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Ibrahim A, Bouvier M, Sadek M, Decousser JW, Poirel L, Nordmann P. A Selective Culture Medium for Screening Cefiderocol Resistance in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii. J Clin Microbiol 2023; 61:e0188322. [PMID: 37338403 PMCID: PMC10358180 DOI: 10.1128/jcm.01883-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/29/2023] [Indexed: 06/21/2023] Open
Abstract
Cefiderocol (FDC) is a siderophore cephalosporin with a broad spectrum of activity against many multidrug-resistant Gram-negative bacteria. Acquired resistance to FDC has been already reported among Gram-negative isolates, thus highlighting the need for rapid and accurate identification of such resistant pathogens, in order to control their spread. Therefore, the SuperFDC medium was developed to screen FDC-resistant Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii. After testing several culture conditions, a selective medium was set up by supplementing an iron-depleted agar medium with 8 μg/mL of FDC and evaluated with a collection of 68 FDC-susceptible and 33 FDC-resistant Gram-negative isolates exhibiting a variety of β-lactam resistance mechanisms. The sensitivity and specificity of detection of this medium were evaluated at 97% and 100%, respectively. In comparison with the reference broth microdilution method, only 3% very major errors were found. In addition, excellent detection performances were obtained by testing spiked stools with a lower limit of detection ranging between 100 and 103 CFU/mL. The SuperFDC medium allows detection of FDC-resistant Gram-negative isolates regardless of their corresponding resistance mechanisms.
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Affiliation(s)
- Ahmad Ibrahim
- Clinical Microbiology Unit, Pasteur Institute of Lille, Lille, France
- European Institute for Emerging Antibiotic Resistance, Pasteur Institute, Lille, France
- European Institute for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Maxime Bouvier
- Medical and Molecular Microbiology, University of Fribourg, Fribourg, Switzerland
| | - Mustafa Sadek
- Medical and Molecular Microbiology, University of Fribourg, Fribourg, Switzerland
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Jean-Winoc Decousser
- Equipe Opérationnelle d’Hygiène, Département Prévention, Diagnostic, Traitement des Infections, Hôpitaux Universitaires Henri-Mondor AP-HP, Créteil, France
- DYNAMYC, University Paris Est Creteil, Créteil, France
- DYNAMYC, EnvA, Maisons-Alfort, France
| | - Laurent Poirel
- European Institute for Emerging Antibiotic Resistance, Pasteur Institute, Lille, France
- Medical and Molecular Microbiology, University of Fribourg, Fribourg, Switzerland
- European Institute for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- European Institute for Emerging Antibiotic Resistance, Pasteur Institute, Lille, France
- Medical and Molecular Microbiology, University of Fribourg, Fribourg, Switzerland
- European Institute for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
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Thatchanamoorthy N, Rukumani Devi V, Chandramathi S, Tay ST. Candida auris: A Mini Review on Epidemiology in Healthcare Facilities in Asia. J Fungi (Basel) 2022; 8:1126. [PMID: 36354893 PMCID: PMC9696804 DOI: 10.3390/jof8111126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 07/28/2023] Open
Abstract
Candida auris, a newly emerging healthcare-associated yeast pathogen from the Metschnikowiaceae family, was first described in the ear canal of an elderly Japanese patient in 2009. The yeast is one of the causative agents of candidemia, which has been linked with nosocomial outbreaks and high mortality rates in healthcare facilities worldwide. Since its first isolation, the occurrence of C. auris in six continents has becomes a grave concern for the healthcare professionals and scientific community. Recent reports showed the identification of five geographically distinct clades and high rates of antifungal resistance associated with C. auris. Till date, there are no effective treatment options, and standardized measures for prevention and control of C. auris infection in healthcare facilities. This leads to frequent therapeutic failures and complicates the eradication of C. auris infection in healthcare facilities. Thus, this review focuses on the recent understanding of the epidemiology, risk factors, diagnosis, transmission and prevention and control strategies of C. auris infection in healthcare facilities in Asia.
