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Spruijtenburg B, Meis JF, Verweij PE, de Groot T, Meijer EFJ. Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential. Mycopathologia 2024; 189:72. [PMID: 39096450 DOI: 10.1007/s11046-024-00877-8] [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: 04/26/2024] [Accepted: 07/11/2024] [Indexed: 08/05/2024]
Abstract
Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.
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Affiliation(s)
- Bram Spruijtenburg
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacques F Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Excellence Center for Medical Mycology, Institute of Translational Research, University of Cologne, Cologne, Germany
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul E Verweij
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Theun de Groot
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
| | - Eelco F J Meijer
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands.
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands.
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
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Karakoyun AS, Spruijtenburg B, Unal N, Meijer EFJ, Sucu M, Hilmioğlu-Polat S, Meis JF, de Groot T, Ilkit M. Molecular typing and antifungal susceptibility profile of Candida krusei bloodstream isolates from Türkiye. Med Mycol 2024; 62:myae005. [PMID: 38289726 DOI: 10.1093/mmy/myae005] [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: 11/29/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
Candida krusei also known as Pichia kudriavzevii is a potentially multidrug-resistant yeast because it is intrinsically resistant to fluconazole and develops acquired resistance to echinocandins and polyenes. Here, we aim to provide a better understanding of the epidemiology and transmission modes of C. krusei infections by comparing invasive bloodstream (n = 35) and non-invasive vaginal (n = 20) C. krusei isolates. The genetic relatedness of the isolates was assessed using a newly described short tandem repeat (STR) analysis and their sensitivity to eight antifungal compounds was evaluated by antifungal susceptibility testing using the CLSI microbroth dilution method. All C. krusei isolates revealed unique STR genotypes, indicating the absence of clonal transmission in the study group. Furthermore, no drug-resistant or non-wild-type isolates were identified. Our findings demonstrated high resolution of STR genotyping for the detection and simultaneous genetic analysis of multiple C. krusei strains in clinical samples and excellent in vitro activity of common antifungal agents against invasive strains.
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Affiliation(s)
- Ayşe Sultan Karakoyun
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Nevzat Unal
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
- University of Health Sciences, Adana City Training and Research Hospital, Laboratory of Medical Microbiology, Adana, Türkiye
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Mete Sucu
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Çukurova University, Adana, Türkiye
| | - Süleyha Hilmioğlu-Polat
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Ege University, Izmir, Türkiye
| | - Jacques F Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Disease, Canisius-Wilhelmina Hospital (CWZ)/Dicoon, SZ Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
| | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, Çukurova University, Adana, Türkiye
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Marek A, Meijer EFJ, Tartari E, Zakhour J, Chowdhary A, Voss A, Kanj SS, Bal AM. Environmental monitoring for filamentous fungal pathogens in hematopoietic cell transplant units. Med Mycol 2023; 61:myad103. [PMID: 37793805 DOI: 10.1093/mmy/myad103] [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: 08/07/2023] [Revised: 09/18/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
The incidence of invasive fungal disease (IFD) is on the rise due to increasing numbers of highly immunocompromized patients. Nosocomial IFD remains common despite our better understanding of its risk factors and pathophysiology. High-efficiency particulate air filtration with or without laminar air flow, frequent air exchanges, a positive pressure care environment, and environmental hygiene, amongst other measures, have been shown to reduce the mould burden in the patient environment. Environmental monitoring for moulds in areas where high-risk patients are cared for, such as hematopoietic cell transplant units, has been considered an adjunct to other routine environmental precautions. As a collaborative effort between authors affiliated to the Infection Prevention and Control Working Group and the Fungal Infection Working Group of the International Society of Antimicrobial Chemotherapy (ISAC), we reviewed the English language literature and international guidance to describe the evidence behind the need for environmental monitoring for filamentous fungi as a quality assurance approach with an emphasis on required additional precautions during periods of construction. Many different clinical sampling approaches have been described for air, water, and surface sampling with significant variation in laboratory methodologies between reports. Importantly, there are no agreed-upon thresholds that correlate with an increase in the clinical risk of mould infections. We highlight important areas for future research to assure a safe environment for highly immunocompromized patients.
