1
|
Kidd SE, Hagen F, Halliday CL, Abdolrasouli A, Boekhout T, Crous PW, Ellis DH, Elvy J, Forrest GN, Groenewald M, Hahn RC, Houbraken J, Rodrigues AM, Scott J, Sorrell TC, Summerbell RC, Tsui CKM, Yurkov A, Chen SCA. Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion. J Clin Microbiol 2024; 62:e0157023. [PMID: 38441055 PMCID: PMC11005369 DOI: 10.1128/jcm.01570-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Sarah E. Kidd
- National Mycology Reference Centre, SA Pathology, Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Alireza Abdolrasouli
- Department of Medical Microbiology, King’s College Hospital, London, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Teun Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Biology, Molecular Microbiology, Utrecht University, Utrecht, the Netherlands
| | - David H. Ellis
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Juliet Elvy
- Awanui Labs, Dunedin Hospital, Dunedin, New Zealand
| | | | | | - Rosane C. Hahn
- Medical Mycology Laboratory/Investigation, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
- Júlio Muller Hospital, EBSERH, Cuiabá, Mato Grosso, Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Anderson M. Rodrigues
- Department of Microbiology, Immunology and Parasitology, Laboratory of Emerging Fungal Pathogens, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - James Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Tania C. Sorrell
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Richard C. Summerbell
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Sporometrics, Toronto, Ontario, Canada
| | - Clement K. M. Tsui
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Andrey Yurkov
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia
| |
Collapse
|
2
|
Abdel Hadi H, Dargham SR, Eltayeb F, Ali MOK, Suliman J, Ahmed SAM, Omrani AS, Ibrahim EB, Chen Y, Tsui CKM, Skariah S, Sultan A. Epidemiology, Clinical, and Microbiological Characteristics of Multidrug-Resistant Gram-Negative Bacteremia in Qatar. Antibiotics (Basel) 2024; 13:320. [PMID: 38666996 PMCID: PMC11047403 DOI: 10.3390/antibiotics13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial resistance is a global healthcare threat with significant clinical and economic consequences peaking at secondary and tertiary care hospitals where multidrug-resistant Gram-negative bacteria (MDR GNB) lead to poor outcomes. A prospective study was conducted between January and December 2019 for all invasive bloodstream infections (BSIs) secondary to MDR GNB in Qatar identified during routine microbiological service to examine their clinical, microbiological, and genomic characteristics. Out of 3238 episodes of GNB BSIs, the prevalence of MDR GNB was 13% (429/3238). The predominant MDR pathogens were Escherichia coli (62.7%), Klebsiella pneumoniae (20.4%), Salmonella species (6.6%), and Pseudomonas aeruginosa (5.3%), while out of 245 clinically evaluated patients, the majority were adult males, with the elderly constituting almost one-third of the cohort and with highest observed risk for prolonged hospital stays. The risk factors identified included multiple comorbidities, recent healthcare contact, previous antimicrobial therapy, and admission to critical care. The in-hospital mortality rate was recorded at 25.7%, associated with multiple comorbidities, admission to critical care, and the acquisition of MDR Pseudomonas aeruginosa. Resistant pathogens demonstrated high levels of antimicrobial resistance but noticeable susceptibility to amikacin and carbapenems. Genomic analysis revealed that Escherichia coli ST131 and Salmonella enterica ST1 were the predominant clones not observed with other pathogens.
Collapse
Affiliation(s)
- Hamad Abdel Hadi
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (S.A.M.A.); (A.S.O.)
- College of Medicine, Qatar University, Doha P.O. Box 2713, Qatar
| | - Soha R. Dargham
- Department of Medical Education, Weill Cornell Medicine, Qatar Foundation, Doha P.O. Box 24144, Qatar;
| | - Faiha Eltayeb
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (F.E.); (E.B.I.)
| | - Mohamed O. K. Ali
- Department of Internal Medicine, University Health Truman Medical Centre, Kansas City, MO 64108, USA;
| | - Jinan Suliman
- Department of Community Medicine, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar;
| | - Shiema Abdalla M. Ahmed
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (S.A.M.A.); (A.S.O.)
| | - Ali S. Omrani
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (S.A.M.A.); (A.S.O.)
- College of Medicine, Qatar University, Doha P.O. Box 2713, Qatar
| | - Emad Bashir Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (F.E.); (E.B.I.)
- Biomedical Research Centre, Qatar University, Doha P.O. Box 2713, Qatar
| | - Yuzhou Chen
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (Y.C.); (C.K.M.T.)
| | - Clement K. M. Tsui
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (Y.C.); (C.K.M.T.)
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Singapore 308442, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Doha 2713, Qatar; (S.S.); (A.S.)
| | - Ali Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Doha 2713, Qatar; (S.S.); (A.S.)
| |
Collapse
|
3
|
Gao M, Xiong C, Tsui CKM, Cai L. Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome. Mol Ecol 2024; 33:e17228. [PMID: 38037712 DOI: 10.1111/mec.17228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.