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Affiliation(s)
- Nishanthinie Thatchanamoorthy
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur 50603, Wilayah Persekutuan, Malaysia
| | - Velayuthan Rukumani Devi
- Department of Medical Microbiology, University Malaya Medical Centre, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur 59100, Wilayah Persekutuan, Malaysia
| | - Samudi Chandramathi
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur 50603, Wilayah Persekutuan, Malaysia
| | - Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Jalan Profesor Diraja Ungku Aziz, Kuala Lumpur 50603, Wilayah Persekutuan, Malaysia
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What Is Candida Doing in My Food? A Review and Safety Alert on Its Use as Starter Cultures in Fermented Foods. Microorganisms 2022; 10:microorganisms10091855. [PMID: 36144457 PMCID: PMC9502980 DOI: 10.3390/microorganisms10091855] [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: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, Saccharomyces cerevisiae has been the most common and widely used microorganism in the food industry. However, Candida species have also been used as an adjuvant in cheese production or as starters for coffee, cocoa, vegetable, meat, beer, and wine fermentations. A thorough screening of candidate Candida is sometimes performed to obtain the best performing strains to enhance specific features. Some commonly selected species include C. pulcherrima (teleomorph Metschnikowia pulcherrima) (wine), C. parapsilosis (teleomorph Monilia parapsilosis) (coffee), C. famata (teleomorph Debaryomyces hansenii) (cheese), and C. zeylanoides (teleomorph Kurtzmaniella zeylanoides) and C. norvegensis (teleomorph Pichia norvegensis) (cocoa). These species are associated with the production of key metabolites (food aroma formation) and different enzymes. However, safety-associated selection criteria are often neglected. It is widely known that some Candida species are opportunistic human pathogens, with important clinical relevance. Here, the physiology and metabolism of Candida species are addressed, initially emphasizing their clinical aspects and potential pathogenicity. Then, Candida species used in food fermentations and their functional roles are reported. We recommended that Candida not be used as food cultures if safety assessments are not performed. Some safety features are highlighted to help researchers choose methods and selection criteria.
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Zerrouki H, Ibrahim A, Rebiahi SA, Elhabiri Y, Benhaddouche DE, de Groot T, Meis JF, Rolain JM, Bittar F. Emergence of Candida auris in intensive care units in Algeria. Mycoses 2022; 65:753-759. [PMID: 35546294 PMCID: PMC9328195 DOI: 10.1111/myc.13470] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
Background Currently, Candida auris is among the most serious emerging pathogens that can be associated with nosocomial infections and outbreaks in intensive care units. Clinicians must be able to identify and manage it quickly. Objective Here, we report for the first time in Algeria seven cases of C. auris infection or colonisation. Methods and Results The strains were isolated from clinical sites including bronchial aspirates (n = 4), wound swabs (n = 1), urine sample (n = 1) and peritoneal fluid (n = 1), in patients admitted to the intensive care unit. Candida auris was identified both by MALDI‐TOF and by sequencing the ITS region and the D1/D2 domain. Antifungal susceptibility testing was performed using the E‐test method. Non‐wildtype susceptibility was observed for five strains against fluconazole, itraconazole, voriconazole and caspofungin. Genotyping showed the presence of four clades (I–IV) in one hospital. Conclusions Appropriate antifungal treatments with rapid and accurate microbial identification are the cornerstone for the management and control of C. auris infections.