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Affiliation(s)
- Aleksandra Marek
- Department of Microbiology, Glasgow Royal Infirmary, Glasgow, UK
- Infection Control Working Group, International Society of Antimicrobial Chemotherapy
| | - Eelco F J Meijer
- Canisius-Wilhelmina Hospital (CWZ), Medical Microbiology and Infectious Diseases, Nijmegen, The Netherlands
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Fungal Infection Working Group, International Society of Antimicrobial Chemotherapy
| | - Ermira Tartari
- Faculty of Health Sciences, University of Malta, Msida, Malta
- Infection Control Working Group, International Society of Antimicrobial Chemotherapy
| | - Johnny Zakhour
- Division of Infectious Diseases, Department of Internal Medicine and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- Fungal Infection Working Group, International Society of Antimicrobial Chemotherapy
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands
- Infection Control Working Group, International Society of Antimicrobial Chemotherapy
| | - Souha S Kanj
- Division of Infectious Diseases, Department of Internal Medicine and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
- Fungal Infection Working Group, International Society of Antimicrobial Chemotherapy
| | - Abhijit M Bal
- Department of Microbiology, Queen Elizabeth University Hospital, Glasgow, UK
- Fungal Infection Working Group, International Society of Antimicrobial Chemotherapy
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Spruijtenburg B, Meijer EFJ, Xiao M, Shawky SM, Meis JF, de Groot T, El-Kholy MA. Genotyping and susceptibility testing uncovers large azole-resistant Candida tropicalis clade in Alexandria, Egypt. J Glob Antimicrob Resist 2023; 34:99-105. [PMID: 37419181 DOI: 10.1016/j.jgar.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/09/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES Candida tropicalis is an emerging medically relevant Candida species. The yeast primarily causes opportunistic infections in intensive care units and is highly prevalent in tropical countries. The genetic diversity within this species is high, and nosocomial transmission has been reported. C. tropicalis genotyping of isolates from low- and middle-income countries is underrepresented when compared with that from high-income countries. Also, in Egypt, only limited genotyping has been conducted for C. tropicalis isolates, while antifungal resistance seems to increase, especially against azoles. METHODS Antifungal susceptibility testing was performed on 64 C. tropicalis isolates from ICU patients collected from multiple hospitals in Alexandria, Egypt. Genotyping by means of short tandem repeat (STR) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis was performed. RESULTS Using antifungal susceptibility testing, fluconazole resistance was observed in 24 isolates (38%), of which 23 harboured an ERG11 G464S substitution, previously shown to cause resistance in Candida albicans. STR genotyping showed that these 23 isolates were related, forming a distinct resistant clade. WGS SNP analysis subsequently confirmed this genetic relationship, although isolates within this clade differed in at least 429 SNPs, suggesting that these were independently introduced. CONCLUSION Overall, STR and WGS SNP analysis of this collection indicates limited C. tropicalis nosocomial transmission in Alexandria, while the presence of this large azole-resistant C. tropicalis clade within this city hampers the treatment of intensive care unit patients.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, People's Republic of China
| | - Sherine M Shawky
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Mohammed A El-Kholy
- Department of Microbiology and Biotechnology, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), Alexandria, Egypt.
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Spruijtenburg B, Rudramurthy SM, Meijer EFJ, van Haren MHI, Kaur H, Chakrabarti A, Meis JF, de Groot T. Application of Novel Short Tandem Repeat Typing for Wickerhamomyces anomalus Reveals Simultaneous Outbreaks within a Single Hospital. Microorganisms 2023; 11:1525. [PMID: 37375027 DOI: 10.3390/microorganisms11061525] [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: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Wickerhamomyces anomalus, previously known as Candida pelliculosa, occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported. W. anomalus outbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme for W. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90 W. anomalus isolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates. ERG11 genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model for W. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multiple W. anomalus outbreak events by applying a novel STR genotyping scheme.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Merlijn H I van Haren
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
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Spruijtenburg B, Baqueiro CCSZ, Colombo AL, Meijer EFJ, de Almeida JN, Berrio I, Fernández NB, Chaves GM, Meis JF, de Groot T. Short Tandem Repeat Genotyping and Antifungal Susceptibility Testing of Latin American Candida tropicalis Isolates. J Fungi (Basel) 2023; 9:jof9020207. [PMID: 36836321 PMCID: PMC9958743 DOI: 10.3390/jof9020207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Candida tropicalis is emerging as one of the most common Candida species causing opportunistic infections in Latin America. Outbreak events caused by C. tropicalis were reported, and antifungal resistant isolates are on the rise. In order to investigate population genomics and look into antifungal resistance, we applied a short tandem repeat (STR) genotyping scheme and antifungal susceptibility testing (AFST) to 230 clinical and environmental C. tropicalis isolates from Latin American countries. STR genotyping identified 164 genotypes, including 11 clusters comprised of three to seven isolates, indicating outbreak events. AFST identified one isolate as anidulafungin-resistant and harboring a FKS1 S659P substitution. Moreover, we identified 24 clinical and environmental isolates with intermediate susceptibility or resistance to one or more azoles. ERG11 sequencing revealed each of these isolates harboring a Y132F and/or Y257H/N substitution. All of these isolates, except one, were clustered together in two groups of closely related STR genotypes, with each group harboring distinct ERG11 substitutions. The ancestral C. tropicalis strain of these isolates likely acquired the azole resistance-associated substitutions and subsequently spread across vast distances within Brazil. Altogether, this STR genotyping scheme for C. tropicalis proved to be useful for identifying unrecognized outbreak events and better understanding population genomics, including the spread of antifungal-resistant isolates.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Cynthea C. S. Z. Baqueiro
