were recorded (type of vials, result, and for positive vials time-to-positivity and Candida species). Overall, 509 episodes of candidemia were included. The main species were C. albicans (55.6%) followed by C. glabrata (17.1%), C. parapsilosis (4.9%), and C. tropicalis (4.5%). An anaerobic vial was positive in 76 (14.9%) of all episodes of which 56 (73.8%) were due to C. glabrata. The number of C. glabrata infections only positive in anaerobic vials was 1 (2.6%), 1 (11.1%), and 15 (37.5%) with the BACT/ALERT 3D the BACT/ALERT VIRTUO and the BACTEC FX instrument respectively (P < 0.01). The initial positivity of an anaerobic vial was highly predictive of the isolation of C. glabrata with the BACTEC FX (sensitivity of 96.8%). C. glabrata time-to-positivity was shorter in anaerobic vial than aerobic vial with all instruments. Anaerobic blood culture vials improve the recovery of Candida spp mainly C. glabrata. This study could be completed by further analyzes including mycological and pediatric vials.
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Affiliation(s)
- Eric Farfour
- Service de biologie clinique, Hôpital Foch, Suresnes, France
| | | | - Assaf Mizrahi
- Service de biologie, GH Paris Saint-Joseph, Paris, France
| | - Pauline Bargain
- Service de biologie, Hôpital A. Mignot, Le Chesnay-Rocquencourt, France
| | | | - Frédérique Boquel
- Unité de parasitologie-mycologie, Département de Prévention, diagnostic et traitement des infections. CHU Henri Mondor, APHP, Créteil, France
| | - Stéphane Corvec
- Service de Bactériologie et des contrôles microbiologiques des produits de santé, CHU de Nantes, Nantes, France
| | - Fakhri Jeddi
- Laboratoire de Parasitologie et Mycologie Médicale, CHU de Nantes, France
| | - Anaëlle Muggeo
- Université de Reims-Champagne-Ardenne, SFR CAP-Santé, Inserm UMR-S 1250 P3Cell, 51097, Reims, France; CHU Reims, Hôpital Robert Debré, France
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, 51100, Reims, France
| | - Antoine Huguenin
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, 51100, Reims, France
- EA 7510, ESCAPE, Laboratoire de Parasitologie-Mycologie, Université de Reims Champagne-Ardenne, 51 rue Cognacq Jay, 51092 Reims CEDEX, France
| | - Olivier Barraud
- Service de bactériologie- virologie-hygiène, CHU Limoges, Limoges, France
| | - Marlène Amara
- Service de biologie, Hôpital A. Mignot, Le Chesnay-Rocquencourt, France
| | - Vincent Fihman
- Bacteriology and Infection control Unit, Department of Prevention, Diagnosis, and Treatment of Infections, Henri-Mondor University Hospital, AP-HP, 94000 Créteil, France
- EA 7380 Dynamyc, EnvA, UPEC, Paris-Est University, Créteil, France
| | - Eric Bailly
- Service de Parasitologie-mycologie, CHU Bretonneau, Tours, France
| | - Françoise Botterel
- Unité de parasitologie-mycologie, Département de Prévention, diagnostic et traitement des infections. CHU Henri Mondor, APHP, Créteil, France
| | - Thomas Guillard
- Université de Reims-Champagne-Ardenne, SFR CAP-Santé, Inserm UMR-S 1250 P3Cell, 51097, Reims, France; CHU Reims, Hôpital Robert Debré, France
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, 51100, Reims, France
| | - Marc Vasse
- Service de biologie clinique, Hôpital Foch, Suresnes, France
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Technical challenges for complete implementation of automated growth-based methods for microbiological examination of advanced therapy medicinal products. What's wrong with Candida albicans? Cytotherapy 2022; 24:320-333. [DOI: 10.1016/j.jcyt.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]
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Tan SJ, Gardam DJ, Radinger A, Le T, Nure M, Boan P. Fungal yield from sterile specimens. Med Mycol 2021; 60:6412528. [PMID: 34718695 DOI: 10.1093/mmy/myab066] [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: 07/15/2021] [Revised: 09/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Clinicians may not request fungal culture when it is indicated. For sterile specimens without a specific request for fungal culture, in addition to bacteriology media, we routinely incubated a Sabouraud dextrose agar (SAB) plate for 4 weeks. From 44635 sterile specimens from years 2011 to 2016, 2722 (6.1%) had fungal request. Fungi were identified from 1037 (2.3%) specimens, 292 (0.6%) from specimens with specific fungal request, 574 (1.3%) from bacteriology media, and 171 (0.4%) solely from SAB plate (of 171, 77 were deemed clinically significant and 55 were treated). Relying on request for fungal studies from sterile specimens underdiagnosed fungal infection. Routine fungal culture had a modest incremental yield at a moderately high cost. LAY SUMMARY Routine fungal culture of sterile specimens had a modest incremental yield to routine bacteriology culture and specific fungal request at a moderately high financial cost.