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Affiliation(s)
- Hanane Zerrouki
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Laboratoire de Microbiologie Appliquée à l'Agroalimentaire, au Biomédical et à l'Environnement, Université de Tlemcen, Tlemcen, Algeria
| | - Ahmad Ibrahim
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Sid-Ahmed Rebiahi
- Laboratoire de Microbiologie Appliquée à l'Agroalimentaire, au Biomédical et à l'Environnement, Université de Tlemcen, Tlemcen, Algeria
| | - Yamina Elhabiri
- Laboratoire de Microbiologie Appliquée à l'Agroalimentaire, au Biomédical et à l'Environnement, Université de Tlemcen, Tlemcen, Algeria
| | | | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands.,Centre of Expertise in Mycology, Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands.,Centre of Expertise in Mycology, Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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ClaID: a Rapid Method of Clade-Level Identification of the Multidrug Resistant Human Fungal Pathogen Candida auris. Microbiol Spectr 2022; 10:e0063422. [PMID: 35343775 PMCID: PMC9045239 DOI: 10.1128/spectrum.00634-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candida auris, the multidrug-resistant human fungal pathogen, emerged as four major distinct geographical clades (clade 1–clade 4) in the past decade. Though isolates of the same species, C. auris clinical strains exhibit clade-specific properties associated with virulence and drug resistance. In this study, we report the identification of unique DNA sequence junctions by mapping clade-specific regions through comparative analysis of whole-genome sequences of strains belonging to different clades. These unique DNA sequence stretches are used to identify C. auris isolates at the clade level in subsequent in silico and experimental analyses. We develop a colony PCR-based clade-identification system (ClaID), which is rapid and specific. In summary, we demonstrate a proof-of-concept for using unique DNA sequence junctions conserved in a clade-specific manner for the rapid identification of each of the four major clades of C. auris. IMPORTANCEC. auris was first isolated in Japan in 2009 as an antifungal drug-susceptible pathogen causing localized infections. Within a decade, it simultaneously evolved in different parts of the world as distinct clades exhibiting resistance to antifungal drugs at varying levels. Recent studies hinted the mixing of isolates belonging to different geographical clades in a single location, suggesting that the area of isolation alone may not indicate the clade status of an isolate. In this study, we compared the genomes of representative strains of the four major clades to identify clade-specific sequences, which were then used to design clade-specific primers. We propose the utilization of whole genome sequence data to extract clade-specific sequences for clade-typing. The colony PCR-based method employed can rapidly distinguish between the four major clades of C. auris, with scope for expanding the panel by adding more primer pairs.
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Abstract
Candida auris is an emerging yeast species that has the unique characteristics of patient skin colonization and rapid transmission within healthcare facilities and the ability to rapidly develop antifungal resistance. When C. auris first started appearing in clinical microbiology laboratories, it could only be identified using DNA sequencing. In the decade since its first identification outside of Japan there have been many improvements in the detection of C. auris. These include the expansion of MALDI-TOF databases to include C. auris, the development of both laboratory-developed tests and commercially available kits for its detection, and special CHROMagar for identification from laboratory specimens. Here we discuss the current tools and resources that are available for C. auris identification and detection.
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Dennis EK, Chaturvedi S, Chaturvedi V. So Many Diagnostic Tests, So Little Time: Review and Preview of Candida auris Testing in Clinical and Public Health Laboratories. Front Microbiol 2021; 12:757835. [PMID: 34691009 PMCID: PMC8529189 DOI: 10.3389/fmicb.2021.757835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/13/2021] [Indexed: 01/13/2023] Open
Abstract
The recognition of a new yeast, Candida auris, in 2009 in East Asia, and its rapid global spread, was a reminder of the threats posed by multidrug-resistant fungal pathogens. C. auris had likely remained unrecognized for a long time as accurate tests were not available. The laboratory community responded to the C. auris challenge by publishing 35 new or revised diagnostic methods between 2014 and early 2021. The commercial sector also modified existing diagnostic devices. These C. auris diagnostic tests run the gamut from traditional culture-based differential and selective media, biochemical assimilations, and rapid protein profiles, as well as culture-independent DNA-based diagnostics. We provide an overview of these developments, especially the tests with validation data that were subsequently adopted for common use. We share a workflow developed in our laboratory to process over 37,000 C. auris surveillance samples and 5,000 C. auris isolates from the outbreak in the New York metropolitan area. Our preview covers new devices and diagnostic approaches on the horizon based on microfluidics, optics, and nanotechnology. Frontline laboratories need rapid, cheap, stable, and easy-to-implement tests to improve C. auris diagnosis, surveillance, patient isolation, admission screening, and environmental control. Among the urgent needs is a lateral flow assay or similar device for presumptive C. auris identification. All laboratories will benefit from devices that allow rapid antifungal susceptibility testing, including detection of mutations conferring drug resistance. Hopefully, multiplex test panels are on the horizon for synergy of C. auris testing with ongoing surveillance of other healthcare-associated infections. C. auris genome analysis has a proven role for outbreak investigations, and diagnostic laboratories need quick access to regional and national genome analysis networks.
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Affiliation(s)
- Emily K Dennis
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States.,Department of Biomedical Sciences, University at Albany, Albany, NY, United States
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, United States
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