Collapse
Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Wang Y, Xu J, Ben Abid F, Salah H, Sundararaju S, Al Ismail K, Wang K, Sara Matthew L, Taj-Aldeen S, Ibrahim EB, Tang P, Perez-Lopez A, Tsui CKM. Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata ( Nakaseomyces glabrata) isolates causing invasive infections. Microb Genom 2024; 10:001179. [PMID: 38226964 PMCID: PMC10868614 DOI: 10.1099/mgen.0.001179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Yue Wang
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Fatma Ben Abid
- Department of Medicine, Division of Infectious Diseases, Hamad Medical Corporation, Doha, Qatar
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Khalil Al Ismail
- Communicable Disease Centre, Hamad Medical Corporation, Doha, Qatar
| | - Kun Wang
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Saad Taj-Aldeen
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Emad B. Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Patrick Tang
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Andres Perez-Lopez
- Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Clement K. M. Tsui
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
- Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
5
|
Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Author Correction: Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2023; 14:6755. [PMID: 37875479 PMCID: PMC10597988 DOI: 10.1038/s41467-023-42557-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
| |
Collapse
|
6
|
Hon P, Ko KKK, Chia JWZ, De PP, Smits THM, Low J, Vasoo S, Tsui CKM. Correction for Hon et al., "Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore". Microbiol Resour Announc 2023; 12:e0068923. [PMID: 37747234 PMCID: PMC10586140 DOI: 10.1128/mra.00689-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
|
7
|
Ben Abid F, Salah H, Sundararaju S, Dalil L, Abdelwahab AH, Salameh S, Ibrahim EB, Almaslmani MA, Tang P, Perez-Lopez A, Tsui CKM. Molecular characterization of Candida auris outbreak isolates in Qatar from patients with COVID-19 reveals the emergence of isolates resistant to three classes of antifungal drugs. Clin Microbiol Infect 2023; 29:1083.e1-1083.e7. [PMID: 37116861 PMCID: PMC10132836 DOI: 10.1016/j.cmi.2023.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/08/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
OBJECTIVES During the COVID-19 pandemic in Qatar, many patients who were severely ill were colonized and infected by Candida auris, an invasive multidrug-resistant yeast pathogen that spreads through nosocomial transmission within healthcare facilities. Here, we investigated the molecular epidemiology of these C. auris isolates and the mechanisms associated with antifungal drug resistance. METHODS Whole genomes of 76 clinical C. auris isolates, including 65 from patients with COVID-19 collected from March 2020 to June 2021, from nine major hospitals were sequenced on Illumina NextSeq. Single nucleotide polymorphisms were used to determine their epidemiological patterns and mechanisms for antifungal resistance. The data were compared with those published prior to the COVID-19 pandemic from 2018 to 2020 in Qatar. RESULTS Genomic analysis revealed low genetic variability among the isolates from patients with and without COVID-19, confirming a clonal outbreak and ongoing dissemination of C. auris among various healthcare facilities. Based on antifungal susceptibility profiles, more than 70% (22/28) of isolates were resistant to both fluconazole and amphotericin B. Variant analysis revealed the presence of multi-antifungal resistant isolates with prominent amino acid substitutions: Y132F in ERG11 and V704L in CDR1 linked to reduced azole susceptibility and the emergence of echinocandin resistance samples bearing mutations in FKS1 in comparison with pre-COVID-19 pandemic samples. One sample (CAS109) was resistant to three classes of antifungal drugs with a unique premature stop codon in ERG3 and novel mutations in CDR2, which may be associated with elevated amphotericin B and azole resistance. DISCUSSION Candida auris isolates from patients with COVID-19 and from most patient samples without COVID-19 in Qatar were highly clonal. The data demonstrated the emergence of multidrug-resistant strains that carry novel mutations linked to enhanced resistance to azoles, echinocandins, and amphotericin B. Understanding the epidemiology and drug resistance will inform the infection control strategy and drug therapy.
Collapse
Affiliation(s)
- Fatma Ben Abid
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar; Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Husam Salah
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Lamya Dalil
- Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Ayman H Abdelwahab
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Sarah Salameh
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar; Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Emad B Ibrahim
- Division of Microbiology, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Muna A Almaslmani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Patrick Tang
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Andres Perez-Lopez
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar.
| | - Clement K M Tsui
- Weill Cornell Medicine-Qatar, Doha, Qatar; Division of Microbiology, Department of Pathology, Sidra Medicine, Doha, Qatar; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Infectious Diseases Research Laboratory, National Center for Infectious Diseases, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
| |
Collapse
|
8
|
Hon P, Ko KKK, Zhong JCW, De PP, Smits THM, Low J, Vasoo S, Tsui CKM. Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore. Microbiol Resour Announc 2023; 12:e0016723. [PMID: 37166299 PMCID: PMC10281117 DOI: 10.1128/mra.00167-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023] Open
Abstract
We report the draft genome sequences of two Phytobacter diazotrophicus isolates recovered from a swab specimen from the water faucet located in the Neonatal Intensive Care Unit (ICU), National University Hospital, Singapore. The isolates were misidentified as Cronobacter sakazakii and Klebsiella oxytoca using biochemical methods. Whole-genome sequencing (WGS) was performed to determine their identity.