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Affiliation(s)
- Shu Jin Tan
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia
| | - Dianne J Gardam
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia
| | - Arron Radinger
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia
| | - Tam Le
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia
| | - Mariyam Nure
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia
| | - Peter Boan
- Department of Microbiology, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Perth, Australia.,Department of Infectious Diseases, Fiona Stanley Fremantle Hospital Group, Perth, Australia
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Wu J, Huang M. Application of mNGS to describe the clinical and microbial characteristics of severe burn a tanker explosion at a tertiary medical center: a retrospective study patients following. BMC Infect Dis 2021; 21:1086. [PMID: 34674664 PMCID: PMC8529367 DOI: 10.1186/s12879-021-06790-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/11/2021] [Indexed: 12/04/2022] Open
Abstract
Background Multiple organ dysfunction syndrome secondary to infection is the leading cause of death in burn patients. Bloodstream infection (BSI) and the prognosis of burn patients are negatively correlated. Metagenomic next-generation sequencing (mNGS) can detect many potential pathogens and may be more valuable for patients with severe burns. Methods We retrospectively explored the utility of mNGS in describing the clinical and microbial characteristics of severely burned patients with BSI. We compared mNGS with blood culture. Results Fourteen patients (127 blood samples) developed 71 episodes of BSIs with 102 unique causative pathogens. The median total body surface area was 93%. The overall 90-day mortality was 43%. In total, 17 (23.9%) episodes were polymicrobial, and 61 (86.1%) episodes originated from the wound. In total, 62/71 cases (87%) showed positive findings by mNGS, while 42/71 cases (59%) showed positive findings using blood culture. We found that mNGS outperformed culture, especially in terms of fungi (27% vs. 6%, p < 0.0001). Conclusions The incidence of BSI and polymicrobial in patients with large-area severe burns is high. mNGS has potential value in the diagnosis of fungal infections and coinfections in such patients. In addition, mNGS may provide unique guidance for antibiotic therapy in complicated BSI.
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Affiliation(s)
- Jing Wu
- Department of Intensive Care Unit, Second Affiliated Hospital, School of Medicine, Zhejiang University, No 1511, Jianghong Rd, Hangzhou, 310009, China
| | - Man Huang
- Department of Intensive Care Unit, Second Affiliated Hospital, School of Medicine, Zhejiang University, No 1511, Jianghong Rd, Hangzhou, 310009, China.
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Fu Y, Xu M, Zhou H, Yao Y, Zhou J, Pan Z. Microbiological and clinical characteristics of cryptococcemia: a retrospective analysis of 85 cases in a Chinese hospital. Med Mycol 2021; 58:478-484. [PMID: 31504739 DOI: 10.1093/mmy/myz089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/26/2019] [Accepted: 08/08/2019] [Indexed: 12/23/2022] Open
Abstract
Cryptococcemia is a life-threatening fungal infection. Sometimes, it is hard to diagnose. The studies to describe the characteristics of cryptococcemia specifically were limited. We performed this retrospective analysis in a Chinese hospital during 2002-2015, including 85 cryptococcemia cases and 52 Cryptococcus spp. isolates. The species, mating type, antifungal susceptibility and multilocus sequence typing of Cryptococcus spp. were determined. C. neoformans var. grubii MATα of sequence type (ST) 5 is the representative strain of cryptococcemia, accounting for 51 isolates. The MIC50/90 values were 0.5/0.5, 1.0/1.0, 2.0/4.0, ≤0.06/0.25, and ≤0.06/≤0.06 μg/ml for amphotericin B, flucytosine, fluconazole, itraconazole, and voriconazole, respectively. Cryptococcemia was the first diagnostic proof of cryptococcosis in 37 patients (43.5%, 37/85). Compared with the patients initially diagnosed of cryptococcosis in other sites (mainly cerebrospinal fluid), the patients firstly diagnosed by blood culture had prolonged time from admission to diagnosis of cryptococcosis (9 days vs. 2 days, P < .001) and higher 30-day mortality (54.1% vs. 20.8%, P = .003), while fewer symptoms of meningitis (45.9% vs. 100%, P < .001). For the patients receiving lumbar puncture, the occurrence of meningitis was similar between the patients firstly diagnosed by blood culture and those firstly diagnosed in other sites (94.1% vs. 100%, P = .26). However, the patients first diagnosed by blood culture had lower baseline intracranial pressure (250 mm H2O vs. 342.5 mm H2O, P = .001). In conclusion, patients with cryptococcemia as the first diagnostic proof of cryptococcosis usually had neglected subtle symptoms of meningitis, which may result in delayed diagnosis and catastrophic outcome.
