Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types
Candida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we ut...
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-12-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2018.02946/full |
| _version_ | 1819266350597537792 |
|---|---|
| author | Chayanika Biswas Chayanika Biswas Vanessa R. Marcelino Vanessa R. Marcelino Vanessa R. Marcelino Sebastiaan Van Hal Catriona Halliday Elena Martinez Elena Martinez Qinning Wang Qinning Wang Sarah Kidd Karina Kennedy Deborah Marriott C. Orla Morrissey Ian Arthur Kerry Weeks Monica A. Slavin Tania C. Sorrell Tania C. Sorrell Tania C. Sorrell Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Wieland Meyer Wieland Meyer Wieland Meyer Wieland Meyer Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen |
| author_facet | Chayanika Biswas Chayanika Biswas Vanessa R. Marcelino Vanessa R. Marcelino Vanessa R. Marcelino Sebastiaan Van Hal Catriona Halliday Elena Martinez Elena Martinez Qinning Wang Qinning Wang Sarah Kidd Karina Kennedy Deborah Marriott C. Orla Morrissey Ian Arthur Kerry Weeks Monica A. Slavin Tania C. Sorrell Tania C. Sorrell Tania C. Sorrell Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Wieland Meyer Wieland Meyer Wieland Meyer Wieland Meyer Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen |
| author_sort | Chayanika Biswas |
| collection | DOAJ |
| description | Candida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we utilized whole genome sequencing (WGS) to study the genetic diversity of 51 Australian C. glabrata isolates and sought associations between STs over two time periods (2002–2004, 2010–2017), and with susceptibility to fluconazole by principal component analysis (PCA). Antifungal susceptibility was determined using Sensititre YeastOneTM Y010 methodology and WGS performed on the NextSeq 500 platform (Illumina) with in silico MLST STs inferred by WGS data. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-fluorocytosine resistance were analyzed. Of 51 isolates, WGS identified 18 distinct STs including four novel STs (ST123, ST124, ST126, and ST127). Four STs accounted for 49% of isolates (ST3, 15.7%; ST83, 13.7%; ST7, 9.8%; ST26, 9.8%). Split-tree network analysis resolved isolates to terminal branches; many of these comprised multiple isolates from disparate geographic settings but four branches contained Australian isolates only. ST3 isolates were common in Europe, United States and now Australia, whilst ST8 and ST19, relatively frequent in the United States, were rare/absent amongst our isolates. There was no association between ST distribution (genomic similarity) and the two time periods or with fluconazole susceptibility. WGS identified mutations in the FKS1 (S629P) and FKS2 (S663P) genes in three, and one, echinocandin-resistant isolate(s), respectively. Both mutations confer phenotypic drug resistance. Twenty-five percent (13/51) of isolates were fluconazole-resistant (MIC ≥ 64 μg/ml) of which 9 (18%) had non wild-type MICs to voriconazole and posaconazole. Multiple SNPs were present in genes linked to azole resistance such as CgPDR1 and CgCDR1, as well as several in MSH2; however, SNPs occurred in both azole-susceptible and azole-resistant isolates. Although no particular SNP in these genes was definitively associated with resistance, azole-resistant/non-wild type isolates had a propensity to harbor SNPs resulting in amino acid substitutions in Pdr1 beyond the first 250 amino acid positions. The presence of SNPs may be markers of STs. Our study shows the value of WGS for high-resolution sequence typing of C. glabrata, discovery of novel STs and potential to monitor trends in genetic diversity. WGS assessment for echinocandin resistance augments phenotypic susceptibility testing. |
| first_indexed | 2024-12-23T20:59:53Z |
| format | Article |
| id | doaj.art-56838ef0ee7e40f7902febcb37bc7766 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-23T20:59:53Z |
| publishDate | 2018-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-56838ef0ee7e40f7902febcb37bc77662022-12-21T17:31:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-12-01910.3389/fmicb.2018.02946424436Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence TypesChayanika Biswas0Chayanika Biswas1Vanessa R. Marcelino2Vanessa R. Marcelino3Vanessa R. Marcelino4Sebastiaan Van Hal5Catriona Halliday6Elena Martinez7Elena Martinez8Qinning Wang9Qinning Wang10Sarah Kidd11Karina Kennedy12Deborah Marriott13C. Orla Morrissey14Ian Arthur15Kerry Weeks16Monica A. Slavin17Tania C. Sorrell18Tania C. Sorrell19Tania C. Sorrell20Vitali Sintchenko21Vitali Sintchenko22Vitali Sintchenko23Vitali Sintchenko24Wieland Meyer25Wieland Meyer26Wieland Meyer27Wieland Meyer28Sharon C.-A. Chen29Sharon C.-A. Chen30Sharon C.-A. Chen31Sharon C.-A. Chen32Sharon C.-A. Chen33Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, AustraliaMarie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, AustraliaDepartment of Infectious Diseases and Microbiology, New South Wales Health Pathology, Royal Prince Alfred Hospital, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaNational Mycology Reference Centre, SA Pathology, Adelaide, SA, AustraliaDepartment of Microbiology and Infectious Diseases, Canberra Hospital & Health Services, Australian National University Medical School, Canberra, ACT, AustraliaDepartment of Microbiology and Infectious Diseases, St Vincent’s Hospital, Sydney, NSW, Australia0Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, VIC, Australia1Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Perth, WA, Australia2Department of Microbiology and Infectious Diseases, Royal North Shore Hospital, Sydney, NSW, Australia3National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, AustraliaMarie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, AustraliaMarie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, AustraliaMarie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, NSW, AustraliaWestmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, AustraliaMarie Bashir Institute for Emerging Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, AustraliaCentre for Infectious Diseases and Microbiology Laboratory Services, ICPMR, New South Wales Health Pathology, Westmead Hospital, Sydney, NSW, AustraliaCandida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we utilized whole genome sequencing (WGS) to study the genetic diversity of 51 Australian C. glabrata isolates and sought associations between STs over two time periods (2002–2004, 2010–2017), and with susceptibility to fluconazole by principal component analysis (PCA). Antifungal susceptibility was determined using Sensititre YeastOneTM Y010 methodology and WGS performed on the NextSeq 500 platform (Illumina) with in silico MLST STs inferred by WGS data. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-fluorocytosine resistance were analyzed. Of 51 isolates, WGS identified 18 distinct STs including four novel STs (ST123, ST124, ST126, and ST127). Four STs accounted for 49% of isolates (ST3, 15.7%; ST83, 13.7%; ST7, 9.8%; ST26, 9.8%). Split-tree network analysis resolved isolates to terminal branches; many of these comprised multiple isolates from disparate geographic settings but four branches contained Australian isolates only. ST3 isolates were common in Europe, United States and now Australia, whilst ST8 and ST19, relatively frequent in the United States, were rare/absent amongst our isolates. There was no association between ST distribution (genomic similarity) and the two time periods or with fluconazole susceptibility. WGS identified mutations in the FKS1 (S629P) and FKS2 (S663P) genes in three, and one, echinocandin-resistant isolate(s), respectively. Both mutations confer phenotypic drug resistance. Twenty-five percent (13/51) of isolates were fluconazole-resistant (MIC ≥ 64 μg/ml) of which 9 (18%) had non wild-type MICs to voriconazole and posaconazole. Multiple SNPs were present in genes linked to azole resistance such as CgPDR1 and CgCDR1, as well as several in MSH2; however, SNPs occurred in both azole-susceptible and azole-resistant isolates. Although no particular SNP in these genes was definitively associated with resistance, azole-resistant/non-wild type isolates had a propensity to harbor SNPs resulting in amino acid substitutions in Pdr1 beyond the first 250 amino acid positions. The presence of SNPs may be markers of STs. Our study shows the value of WGS for high-resolution sequence typing of C. glabrata, discovery of novel STs and potential to monitor trends in genetic diversity. WGS assessment for echinocandin resistance augments phenotypic susceptibility testing.https://www.frontiersin.org/article/10.3389/fmicb.2018.02946/fullwhole genome sequencingCandida glabrataMLSTsequence typeAustralia |
| spellingShingle | Chayanika Biswas Chayanika Biswas Vanessa R. Marcelino Vanessa R. Marcelino Vanessa R. Marcelino Sebastiaan Van Hal Catriona Halliday Elena Martinez Elena Martinez Qinning Wang Qinning Wang Sarah Kidd Karina Kennedy Deborah Marriott C. Orla Morrissey Ian Arthur Kerry Weeks Monica A. Slavin Tania C. Sorrell Tania C. Sorrell Tania C. Sorrell Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Vitali Sintchenko Wieland Meyer Wieland Meyer Wieland Meyer Wieland Meyer Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Sharon C.-A. Chen Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types Frontiers in Microbiology whole genome sequencing Candida glabrata MLST sequence type Australia |
| title | Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types |
| title_full | Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types |
| title_fullStr | Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types |
| title_full_unstemmed | Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types |
| title_short | Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types |
| title_sort | whole genome sequencing of australian candida glabrata isolates reveals genetic diversity and novel sequence types |
| topic | whole genome sequencing Candida glabrata MLST sequence type Australia |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2018.02946/full |
| work_keys_str_mv | AT chayanikabiswas wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT chayanikabiswas wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vanessarmarcelino wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vanessarmarcelino wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vanessarmarcelino wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sebastiaanvanhal wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT catrionahalliday wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT elenamartinez wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT elenamartinez wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT qinningwang wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT qinningwang wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sarahkidd wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT karinakennedy wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT deborahmarriott wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT corlamorrissey wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT ianarthur wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT kerryweeks wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT monicaaslavin wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT taniacsorrell wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT taniacsorrell wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT taniacsorrell wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vitalisintchenko wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vitalisintchenko wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vitalisintchenko wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT vitalisintchenko wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT wielandmeyer wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT wielandmeyer wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT wielandmeyer wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT wielandmeyer wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sharoncachen wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sharoncachen wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sharoncachen wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sharoncachen wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes AT sharoncachen wholegenomesequencingofaustraliancandidaglabrataisolatesrevealsgeneticdiversityandnovelsequencetypes |