Collapse
Affiliation(s)
- Peiyun Hon
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Karrie K. K. Ko
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Partha P. De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Jiaming Low
- Department of Neonatology, National University Hospital, Singapore, Singapore
| | - Shawn Vasoo
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Clement K. M. Tsui
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
9
|
Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
Collapse
Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
10
|
Fan X, Tsui CKM, Chen X, Wang P, Liu ZJ, Yang CX. High prevalence of fluconazole resistant Candida tropicalis among candiduria samples in China: An ignored matter of concern. Front Microbiol 2023; 14:1125241. [PMID: 36937265 PMCID: PMC10017723 DOI: 10.3389/fmicb.2023.1125241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction The rapid rise of azole resistance in Candida tropicalis causing invasive infections has become a public health concern; however, the prevalence of resistant isolates in urine samples was not well studied, because the clinical significance of candiduria was not unambiguous due to possible host colonization. Methods We performed a 12-year laboratory-based surveillance study of C. tropicalis causing either invasive infection or candiduria and studied their susceptibility profiles to common antifungal drugs. The complete coding domain sequence of the ERG11 gene was amplified in all fluconazole resistant isolates, and aligned with the wild-type sequence to detect nucleotide mutations. Results A total of 519 unique C. tropicalis strains isolates, 69.9% of which were isolated from urine samples and remaining 30.1% were invasive strains. Overall, 16.5% isolates were confirmed to be resistant to fluconazole, of which 91.9% were cross-resistant voriconazole. Of note, at the beginning of surveillance (2010-2011), the fluconazole resistance rates were low in both candiduria and invasive groups (6.8% and 5.9%, respectively). However, the resistant rate in the candiduria group significantly increased to 29.5% since 2012-2013 (p = 0.001) and stayed high since then, whilst the resistance rate in the invasive group only showed a gradually increasing trends till 2021 (p > 0.05). Sequence analysis of ERG11 from fluconazole-resistant strains revealed the prevalence of A395T/W mutations were relatively low (16.7%) in the beginning but reached 87.5-100% after 2014. Moreover, the A395W heterozygous mutation isolates became predominant (>60% of resistant strains) after 2016, and indeed isolates carrying corresponding amino acid substitution (Y132F) was highly resistant to fluconazole with MIC50 exceeded 256 μg/ml. Conclusion Our study revealed high azole resistant rate in candiduria with its increasing trends observed much earlier than stains causing invasive infections. Given antimicrobial resistance as a critical "One Health" issue, the emergence of antifungal resistance in Candida species that are common commensal colonizers in the human body should be concerned.
Collapse
Affiliation(s)
- Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Clement K. M. Tsui
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Xi Chen
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Peng Wang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhen-jia Liu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Zhen-jia Liu,
| | - Chun-xia Yang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Chun-xia Yang,
| |
Collapse
|
11
|
Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2022; 13:7890. [PMID: 36550095 PMCID: PMC9780251 DOI: 10.1038/s41467-022-35452-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
Collapse
Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
| |
Collapse
|
12
|
Huang JJ, Chen XF, Tsui CKM, Pang CJ, Hu ZD, Shi Y, Wang WP, Cui LY, Xiao YL, Gong J, Fan X, Li YX, Zhang G, Xiao M, Xu YC. Persistence of an epidemic cluster of Rhodotorula mucilaginosa in multiple geographic regions in China and the emergence of a 5-flucytosine resistant clone. Emerg Microbes Infect 2022; 11:1079-1089. [PMID: 35343400 PMCID: PMC9009924 DOI: 10.1080/22221751.2022.2059402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rhodotorula mucilaginosa, an environmental yeast widely used in industry and agriculture, is also an opportunistic pathogen resistant to multi-antifungals. During the national surveillance in China, R. mucilaginosa has been documented from various hospitals and regions. At present, the molecular epidemiology of invasive infections caused by R. mucilaginosa and their resistance profiles to antifungals were unknown. Here we collected 49 strains from four hospitals located in different geographic regions from 2009 to 2019 in China, determined their genotypes using different molecular markers and quantified susceptibilities to various antifungals. Sequencing of ITS and D1/D2 regions in rDNA indicated that 73.5% (36/49) of clinical strains belong to same sequence type (rDNA type 2). Microsatellite (MT) genotyping with 15 (recently developed) tandem repeat loci identified 5 epidemic MT types, which accounted for 44.9% (22/49) of clinical strains, as well as 27 sporadic MT types. Microsatellite data indicated that the presence of an epidemic cluster including 35 strains (71.4%) repeatedly isolated in four hospitals for eight years. Single nucleotide variants (SNVs) from the whole genome sequence data also supported the clustering of these epidemic strains due to low pairwise distance. In addition, phylogenetic analysis of SNVs from these clinical strains, together with environmental and animal strains showed that the closely related epidemic cluster strains may be opportunistic, zoonotic pathogens. Also, molecular data indicated a possible clonal transmission of pan echinocandins-azoles-5-flucytosine resistant R. mucilaginosa strains in hospital H01. Our study demonstrated that R. mucilaginosa is a multi-drug resistant pathogen with the ability to cause nosocomial infection.