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Affiliation(s)
- Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Min Xu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yake Yao
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhijie Pan
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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14
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Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering. Nat Commun 2020; 11:4774. [PMID: 32963224 PMCID: PMC7508858 DOI: 10.1038/s41467-020-18574-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023] Open
Abstract
Detection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL−1 (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT’s clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood. Culture-based diagnostic methods for microorganism detection are time-consuming but still the gold standard for conditions such as sepsis. Here the authors present an amplification and purification-free method to detect microorganisms in bodily fluids with high sensitivity: Single MOLecule Tethering (SMOLT).
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15
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Xu Y, Xia W, Ni F. False-Negative Serum Cryptococcal Antigen Lateral Flow Immunoassay Result for a Patient with Disseminated Cryptococcal Disease. Infect Drug Resist 2020; 13:2877-2881. [PMID: 32903771 PMCID: PMC7445500 DOI: 10.2147/idr.s265784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/28/2020] [Indexed: 11/23/2022] Open
Abstract
Cryptococcus neoformans (C. neoformans) is an opportunistic fungal pathogen to humans, which can be acquired from environmental sources. Its most important virulence factor is its polysaccharide capsule, which can be used for diagnostic tests that identify the cryptococcal antigen (CrAg). The CrAg lateral flow assay (LFA) is a dipstick immunochromatographic assay with high sensitivity and specificity; however, several false-negative cases have been reported. Here, we present a case of a false-negative serum CrAg LFA, in which the blood culture from a matched sample was positive for C. neoformans, thus demonstrating the postzone phenomenon.
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Affiliation(s)
- Yuqiao Xu
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Wenying Xia
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Fang Ni
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
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16
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Carlesse F, Daudt LE, Seber A, Dutra ÁP, Melo ASDA, Simões B, Macedo CRD, Bonfim C, Benites E, Gregianin L, Batista MV, Abramczyk M, Tostes V, Lederman HM, Lee MLDM, Loggetto S, Galvão de Castro Junior C, Colombo AL. A consensus document for the clinical management of invasive fungal diseases in pediatric patients with hematologic cancer and/or undergoing hematopoietic stem cell transplantation in Brazilian medical centers. Braz J Infect Dis 2019; 23:395-409. [PMID: 31738887 PMCID: PMC9428207 DOI: 10.1016/j.bjid.2019.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 09/10/2019] [Accepted: 09/28/2019] [Indexed: 01/05/2023] Open
Abstract
In the present paper we summarize the suggestions of a multidisciplinary group including experts in pediatric oncology and infectious diseases who reviewed the medical literature to elaborate a consensus document (CD) for the diagnosis and clinical management of invasive fungal diseases (IFDs) in children with hematologic cancer and those who underwent hematopoietic stem-cell transplantation. All major multicenter studies designed to characterize the epidemiology of IFDs in children with cancer, as well as all randomized clinical trials addressing empirical and targeted antifungal therapy were reviewed. In the absence of randomized clinical trials, the best evidence available to support the recommendations were selected. Algorithms for early diagnosis and best clinical management of IFDs are also presented. This document summarizes practical recommendations that will certainly help pediatricians to best treat their patients suffering of invasive fungal diseases.