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Arnaldo L. Colombo
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Eelco F. J. Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - João N. de Almeida
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
| | - Indira Berrio
- Hospital General de Medellín Luz Castro de Gutiérrez ESE, Medellín 050015, Colombia
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín 050015, Colombia
| | - Norma B. Fernández
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires 2351, Argentina
| | - Guilherme M. Chaves
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba 80060-000, PR, Brazil
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Excellence Center for Medical Mycology, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Correspondence:
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Spruijtenburg B, van Haren MHI, Chowdhary A, Meis JF, de Groot T. Development and Application of a Short Tandem Repeat Multiplex Typing Assay for Candida tropicalis. Microbiol Spectr 2023; 11:e0461822. [PMID: 36715547 PMCID: PMC10100945 DOI: 10.1128/spectrum.04618-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Candida tropicalis is a clinically important yeast that causes candidemia in humans with a high mortality rate. The yeast primarily infects immunocompromised patients, and causes outbreaks in health care facilities. Antifungal resistant isolates have been reported. We developed a short tandem repeat (STR) typing scheme for C. tropicalis to enable fast, cost-effective, and high-resolution genotyping. For the development of the typing scheme, 6 novel STR markers were selected, combined into 2 multiplex PCRs. In total, 117 C. tropicalis isolates were typed, resulting in the identification of 104 different genotypes. Subsequently, the outcome of STR typing of 10 isolates was compared to single nucleotide polymorphism (SNP) calling from whole-genome sequencing (WGS). Isolates with more than 111 SNPs were differentiated by the typing assay. Two isolates, which were identical according to SNP analysis, were separated by STR typing in 1 marker. To test specificity, the STR typing was applied to 15 related yeast species, and we found no amplification of these targets. For reproducibility testing, 2 isolates were independently typed five times, which showed identical results in each experiment. In summary, we developed a reliable and multiplex STR genotyping for C. tropicalis, which was found to correlate well to SNP calling by WGS. WGS analysis from and extensive collection of isolates is required to establish the precise resolution of this STR assay. IMPORTANCE Candida tropicalis frequently causes candidemia in immunocompromised patients. C. tropicalis infections have a high mortality rate, and the yeast is able to cause outbreaks in health care facilities. Further, antifungal resistant isolates are on the rise. Genotyping is necessary to investigate potential outbreaks. Here, we developed and applied a STR genotyping scheme in order to rapidly genotype isolates with a high-resolution. WGS SNP outcomes were highly comparable with STR typing results. Altogether, we developed a rapid, high-resolution, and specific STR genotyping scheme for C. tropicalis.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Merlijn H. I. van Haren
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Medical Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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de Groot T, Spruijtenburg B, Parnell LA, Chow NA, Meis JF. Optimization and Validation of Candida auris Short Tandem Repeat Analysis. Microbiol Spectr 2022; 10:e0264522. [PMID: 36190407 PMCID: PMC9603409 DOI: 10.1128/spectrum.02645-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Candida auris is an easily transmissible yeast with resistance to different antifungal compounds. Outbreaks of C. auris are mostly observed in intensive care units. To take adequate measures during an outbreak, it is essential to understand the transmission route, which requires isolate genotyping. In 2019, a short tandem repeat (STR) genotyping analysis was developed for C. auris. To determine the discriminatory power of this method, we performed STR analysis of 171 isolates with known whole-genome sequencing (WGS) data using Illumina reads, and we compared their resolutions. We found that STR analysis separated the 171 isolates into four clades (clades I to IV), as was also seen with WGS analysis. Then, to improve the separation of isolates in clade IV, the STR assay was optimized by the addition of 2 STR markers. With this improved STR assay, a total of 32 different genotypes were identified, while all isolates with differences of >50 single-nucleotide polymorphisms (SNPs) were separated by at least 1 STR marker. Altogether, we optimized and validated the C. auris STR panel for clades I to IV and established its discriminatory power, compared to WGS SNP analysis using Illumina reads. IMPORTANCE The emerging fungal pathogen Candida auris poses a threat to public health, mainly causing outbreaks in intensive care units. Genotyping is essential for investigating potential outbreaks and preventing further spread. Previously, we developed a STR genotyping scheme for rapid and high-resolution genotyping, and WGS SNP outcomes for some isolates were compared to STR data. Here, we compared WGS SNP and STR outcomes for a larger sample cohort. Also, we optimized the resolution of this typing scheme with the addition of 2 STR markers. Altogether, we validated and optimized this rapid, reliable, and high-resolution typing scheme for C. auris.