Collapse
Affiliation(s)
- Jing-Jing Huang
- 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.,Graduate School, 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
| | - Xin-Fei Chen
- 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.,Graduate School, 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
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Education City, Al Rayyan Municipality, Qatar.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.,Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Chong-Jie Pang
- Department of Infection Diseases, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Zhi-Dong Hu
- Department of Clinical Laboratories, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Wei-Ping Wang
- Department of Clinical Laboratory, Jinling Hospital, Medical School of Nanjing University, Nanjing, People's Republic of China
| | - Lan-Ying Cui
- Department of Laboratory Diagnosis, the first Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Yu-Ling Xiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Ying-Xing Li
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, People's Republic of China.,Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, People's Republic of China
| | - Ge Zhang
- 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
| | - 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
| | - Ying-Chun Xu
- 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
| |
Collapse
|
13
|
Tsui CKM, Sorrentino F, Narula G, Mendoza-Losana A, del Rio RG, Herrán EP, Lopez A, Bojang A, Zheng X, Remuiñán-Blanco MJ, Av-Gay Y. Hit Compounds and Associated Targets in Intracellular Mycobacterium tuberculosis. Molecules 2022; 27:molecules27144446. [PMID: 35889319 PMCID: PMC9324642 DOI: 10.3390/molecules27144446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is one of the most devastating infectious agents in the world. Chemical-genetic characterization through in vitro evolution combined with whole genome sequencing analysis was used identify novel drug targets and drug resistance genes in Mtb associated with its intracellular growth in human macrophages. We performed a genome analysis of 53 Mtb mutants resistant to 15 different hit compounds. We found nonsynonymous mutations/indels in 30 genes that may be associated with drug resistance acquisitions. Beyond confirming previously identified drug resistance mechanisms such as rpoB and lead targets reported in novel anti-tuberculosis drug screenings such as mmpL3, ethA, and mbtA, we have discovered several unrecognized candidate drug targets including prrB. The exploration of the Mtb chemical mutant genomes could help novel drug discovery and the structural biology of compounds and associated mechanisms of action relevant to tuberculosis treatment.
Collapse
Affiliation(s)
- Clement K. M. Tsui
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore 308442, Singapore
| | - Flavia Sorrentino
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Gagandeep Narula
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Alfonso Mendoza-Losana
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
- Department of Bioengineering and Aerospace Engineering, Carlos III University of Madrid, 28040 Madrid, Spain
| | - Ruben Gonzalez del Rio
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Esther Pérez Herrán
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Abraham Lopez
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Adama Bojang
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Xingji Zheng
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Modesto Jesus Remuiñán-Blanco
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Yossef Av-Gay
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- Correspondence: ; Tel.: +1-604-822-3432
| |
Collapse
|
14
|
Wang R, Tsui CKM, You C. Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China. J Fungi (Basel) 2022; 8:83. [PMID: 35050023 PMCID: PMC8781690 DOI: 10.3390/jof8010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.
Collapse
Affiliation(s)
- Rui Wang
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China;
| | - Clement K. M. Tsui
- Department of Pathology, Sidra Medicine, Doha 2713, Qatar;
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha 2713, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Chongjuan You
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing 100083, China;
| |
Collapse
|
15
|
Gao M, Xiong C, Gao C, Tsui CKM, Wang MM, Zhou X, Zhang AM, Cai L. Disease-induced changes in plant microbiome assembly and functional adaptation. Microbiome 2021; 9:187. [PMID: 34526096 PMCID: PMC8444440 DOI: 10.1186/s40168-021-01138-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/27/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. RESULTS The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants. CONCLUSIONS Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.
Collapse
Affiliation(s)
- Min Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Meng-Meng Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ai-Min Zhang
- Pepper Research Institute, Guizhou Provincial Academy of Agricultural Sciences, 550009, Guiyang, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
16
|
Barrett TM, Tsui CKM. Emerging fungal pathogen: Candida auris. Evol Med Public Health 2021; 9:246-247. [PMID: 34447574 DOI: 10.1093/emph/eoab021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/15/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Tyler M Barrett
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.,Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
17
|
Al Mana H, Sundararaju S, Tsui CKM, Perez-Lopez A, Yassine H, Al Thani A, Al-Ansari K, Eltai NO. Whole-Genome Sequencing for Molecular Characterization of Carbapenem-Resistant Enterobacteriaceae Causing Lower Urinary Tract Infection among Pediatric Patients. Antibiotics (Basel) 2021; 10:antibiotics10080972. [PMID: 34439022 PMCID: PMC8388976 DOI: 10.3390/antibiotics10080972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistance is a growing public health problem globally, incurring health and cost burdens. The occurrence of antibiotic-resistant bacterial infections has increased significantly over the years. Gram-negative bacteria display the broadest resistance range, with bacterial species expressing extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases. All carbapenem-resistant Enterobacteriaceae (CRE) isolates from pediatric urinary tract infections (UTIs) between October 2015 and November 2019 (n = 30). All isolates underwent antimicrobial resistance phenotypic testing using the Phoenix NMIC/ID-5 panel, and carbapenemase production was confirmed using the NG-Test CARBA 5 assay. Whole-genome sequencing was performed on the CREs. The sequence type was identified using the Achtman multi-locus sequence typing scheme, and antimicrobial resistance markers were identified using ResFinder and the CARD database. The most common pathogens causing CRE UTIs were E. coli (63.3%) and K. pneumoniae (30%). The most common carbapenemases produced were OXA-48-like enzymes (46.6%) and NDM enzymes (40%). Additionally, one E. coli harbored IMP-26, and two K. pneumoniae possessed mutations in ompK37 and/or ompK36. Lastly, one E. coli had a mutation in the marA porin and efflux pump regulator. The findings highlight the difference in CRE epidemiology in the pediatric population compared to Qatar's adult population, where NDM carbapenemases are more common.