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Affiliation(s)
- Fabianne Carlesse
- Instituto de Oncologia Pediátrica, UNIFESP, São Paulo, SP, Brazil; Universidade Federal de São Paulo, Escola Paulista de Medicina (EPM), UNIFESP, São Paulo, SP, Brazil.
| | - Liane Esteves Daudt
- Universidade do Rio Grande do Sul, Hospital das Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.
| | - Adriana Seber
- Hospital Samaritano de São Paulo, São Paulo, SP, Brazil; ABHH, Brazil.
| | | | | | - Belinda Simões
- Hospital das Clínicas de Ribeirão Preto-USP, São Paulo, SP, Brazil.
| | | | - Carmem Bonfim
- Hospital das Clínicas de Curitiba, Paraná, PR, Brazil.
| | | | - Lauro Gregianin
- Hospital das Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.
| | - Marjorie Vieira Batista
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, São Paulo, SP, Brazil.
| | - Marcelo Abramczyk
- Hospital Infantil Darcy Vargas, Morumbi, SP, Brazil; Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Pediatria, São Paulo, SP, Brazil.
| | - Vivian Tostes
- Pro-Imagem medicina diagnóstica Ribeirão Preto, SP, Brazil.
| | | | - Maria Lúcia de Martino Lee
- Hospital Santa Marcelina TUCA, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
| | | | | | - Arnaldo Lopes Colombo
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Disciplina de Infectologia, Brazil.
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17
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Wilson ML. Critical factors in the recovery of pathogenic microorganisms in blood. Clin Microbiol Infect 2019; 26:174-179. [PMID: 31377231 DOI: 10.1016/j.cmi.2019.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/15/2019] [Accepted: 07/20/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND The critical factors for optimal recovery of microbial pathogens from blood are not only the basis for how we perform blood cultures on a daily basis, but are also important for development of all current blood-culture systems. Because much of this research was conducted and published between 1975 and 2010 there is a general sense that many physicians and scientists may not be familiar with it, but it is critical for performing and interpreting blood cultures. OBJECTIVES To review the critical factors in the laboratory recovery and isolation of pathogenic microorganisms in blood. SOURCES Literature review of published papers, select reviews and updated guidelines. CONTENT This review focuses on the critical factors that affect the recovery isolation of pathogenic microorganisms from individuals with bloodstream infections. Contemporary blood-culture systems, and current methods for blood-culture collection, have been designed to incorporate these critical factors so as to optimize recovery and isolation of pathogens while minimizing contamination. IMPLICATIONS It is important for microbiologists and practitioners to understand how and why these critical factors affect current blood-culture practices to improve patient management. Future research should emphasize which of these critical factors will still play a role in the era of molecular diagnostic tests, which will no longer be relevant, and which new critical factors have yet to be defined.
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Affiliation(s)
- M L Wilson
- Department of Pathology & Laboratory Services, Denver Health, Denver, CO, USA; Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA.
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18
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Honarvar B, Bagheri Lankarani K, Taghavi M, Vahedi G, Mortaz E. Biomarker-guided antifungal stewardship policies for patients with invasive candidiasis. Curr Med Mycol 2018; 4:37-44. [PMID: 30815616 PMCID: PMC6386506 DOI: 10.18502/cmm.4.4.385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/10/2018] [Accepted: 01/02/2018] [Indexed: 02/05/2023] Open
Abstract
Invasive fungal infections (IFIs) are among the life-threatening issues in patients with impaired immune system. High administration of antifungals in these patients imposes a heavy economic burden on the national health system. In addition, despite the usually expensive antifungal regimens, the mortality rate due to fungal infections is still high, resulting in the loss of hundreds of lives per year. Survival rate is an indicator of the success of national healthcare policies. Early diagnosis of IFI is critical because any delays may be fatal. The weakness of the old-fashioned culture-based diagnostic methods lies in their time-consuming laboratory procedures. To overcome this problem, several diagnostic approaches have been developed to facilitate the early diagnosis of invasive candidiasis as the most prevalent IFI. These methods are based on the detection of serologic and molecular footprints. However, nowadays, antibiotic resistance and proper and cost-effective use of antibiotics are given special attention in national healthcare policies. The instructions for controlling these indices have been collected under the name of antibiotic stewardship. The present review study was targeted toward providing insight into novel diagnostic biomarkers and antifungal stewardship programs. The simultaneous investigation of these two issues facilitates the achievement of a novel health policy for the treatment of systemic candidiasis in immunocompromised patients.
