Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections
Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C....
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2024
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/178591 |
| _version_ | 1826121784833867776 |
|---|---|
| author | Wang, Yue Xu, Jianping Abid, Fatma Ben Salah, Husam Sundararaju, Sathyavathi Al Ismail, Khalil Wang, Kun Matthew, Lisa Sara Taj-Aldeen, Saad Ibrahim, Emad B. Tang, Patrick Perez-Lopez, Andres Tsui, Clement K. M. |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) Wang, Yue Xu, Jianping Abid, Fatma Ben Salah, Husam Sundararaju, Sathyavathi Al Ismail, Khalil Wang, Kun Matthew, Lisa Sara Taj-Aldeen, Saad Ibrahim, Emad B. Tang, Patrick Perez-Lopez, Andres Tsui, Clement K. M. |
| author_sort | Wang, Yue |
| collection | NTU |
| description | Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world. |
| first_indexed | 2024-10-01T05:38:09Z |
| format | Journal Article |
| id | ntu-10356/178591 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:38:09Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1785912024-06-30T15:39:33Z Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections Wang, Yue Xu, Jianping Abid, Fatma Ben Salah, Husam Sundararaju, Sathyavathi Al Ismail, Khalil Wang, Kun Matthew, Lisa Sara Taj-Aldeen, Saad Ibrahim, Emad B. Tang, Patrick Perez-Lopez, Andres Tsui, Clement K. M. Lee Kong Chian School of Medicine (LKCMedicine) Medicine, Health and Life Sciences Antifungal susceptibility Nosocomial Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world. Published version This study was funded by the Sidra Medicine Internal Research Grant (SDR_200052 to A.P- L. and K.M.T.), the Medical Research Centre at Hamad Medical Corporation (MRC- 01019–420 to F.B.A.), and the Global Science Initiative at McMaster University (2020–3 to J.X.). 2024-06-27T05:14:54Z 2024-06-27T05:14:54Z 2024 Journal Article Wang, Y., Xu, J., Abid, F. B., Salah, H., Sundararaju, S., Al Ismail, K., Wang, K., Matthew, L. S., Taj-Aldeen, S., Ibrahim, E. B., Tang, P., Perez-Lopez, A. & Tsui, C. K. M. (2024). Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections. Microbial Genomics, 10(1), 001179-. https://dx.doi.org/10.1099/mgen.0.001179 2057-5858 https://hdl.handle.net/10356/178591 10.1099/mgen.0.001179 38226964 2-s2.0-85182546353 1 10 001179 en Microbial Genomics © 2024 The Authors. This is an open- access article distributed under the terms of the Creative Commons Attribution License. application/pdf |
| spellingShingle | Medicine, Health and Life Sciences Antifungal susceptibility Nosocomial Wang, Yue Xu, Jianping Abid, Fatma Ben Salah, Husam Sundararaju, Sathyavathi Al Ismail, Khalil Wang, Kun Matthew, Lisa Sara Taj-Aldeen, Saad Ibrahim, Emad B. Tang, Patrick Perez-Lopez, Andres Tsui, Clement K. M. Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title | Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title_full | Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title_fullStr | Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title_full_unstemmed | Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title_short | Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections |
| title_sort | population genomic analyses reveal high diversity recombination and nosocomial transmission among candida glabrata nakaseomyces glabrata isolates causing invasive infections |
| topic | Medicine, Health and Life Sciences Antifungal susceptibility Nosocomial |
| url | https://hdl.handle.net/10356/178591 |
| work_keys_str_mv | AT wangyue populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT xujianping populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT abidfatmaben populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT salahhusam populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT sundararajusathyavathi populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT alismailkhalil populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT wangkun populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT matthewlisasara populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT tajaldeensaad populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT ibrahimemadb populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT tangpatrick populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT perezlopezandres populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections AT tsuiclementkm populationgenomicanalysesrevealhighdiversityrecombinationandnosocomialtransmissionamongcandidaglabratanakaseomycesglabrataisolatescausinginvasiveinfections |