Collapse
Affiliation(s)
- Hassan Al Mana
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; (H.A.M.); (H.Y.); (A.A.T.)
| | - Sathyavathi Sundararaju
- Division of Microbiology, Department of Pathology Sidra Medicine, Doha 2713, Qatar; (S.S.); (C.K.M.T.); (A.P.-L.)
| | - Clement K. M. Tsui
- Division of Microbiology, Department of Pathology Sidra Medicine, Doha 2713, Qatar; (S.S.); (C.K.M.T.); (A.P.-L.)
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College in Qatar, Doha 2713, Qatar;
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andres Perez-Lopez
- Division of Microbiology, Department of Pathology Sidra Medicine, Doha 2713, Qatar; (S.S.); (C.K.M.T.); (A.P.-L.)
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College in Qatar, Doha 2713, Qatar;
| | - Hadi Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; (H.A.M.); (H.Y.); (A.A.T.)
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar
| | - Asmaa Al Thani
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; (H.A.M.); (H.Y.); (A.A.T.)
| | - Khalid Al-Ansari
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College in Qatar, Doha 2713, Qatar;
- Department of Emergency, Sidra Medicine, Doha 2713, Qatar
| | - Nahla O. Eltai
- Biomedical Research Center, Qatar University, Doha 2713, Qatar; (H.A.M.); (H.Y.); (A.A.T.)
- Correspondence:
| |
Collapse
|
18
|
Liang J, Liu X, Tsui CKM, Ma Z, Luo Y. Genetic Structure and Asymmetric Migration of Wheat Stripe Rust Pathogen in Western Epidemic Areas of China. Phytopathology 2021; 111:1252-1260. [PMID: 33210988 DOI: 10.1094/phyto-06-20-0236-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Puccinia striiformis f. sp. tritici causes severe global epidemics of wheat stripe rust primarily by airborne urediniospores. Understanding long-distance migration patterns of P. striiformis f. sp. tritici is critical for disease forecasting and management. Although the western epidemic areas in China have been considered as the source of inoculum spread eastward across the country, migration pathways among different populations within the western epidemic areas are poorly understood. In this study, we investigated the population genetics of 200 P. striiformis f. sp. tritici isolates from western epidemic areas using amplified fragment length polymorphism and simple sequence repeat markers. A coalescent approach was also used to calculate the migration rates among populations. Data analyses with both marker systems indicated high genetic diversity in each regional population. The Mantel test revealed significant positive correlation between genetic and geographic distances. Both discriminant analysis of principal components and STRUCTURE analysis supported moderate population structure shaped by seasonality and geography. The calculated migration rates indicated the presence of asymmetric migration between major populations in western epidemic areas, with greater migration rates from high elevation, oversummering areas to low elevation, overwintering areas. Sichuan Basin, one of the low elevation, overwintering areas, sampled in both fall and spring, was inferred as a recipient in fall but a donor in spring. Migration among P. striiformis f. sp. tritici populations may be partly attributable to terrace farming and prevailing wind direction in different seasons. Our study provides a better understanding of fine-scale population structure and the interregional migration pattern of P. striiformis f. sp. tritici in northwestern China and will inform future rust management.
Collapse
Affiliation(s)
- Junmin Liang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiufeng Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yong Luo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
19
|
Al Malki A, Brumfield KD, Tsui CKM, Anand A, Rashed SM, Ibrahim E, Al Shamari H, Huq A, Colwell RR, Fotedar R. Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar. Microbiol Resour Announc 2021; 10:e01489-20. [PMID: 33664147 PMCID: PMC7936645 DOI: 10.1128/mra.01489-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/11/2021] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequences of seven Vibrio cholerae isolates from patients. Four isolates were profiled as multilocus sequence type 69, serogroup O1, a subset of seventh-pandemic El Tor clonal isolates. Presented here are genome assemblies and evidence for major pathogenicity islands, virulence factors, and antimicrobial resistance genes.