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Affiliation(s)
- Behnam Honarvar
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Bagheri Lankarani
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Taghavi
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ghasem Vahedi
- Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Esmaeil Mortaz
- Department of Immunology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Utrecht, the Netherlands
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19
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García J, Pemán J. [Microbiological diagnosis of invasive mycosis]. Rev Iberoam Micol 2018; 35:179-185. [PMID: 30471895 DOI: 10.1016/j.riam.2018.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/11/2018] [Accepted: 05/08/2018] [Indexed: 11/17/2022] Open
Abstract
The prognosis of invasive fungal infections (IFI) depends on the speed of diagnosis and treatment. Conventional diagnostic methods are of low sensitivity, laborious and too slow, leading to the need for new, faster, and more efficient diagnostic strategies. There are several techniques for diagnosing a candidemia that are faster than the conventional blood culture (BC). Once yeast growth in BC is detected, species identification can be speeded up by mass spectrometry (30minutes), commercialised molecular techniques (60-80minutes) or fluorescent in situ hybridization (90minutes). The combined detection of biomarkers (antimicellium, mannan and anti-mannan or β-glucan) has shown to be of greater use than their individual use. Commercialised nucleic acid amplification techniques (Septifast®, T2Candida®) are very reliable alternatives to BC. The detection of the capsular antigen of Cryptococcus, by means of latex agglutination or immuno-chromatography, is a valuable technique for cryptococcosis diagnosis. Direct microscopic examination and culture of representative specimens is used for the conventional diagnosis of IFI by filamentous fungi. Detection of galactomannan and β-glucan are considered diagnostic criteria for probable invasive aspergillosis and probable IFI, respectively, despite the lack of specificity of the latter. The detection of fungal volatile organic compounds in breath is an interesting diagnostic strategy in pulmonary infections. Although widely used, nucleic acid detection techniques are not considered diagnostic criteria for IFIs caused by moulds in consensus documents, due to their lack of standardisation. However, they are the only alternative to culture methods in invasive infections by Scedosporium/Lomentospora, Fusarium, zygomycetes, or dematiaceous fungi.
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Affiliation(s)
- Julio García
- Servicio de Microbiología, Hospital Universitario La Paz, Madrid, España
| | - Javier Pemán
- Servicio de Microbiología, Hospital Universitari i Politècnic La Fe, Valencia, España.
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20
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Evidence-based consensus on opportunistic infections in inflammatory bowel disease (republication). Intest Res 2018; 16:178-193. [PMID: 29743831 PMCID: PMC5934591 DOI: 10.5217/ir.2018.16.2.178] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/08/2018] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) patients are a high-risk population for opportunistic infections. The IBD group of the Chinese Society of Gastroenterology of the Chinese Medical Association organized an expert group to discuss and develop this consensus opinion. This consensus opinion referenced clinical study results from China and other countries to provide guidance for clinical practices. Eight major topics, including cytomegalovirus infection, Epstein-Barr virus infection, viral hepatitis, bacterial infection, Mycobacterium tuberculosis infection, fungal infection, parasitic infection, and vaccines were introduced in this article.
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21
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Sinha M, Jupe J, Mack H, Coleman TP, Lawrence SM, Fraley SI. Emerging Technologies for Molecular Diagnosis of Sepsis. Clin Microbiol Rev 2018; 31:e00089-17. [PMID: 29490932 PMCID: PMC5967692 DOI: 10.1128/cmr.00089-17] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rapid and accurate profiling of infection-causing pathogens remains a significant challenge in modern health care. Despite advances in molecular diagnostic techniques, blood culture analysis remains the gold standard for diagnosing sepsis. However, this method is too slow and cumbersome to significantly influence the initial management of patients. The swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h. The administration of appropriate, narrow-spectrum antibiotics demands that such a test be extremely sensitive with a high negative predictive value. In addition, it should utilize small sample volumes and detect polymicrobial infections and contaminants. All of this must be accomplished with a platform that is easily integrated into the clinical workflow. In this review, we outline the limitations of routine blood culture testing and discuss how emerging sepsis technologies are converging on the characteristics of the ideal sepsis diagnostic test. We include seven molecular technologies that have been validated on clinical blood specimens or mock samples using human blood. In addition, we discuss advances in machine learning technologies that use electronic medical record data to provide contextual evaluation support for clinical decision-making.