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Affiliation(s)
- Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Lindsay A. Parnell
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
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Abstract
Revealing the phylogenetic relationships of Candida krusei strains (sexual form Pichia kudriavzevii) is a prerequisite for understanding the evolution of its virulence-associated mechanisms and ecological lifestyles. Molecular phylogenetic analyses based on entire internal transcribed spacer region (ITS) and multilocus sequence typing (MLST) data were carried out with sequences available in public databases and Hungarian isolates from animals obtained for the study. The ITS haplotype network yielded a high frequency haplotype at the centre of the network (H1; n = 204) indicating that various selective pressure might resulted in population expansion from H1. MLST analysis identified three new genotypes among animal-derived isolates, therefore overall 203 sequence types were investigated to determine the population structure of C. krusei. The most commonly encountered sequence types were ST 17 and ST 67. Phylogenetic analyses showed diverse genetic construction of C. krusei population. Evidence of potential recombination events were also observed that might play some role in high intraspecies genetic variability among strains, however, the limited data of C. krusei genotypes from different countries prevented us to identify accurate evolutionary routes of commensal and pathogenic strains or species-specific lineages. Further expansion of C. krusei MLST database may promote the better understanding of the mixed evolutionary history of this species.
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Kim H, Bae SY. Talus osteomyelitis by Candida krusei with multiple huge cystic lesions: a case report and review of literatures. BMC Musculoskelet Disord 2022; 23:687. [PMID: 35854259 PMCID: PMC9295485 DOI: 10.1186/s12891-022-05648-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/13/2022] [Indexed: 11/12/2022] Open
Abstract
Background Osteomyelitis due to Candida krusei are extremely rare, given that only six cases have been reported, all of which are limited to the patients with immunocompromising risk factors. Here we report a case of C. krusei osteomyelitis in an immunocompetent patient, presenting with multiple huge cystic lesions of talus. Case presentation A 66-year-old female presented with one year history of painful swelling of right ankle and a draining sinus around lateral malleolus. Five months and three months ago, she had undergone arthroscopic synovectomy and bursectomy which revealed no causative organism. Open bursectomy with sinus tract excision was performed and intravenous antibiotic was administered. Two year after the surgery, the patient revisited the clinic for recurrent painful swelling with pus drainage at the same location. Multiple huge cystic lesions with osteolysis and sclerotic rim of talus were found and C. krusei was isolated from tissue culture. The patient received surgical debridement and prolonged antifungal treatment comprising caspofungin and voriconazole. Conclusions In this case, C. krusei infection showed atypically aggressive osteolysis shown as multiple huge cystic abscess. High index of suspicion is critical for early diagnosis and treatment to prevent such devastating results even in an immunocompetent patient.
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Affiliation(s)
- Hyungtae Kim
- Department of Orthopaedic Surgery, Inje University Sanggye Paik Hospital, College of Medicine, Inje University, 1342, Dongil-Ro, Nowon-Gu, Seoul, 01757, Republic of Korea
| | - Su-Young Bae
- Department of Orthopaedic Surgery, Inje University Sanggye Paik Hospital, College of Medicine, Inje University, 1342, Dongil-Ro, Nowon-Gu, Seoul, 01757, Republic of Korea.
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