Collapse
Affiliation(s)
- Ameena Al Malki
- Department of Genetic Engineering, Biotechnology Centre, Doha, Qatar
| | - Kyle D Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
- University of Maryland Institute for Advance Computer Studies, University of Maryland, College Park, Maryland, USA
| | - Clement K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Anjana Anand
- Department of Genetic Engineering, Biotechnology Centre, Doha, Qatar
| | - Shah M Rashed
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Emad Ibrahim
- Department of Microbiology, Hamad Medical Corporation, Doha, Qatar
- Qatar University, Biomedical Research Centre, Doha, Qatar
| | - Hamad Al Shamari
- Department of Genetic Engineering, Biotechnology Centre, Doha, Qatar
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
- University of Maryland Institute for Advance Computer Studies, University of Maryland, College Park, Maryland, USA
| | - Rashmi Fotedar
- Department of Genetic Engineering, Biotechnology Centre, Doha, Qatar
| |
Collapse
|
20
|
Abid FB, Tsui CKM, Doi Y, Deshmukh A, McElheny CL, Bachman WC, Fowler EL, Albishawi A, Mushtaq K, Ibrahim EB, Doiphode SH, Hamed MM, Almaslmani MA, Alkhal A, Butt AA, Omrani AS. Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar. Eur J Clin Microbiol Infect Dis 2021; 40:1779-1785. [PMID: 33616788 PMCID: PMC8295067 DOI: 10.1007/s10096-021-04185-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/03/2021] [Indexed: 02/08/2023]
Abstract
One hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).
Collapse
Affiliation(s)
- Fatma Ben Abid
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar. .,Communicable Diseases Center, Hamad Medical Corporation, PO Box 3050, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar.
| | - Clement K M Tsui
- Weill Cornell Medicine-Qatar, Doha, Qatar.,Department of Pathology, Sidra Medicine, Doha, Qatar.,Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
| | - Anand Deshmukh
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Christi L McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - William C Bachman
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Erin L Fowler
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ahmed Albishawi
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar.,Communicable Diseases Center, Hamad Medical Corporation, PO Box 3050, Doha, Qatar
| | - Kamran Mushtaq
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Emad B Ibrahim
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Sanjay H Doiphode
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Manal M Hamed
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Muna A Almaslmani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar.,Communicable Diseases Center, Hamad Medical Corporation, PO Box 3050, Doha, Qatar
| | - Abdullatif Alkhal
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar.,Communicable Diseases Center, Hamad Medical Corporation, PO Box 3050, Doha, Qatar
| | - Adeel A Butt
- Weill Cornell Medicine-Qatar, Doha, Qatar.,Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Ali S Omrani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar.,Communicable Diseases Center, Hamad Medical Corporation, PO Box 3050, Doha, Qatar.,Clinical Epidemiology Research Unit, Hamad Medical Corporation, Doha, Qatar
| |
Collapse
|
21
|
Yang H, You CJ, Tsui CKM, Tembrock LR, Wu ZQ, Yang DP. Phylogeny and biogeography of the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers. Ecol Evol 2021; 11:153-173. [PMID: 33437420 PMCID: PMC7790660 DOI: 10.1002/ece3.6982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/05/2022] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.
Collapse
Affiliation(s)
- Huan Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Chong Juan You
- Beijing Key Laboratory for Forest Pest ControlBeijing Forestry UniversityBeijingChina
| | - Clement K. M. Tsui
- Department of PathologySidra MedicineDohaQatar
- Department of Pathology and Laboratory MedicineWeill Cornell Medicine‐QatarAr‐RayyanQatar
- Division of Infectious DiseasesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Luke R. Tembrock
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Zhi Qiang Wu
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - De Po Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| |
Collapse
|
22
|
Tsui CKM, Sundararaju S, Mana HA, Hasan MR, Tang P, Perez-Lopez A. Corrigendum to "Plasmid-mediated colistin resistance encoded by mcr-1 gene in Escherichia coli co-carrying bla CTX-M-15 and bla NDM-1 genes in pediatric patients in Qatar" [J Global Antimicrob Resist 22 (2020) 662-663]. J Glob Antimicrob Resist 2020; 23:472. [PMID: 33357977 DOI: 10.1016/j.jgar.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Clement K M Tsui
- Department of Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | | | - Hassan Al Mana
- Department of Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Andres Perez-Lopez
- Department of Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| |
Collapse
|
23
|
Huang C, Tsui CKM, Chen M, Pan K, Li X, Wang L, Chen M, Zheng Y, Zheng D, Chen X, Jiang L, Wei L, Liao W, Cao C. Emerging Cryptococcus gattii species complex infections in Guangxi, southern China. PLoS Negl Trop Dis 2020; 14:e0008493. [PMID: 32845884 PMCID: PMC7449396 DOI: 10.1371/journal.pntd.0008493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