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Affiliation(s)
- Mridu Sinha
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, Saint Louis, Missouri, USA
| | - Hannah Mack
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
| | - Todd P Coleman
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Shelley M Lawrence
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of California, San Diego, San Diego, California, USA
- Rady Children's Hospital of San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
| | - Stephanie I Fraley
- Bioengineering Department, University of California, San Diego, San Diego, California, USA
- Clinical Translational Research Institute, University of California, San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, San Diego, California, USA
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22
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Evidence-based consensus on opportunistic infections in inflammatory bowel disease. J Dig Dis 2018; 19:54-65. [PMID: 29330905 DOI: 10.1111/1751-2980.12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 01/30/2023]
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23
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Saraiva JP, Oswald M, Biering A, Röll D, Assmann C, Klassert T, Blaess M, Czakai K, Claus R, Löffler J, Slevogt H, König R. Fungal biomarker discovery by integration of classifiers. BMC Genomics 2017; 18:601. [PMID: 28797245 PMCID: PMC5553868 DOI: 10.1186/s12864-017-4006-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 08/02/2017] [Indexed: 02/01/2023] Open
Abstract
Background The human immune system is responsible for protecting the host from infection. However, in immunocompromised individuals the risk of infection increases substantially with possible drastic consequences. In extreme, systemic infection can lead to sepsis which is responsible for innumerous deaths worldwide. Amongst its causes are infections by bacteria and fungi. To increase survival, it is mandatory to identify the type of infection rapidly. Discriminating between fungal and bacterial pathogens is key to determine if antifungals or antibiotics should be administered, respectively. For this, in situ experiments have been performed to determine regulation mechanisms of the human immune system to identify biomarkers. However, these studies led to heterogeneous results either due different laboratory settings, pathogen strains, cell types and tissues, as well as the time of sample extraction, to name a few. Methods To generate a gene signature capable of discriminating between fungal and bacterial infected samples, we employed Mixed Integer Linear Programming (MILP) based classifiers on several datasets comprised of the above mentioned pathogens. Results When combining the classifiers by a joint optimization we could increase the consistency of the biomarker gene list independently of the experimental setup. An increase in pairwise overlap (the number of genes that overlap in each cross-validation) of 43% was obtained by this approach when compared to that of single classifiers. The refined gene list was composed of 19 genes and ranked according to consistency in expression (up- or down-regulated) and most of them were linked either directly or indirectly to the ERK-MAPK signalling pathway, which has been shown to play a key role in the immune response to infection. Testing of the identified 12 genes on an unseen dataset yielded an average accuracy of 83%. Conclusions In conclusion, our method allowed the combination of independent classifiers and increased consistency and reliability of the generated gene signatures. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4006-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Pedro Saraiva
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Marcus Oswald
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Antje Biering
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Daniela Röll
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Cora Assmann
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Tilman Klassert
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Markus Blaess
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | | | - Ralf Claus
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | | | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Rainer König
- Network Modelling, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, Germany. .,Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
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24
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Gokbolat E, Oz Y, Metintas S. Evaluation of three different bottles in BACTEC 9240 automated blood culture system and direct identification of Candida species to shorten the turnaround time of blood culture. J Med Microbiol 2017; 66:470-476. [DOI: 10.1099/jmm.0.000434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Egemen Gokbolat
- Department of Microbiology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
- Present address: Department of Microbiology, Burdur State Hospital, Burdur, Turkey
| | - Yasemin Oz
- Department of Microbiology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Selma Metintas
- Department of Public Health, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
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25
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Rapid Detection and Identification of Candidemia by Direct Blood Culturing on Solid Medium by Use of Lysis-Centrifugation Method Combined with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). J Clin Microbiol 2016; 55:97-100. [PMID: 27795344 DOI: 10.1128/jcm.01787-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/09/2016] [Indexed: 11/20/2022] Open
Abstract
Candida sepsis is a life-threatening condition with increasing prevalence. In this study, direct blood culturing on solid medium using a lysis-centrifugation procedure enabled successful Candida species identification by matrix-assisted laser desorption-ionization time of flight mass spectrometry on average 3.8 h (Sabouraud agar) or 7.4 h (chocolate agar) before the positivity signal for control samples in Bactec mycosis-IC/F or Bactec Plus aerobic/F bottles, respectively. Direct culturing on solid medium accelerated candidemia diagnostics compared to that with automated broth-based systems.
