1
|
Hady RE, Fattouh N, Finianos M, Bitar I, Husni R, Khalaf R. Phenotypic and Genotypic Characterization of Candida parapsilosis complex isolates from a Lebanese Hospital. RESEARCH SQUARE 2024:rs.3.rs-4169036. [PMID: 38903078 PMCID: PMC11188110 DOI: 10.21203/rs.3.rs-4169036/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The opportunistic fungal pathogen Candida parapsilosis is a major causative agent of candidiasis leading to death in immunocompromised individuals. Azoles are the first line of defense in treatment by inhibiting ERG11, involved in the synthesis of ergosterol, the main sterol fungal sterol. Resistance to azoles is on the increase worldwide including in Lebanon. The purpose of this study is to characterize nine hospital isolates labeled as C. parapsilosis: four resistant and five sensitive to fluconazole. Phenotypic characterization was achieved through a battery of tests that target pathogenicity attributes such as virulence, biofilm formation, stress resistance, and ergosterol content. Genotypic analysis was done through whole genome sequencing to mutations in key virulence and resistance genes. Phylogenetic comparison was performed to determine strain relatedness and clonality. Genomic data and phylogenetic analysis revealed that three of the nine C. parapsilosis isolates were misidentified; two as C. orthopsilosis and C. metapsilosis belonging to the C. parapsilosis complex, while the third was C. albicans. Moreover, several known and novel mutations in key drug resistance and virulence genes were identified such as ERG11, ERG3, ERG6, CDR1, and FAS2. Phylogenetic analysis revealed a high degree of relatedness and clonality within our C. parapsilosis isolates. Our results showed that resistant isolates had no increased ergosterol content, no statistically significant difference in virulence, but exhibited an increase in biofilm content compared to the sensitive isolates. In conclusion, our study, the first of its kind in Lebanon, suggests several mechanisms of antifungal drug resistance in C. parapsilosis hospital isolates.
Collapse
Affiliation(s)
| | | | | | | | - Rola Husni
- Lebanese American University School of Medicine
| | - Roy Khalaf
- Lebanese American University - Byblos Campus
| |
Collapse
|
2
|
Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. Antimicrob Agents Chemother 2024:e0161923. [PMID: 38712935 DOI: 10.1128/aac.01619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show that the annotated telomeric gene CDR1B is actually an artifactual in silico fusion of two highly similar neighboring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased the expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
Collapse
Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
3
|
Govrins M, Lass-Flörl C. Candida parapsilosis complex in the clinical setting. Nat Rev Microbiol 2024; 22:46-59. [PMID: 37674021 DOI: 10.1038/s41579-023-00961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Representatives of the Candida parapsilosis complex are important yeast species causing human infections, including candidaemia as one of the leading diseases. This complex comprises C. parapsilosis, Candida orthopsilosis and Candida metapsilosis, and causes a wide range of clinical presentations from colonization to superficial and disseminated infections with a high prevalence in preterm-born infants and the potential to cause outbreaks in hospital settings. Compared with other Candida species, the C. parapsilosis complex shows high minimal inhibitory concentrations for echinocandin drugs due to a naturally occurring FKS1 polymorphism. The emergence of clonal outbreaks of strains with resistance to commonly used antifungals, such as fluconazole, is causing concern. In this Review, we present the latest medical data covering epidemiology, diagnosis, resistance and current treatment approaches for the C. parapsilosis complex. We describe its main clinical manifestations in adults and children and highlight new treatment options. We compare the three sister species, examining key elements of microbiology and clinical characteristics, including the population at risk, disease manifestation and colonization status. Finally, we provide a comprehensive resource for clinicians and researchers focusing on Candida species infections and the C. parapsilosis complex, aiming to bridge the emerging translational knowledge and future therapeutic challenges associated with this human pathogen.
Collapse
Affiliation(s)
- Miriam Govrins
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
4
|
Bergin S, Doorley LA, Rybak JM, Wolfe KH, Butler G, Cuomo CA, Rogers PD. Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571446. [PMID: 38168157 PMCID: PMC10760152 DOI: 10.1101/2023.12.13.571446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We used whole-genome sequencing to analyse a collection of 35 fluconazole resistant and 7 susceptible Candida parapsilosis isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two probable outbreak groups were identified. We identified copy number variation of two genes, ERG11 and CDR1B, in resistant isolates. Two strains have a CNV at the ERG11 locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show the annotated telomeric gene CDR1B is actually an artefactual in silico fusion of two highly similar neighbouring CDR genes due to an assembly error in the C. parapsilosis CDC317 reference genome. We report highly variable copy numbers of the CDR1B region across the collection. Several strains have increased expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the CDR gene family in the C. parapsilosis species complex, showing that it is a highly dynamic family.