The emergence and spread of cryptococcosis caused by the Cryptococcus gattii species complex has become a major public concern worldwide. C. deuterogattii (VGIIa) outbreaks in the Pacific Northwest region demonstrate the expansion of this fungal infection to temperate climate regions. However, infections due to the C. gattii species complex in China have rarely been reported. In this study, we studied eleven clinical strains of the C. gattii species complex isolated from Guangxi, southern China. The genetic identity and variability of these isolates were analyzed via multi-locus sequence typing (MLST), and the phylogenetic relationships among these isolates and global isolates were evaluated. The mating type, physiological features and antifungal susceptibilities of these isolates were also characterized. Among the eleven isolates, six belonged to C. deuterogattii, while five belonged to C. gattii sensu stricto. The C. deuterogattii strains from Guangxi, southern China were genetically variable and clustered with different clinical isolates from Brazil. All strains were MATα, and three C. deuterogattii isolates (GX0104, GX0105 and GX0147) were able to undergo sexual reproduction. Moreover, most strains had capsule and were capable of melanin production when compared to the outbreak strain from Canada. Most isolates were susceptible to antifungal drugs; yet one of eleven immunocompetent patients died of cryptococcal meningitis caused by C. deuterogattii (GX0147). Our study indicated that the highly pathogenic C. deuterogattii may be emerging in southern China, and effective nationwide surveillance of C. gattii species complex infection is necessary. Cryptococcosis is a fatal systemic fungal disease caused by Cryptococcus neoformans/gattii species complexes. As a former member of the C. neoformans, C. gattii had been easily neglected before being elevated to species level. Human C. gattii species complex infection was previously confined to the tropical and subtropical regions worldwide. However, in 1999, an outbreak of C. gattii species complex occurred on Vancouver Island in Canada then expanded to the Pacific Northwest in the USA, causing over 200 infections. The highly virulent, highly pathogenic and more resistant to antifungal drugs of this species have become a therapeutic problem. To initiate a better understanding of the infection characteristics and pathogenicity of C. gattii species complex in Guangxi, southern China, the current study aimed to characterize the C. gattii species complex isolates genetically and phenotypically. The ISHAM consensus MLST scheme was utilized to investigate the genetic structure of C. gattii species complex and to correlate their geographic origin, clinical source, virulence factors and antifungal susceptibility. The authors expect that this work can support surveillance and encourage more research and public health initiatives to prevent and control the cryptococcosis cause by C. gattii species complex.
Collapse
Affiliation(s)
- Chunyang Huang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Clement K. M. Tsui
- Department of Pathology, Sidra Medicine, Qatar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine–Qatar, Doha, Qatar
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Kaisu Pan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Xiuying Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Meini Chen
- Clinical Medicine (8-year program), XiangYa School of Medicine, Central South University, Changsha, P. R. China
| | - Yanqing Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Dongyan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Xingchun Chen
- The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, P. R. China
| | - Li Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Lili Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
- * E-mail: (WL); (CC)
| | - Cunwei Cao
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
- * E-mail: (WL); (CC)
| |
Collapse
|
24
|
Jiang Y, Tsui CKM, Ahmed SA, Hagen F, Shang Z, Gerrits van den Ende AHG, Verweij PE, Lu H, de Hoog GS. Intraspecific Diversity and Taxonomy of Emmonsia crescens. Mycopathologia 2020; 185:613-627. [PMID: 32710392 DOI: 10.1007/s11046-020-00475-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/06/2020] [Indexed: 12/24/2022]
Abstract
Emmonsia crescens is known as an environmental pathogen causing adiaspiromycosis in small rodents. As the generic name Emmonsia is no longer available for this species, its taxonomic position is re-evaluated. The intraspecific variation of Emmonsia crescens was analyzed using molecular, morphological, and physiological data, and the relationship between frequency of adiaspiromycosis and body temperature of host animals was explored. A North American and a pan-global lineage could be discerned, each with subclusters at low genetic distance. European strains produced the classical type of very large adiaspores, while in the North American lineage adiaspores relatively small, resembling the broad-based budding cells of Blastomyces. Members of the closely related genus Emergomyces may exhibit large, broad-based in addition to small, narrow-based budding cells. We conclude that the morphology of the pathogenic phase in these fungi differs gradationally between species and even populations, and is therefore less suitable as a diagnostic criterion for generic delimitation. Two Emmonsia species are reclassified in Emergomyces.
Collapse
Affiliation(s)
- Y Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China. .,Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
| | - C K M Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.,Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - S A Ahmed
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - F Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Z Shang
- Department of Immunology, Basic Medical School, Guizhou Medical University, Guiyang, China
| | | | - P E Verweij
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - H Lu
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China.