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26
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Datcu R, Boel J, Jensen IM, Arpi M. Comparison of BACTEC™ blood culture media for the detection of fungemia. Eur J Clin Microbiol Infect Dis 2016; 36:131-137. [PMID: 27677278 DOI: 10.1007/s10096-016-2781-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/05/2016] [Indexed: 02/05/2023]
Abstract
The aim of the present study was to investigate whether addition of the BACTEC™ Mycosis bottle to the standard BACTEC™ aerobic and anaerobic bottles contributed to a higher detection rate and a faster time to detection (TTD) of fungi. This was a retrospective cohort study of all patients with a positive blood culture with Candida species delivered to the Department of Clinical Microbiology, Herlev and Gentofte Hospital, Denmark in the 8-year period 2006 through 2014. The patients had at least one BACTEC™ aerobic and one Mycosis bottle sampled at the same time and at least one of the bottles yielded growth of fungi. Among 184 patients included, 173 were examined using BACTEC™ aerobic, anaerobic and Mycosis bottles. The anaerobic vial generally had the lowest detection rate and the longest TTD. The detection rate of BACTEC™ aerobic plus anaerobic with the BACTEC™ Mycosis bottle was significantly higher than the detection rate of BACTEC™ aerobic plus anaerobic without BACTEC™ Mycosis bottle for all species after 1-5 days, and specially for Candida glabrata at 2, 3, 4 and 5 days. TTD for C. glabrata was significantly shorter for BACTEC™ Mycosis than TTD for BACTEC™ aerobic or anaerobic bottles after ½ to 4 days. When combining "first or only" detection, the BACTEC™ Mycosis bottle had a significantly higher detection as compared to the aerobic bottle. Addition of the BACTEC™ Mycosis bottle to the standard BACTEC™ aerobic and anaerobic bottles significantly contributed to a higher detection rate and a faster TTD of fungemia.
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Affiliation(s)
- R Datcu
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark.
| | - J Boel
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - I M Jensen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
| | - M Arpi
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Herlev, Denmark
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27
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Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections. J Clin Microbiol 2016; 54:1295-303. [PMID: 26935732 DOI: 10.1128/jcm.00118-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.
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28
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Cost-Effectiveness Analysis of Multiplex PCR with Magnetic Resonance Detection versus Empiric or Blood Culture-Directed Therapy for Management of Suspected Candidemia. J Clin Microbiol 2016; 54:718-26. [PMID: 26739159 DOI: 10.1128/jcm.02971-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/04/2016] [Indexed: 02/03/2023] Open
Abstract
Candida bloodstream infections (BSI) are associated with significant morbidity, mortality, and increased health care costs. Early treatment is essential, because delayed therapy detrimentally impacts clinical outcomes. The FDA recently approved the first culture-independent direct molecular detection method for Candida BSIs (T2Candida). The speed and sensitivity of this assay give it the potential to improve patient care, but the reagents and instrumentation are expensive. We used an analytic decision tree model to compare the cost-effectiveness of T2Candida-directed antifungal therapy (T2DT) to that of either empirical therapy (ET) or blood culture-directed therapy (BCDT). The costs included those of T2Candida testing, antifungal treatment, and hospital length of stay. The effectiveness measure was survival status at hospital discharge. T2DT was less costly and more effective than BCDT but was less costly and less effective than ET with an echinocandin (incremental cost-effectiveness ratio, $111,084 per additional survivor). One-way sensitivity analyses demonstrated that the cost-effectiveness of T2DT was highly dependent on Candida BSI prevalence and the cost of antifungal therapy and T2Candida test reagents. The use of T2DT reduced the number of unnecessarily treated patients by 98% relative to that with ET. Reduced drug exposure might lessen the possibility of drug-related adverse events and may also prevent the development of antifungal resistance or emergence of drug-resistant Candida species. The greatest benefit of T2Candida appears to be the ability to confidently withhold or stop empirical antifungal therapy in low-to-moderate-risk patients who are unlikely to benefit from treatment.
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