Collapse
Affiliation(s)
- Sean Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laura A Doorley
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey M Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kenneth H Wolfe
- School of Medicine, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI, USA
| | - P David Rogers
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
5
|
Del Olmo V, Mixão V, Fotedar R, Saus E, Al Malki A, Księżopolska E, Nunez-Rodriguez JC, Boekhout T, Gabaldón T. Origin of fungal hybrids with pathogenic potential from warm seawater environments. Nat Commun 2023; 14:6919. [PMID: 37903766 PMCID: PMC10616089 DOI: 10.1038/s41467-023-42679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.
Collapse
Affiliation(s)
- Valentina Del Olmo
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Verónica Mixão
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ester Saus
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amina Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Ministry of Municipality and Environment, P.O Box 20022, Doha, Qatar
| | - Ewa Księżopolska
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Toni Gabaldón
- Life Sciences Department. Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.
- , Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
| |
Collapse
|
6
|
Mixão V, Nunez-Rodriguez JC, Del Olmo V, Ksiezopolska E, Saus E, Boekhout T, Gacser A, Gabaldón T. Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens. BMC Biol 2023; 21:105. [PMID: 37170256 PMCID: PMC10173528 DOI: 10.1186/s12915-023-01608-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Hybrids are chimeric organisms with highly plastic heterozygous genomes that may confer unique traits enabling the adaptation to new environments. However, most evolutionary theory frameworks predict that the high levels of genetic heterozygosity present in hybrids from divergent parents are likely to result in numerous deleterious epistatic interactions. Under this scenario, selection is expected to favor recombination events resulting in loss of heterozygosity (LOH) affecting genes involved in such negative interactions. Nevertheless, it is so far unknown whether this phenomenon actually drives genomic evolution in natural populations of hybrids. To determine the balance between selection and drift in the evolution of LOH patterns in natural yeast hybrids, we analyzed the genomic sequences from fifty-five hybrid strains of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis, which derived from at least six distinct natural hybridization events. RESULTS We found that, although LOH patterns in independent hybrid clades share some level of convergence that would not be expected from random occurrence, there is an apparent lack of strong functional selection. Moreover, while mitosis is associated with a limited number of inter-homeologous chromosome recombinations in these genomes, induced DNA breaks seem to increase the LOH rate. We also found that LOH does not accumulate linearly with time in these hybrids. Furthermore, some C. orthopsilosis hybrids present LOH patterns compatible with footprints of meiotic recombination. These meiotic-like patterns are at odds with a lack of evidence of sexual recombination and with our inability to experimentally induce sporulation in these hybrids. CONCLUSIONS Our results suggest that genetic drift is the prevailing force shaping LOH patterns in these hybrid genomes. Moreover, the observed LOH patterns suggest that these are likely not the result of continuous accumulation of sporadic events-as expected by mitotic repair of rare chromosomal breaks-but rather of acute episodes involving many LOH events in a short period of time.
Collapse
Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Present address: Genomics and Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Juan Carlos Nunez-Rodriguez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentina Del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE "Lendület" Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034, Barcelona, Spain.
- Mechanisms of Disease Program, Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain.
| |
Collapse
|
7
|
Mixão V, del Olmo V, Hegedűsová E, Saus E, Pryszcz L, Cillingová A, Nosek J, Gabaldón T. Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex. DNA Res 2022; 29:6570588. [PMID: 35438177 PMCID: PMC9046093 DOI: 10.1093/dnares/dsac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Indexed: 01/27/2023] Open
Abstract
Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C. metapsilosis isolates sequenced thus far are hybrids, and most of the parental lineages remain unidentified. This led to the hypothesis that hybrids with pathogenic potential were formed by the hybridization of non-pathogenic lineages that thrive in the environment. In a search for the missing hybrid parentals, and aiming to get a better understanding of the evolution of the species complex, we sequenced, assembled and analysed the genome of five close relatives isolated from the environment: Candida jiufengensis, Candida pseudojiufengensis, Candida oxycetoniae, Candida margitis and Candida theae. We found that the linear conformation of mitochondrial genomes in Candida species emerged multiple times independently. Furthermore, our analyses discarded the possible involvement of these species in the mentioned hybridizations, but identified C. theae as an additional hybrid in the species complex. Importantly, C. theae was recently associated with a case of infection, and we also uncovered the hybrid nature of this clinical isolate. Altogether, our results reinforce the hypothesis that hybridization is widespread among Candida species, and potentially contributes to the emergence of lineages with opportunistic pathogenic behaviour.
Collapse
Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Valentina del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Eva Hegedűsová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Leszek Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Barcelona 08010, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain
| |
Collapse
|