| | - G S de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| |
Collapse
|
25
|
Tsui CKM, Sundararaju S, Mana HA, Hasan MR, Tang P, Perez-Lopez A. Plasmid-mediated colistin resistance encoded by mcr-1 gene in Escherichia coli co-carrying bla CTX-M-15 and bla NDM-1 genes in pediatric patients in Qatar. J Glob Antimicrob Resist 2020; 22:662-663. [PMID: 32650133 DOI: 10.1016/j.jgar.2020.06.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Clement K M Tsui
- Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | | | - Hassan Al Mana
- Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713 Doha, Qatar
| | - Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Andres Perez-Lopez
- Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar
| |
Collapse
|
26
|
Moure AL, Narula G, Sorrentino F, Bojang A, Tsui CKM, Sao Emani C, Porras-De Francisco E, Díaz B, Rebollo-López MJ, Torres-Gómez PA, López-Román EM, Camino I, Casado Castro P, Guijarro López L, Ortega F, Ballell L, Barros-Aguirre D, Remuiñán Blanco M, Av-Gay Y. MymA Bioactivated Thioalkylbenzoxazole Prodrug Family Active against Mycobacterium tuberculosis. J Med Chem 2020; 63:4732-4748. [DOI: 10.1021/acs.jmedchem.0c00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Abraham L. Moure
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | - Flavia Sorrentino
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | | | | | - Esther Porras-De Francisco
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Beatriz Díaz
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - María José Rebollo-López
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Pedro Alfonso Torres-Gómez
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Eva María López-Román
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Isabel Camino
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Patricia Casado Castro
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Laura Guijarro López
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Fátima Ortega
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - David Barros-Aguirre
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Modesto Remuiñán Blanco
- Diseases of the Developing World (DDW), Global Health Catalyst, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | |
Collapse
|
27
|
Tsui CKM, Hyde KD, Hodgkiss IJ. Paraniesslia tuberculata gen. et sp. nov., and new records or species of Clypeosphaeria, Leptosphaeria and Astrosphaeriella in Hong Kong freshwater habitats. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Clement K. M. Tsui
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kevin D. Hyde
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - I. John Hodgkiss
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| |
Collapse
|
28
|
Tsui CKM, Goh TK, Hyde KD, Hodgkiss IJ. New species or records of Cacumisporium, Helicosporium, Monotosporella and Bahusutrabeeja on submerged wood in Hong Kong streams. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Clement K. M. Tsui
- Center for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Teik Khiang Goh
- Center for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kevin D. Hyde
- Center for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - I. John Hodgkiss
- Center for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| |
Collapse
|
29
|
Ranghoo VM, Hyde KD, Wong SW, Tsui CKM, Jones EBG. Vertexicola caudatusgen. et sp. nov., and a new species ofRivulicolafrom submerged wood in freshwater habitats. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- V. Mala Ranghoo
- Centre for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Kevin D. Hyde
- Centre for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Sze-Wing Wong
- Centre for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Clement K. M. Tsui
- Centre for Research in Fungal Diversity, Department of Ecology and Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - E. B. Gareth Jones
- BIOTEC, National Centre for Genetical Engineering and Biotechnology, 73/1 Rama 6 Road, Bangkok 10400, Thailand
| |
Collapse
|
30
|
Xu W, Peng J, Li D, Tsui CKM, Long Z, Wang Q, Mei H, Liu W. Transcriptional profile of the human skin pathogenic fungus Mucor irregularis in response to low oxygen. Med Mycol 2019; 56:e2. [PMID: 29182775 DOI: 10.1093/mmy/myx132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Wenqi Xu
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Jingwen Peng
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Zhimin Long
- Demo Lab, Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, IBP, Shanghai, 200335, People's Republic of China
| | - Qiong Wang
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Huan Mei
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Weida Liu
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| |
Collapse
|
31
|
Leal I, Bergeron MJ, Feau N, Tsui CKM, Foord B, Pellow K, Hamelin RC, Sturrock RN. Cryptic Speciation in Western North America and Eastern Eurasia of the Pathogens Responsible for Laminated Root Rot. Phytopathology 2019; 109:456-468. [PMID: 30145938 DOI: 10.1094/phyto-12-17-0399-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coniferiporia sulphurascens is a facultative fungal pathogen that causes laminated root rot (LRR) in commercially important coniferous species worldwide. This fungus spreads primarily by way of vegetative mycelium transferring at points of contact between infected and healthy roots. Successful intervention to control LRR requires a better understanding of the population structure and genetic variability of C. sulphurascens. In this study, we investigated the population genetic structure and origin of C. sulphurascens populations in western North America and eastern Eurasia collected from multiple coniferous hosts. By analyzing the small and large mitochondrial ribosomal RNA subunit genes combined with six nuclear loci (internal transcribed spacer region, actin, RNA polymerase II largest subunit, RNA polymerase II second-largest subunit, laccase-like multicopper oxidase, and translation elongation factor 1-α), we observed that none of the alleles among the loci were shared between North American (NA) and Eurasian C. sulphurascens populations. In total, 55 multilocus genotypes (MLGs) were retrieved in C. sulphurascens isolates occurring in these two continental regions. Of these, 41 MLGs were observed among 58 isolates collected from widespread locations in British Columbia (Canada) and the northwestern United States, while 14 MLGs were observed among 16 isolates sampled in Siberia and Japan. Our data showed that the levels of genetic differentiation between the NA and Eurasian populations are much greater than the populations from within each continental region; the two continental populations formed clearly divergent phylogenetic clades or lineages since they were separated approximately 7.5 million years ago. Moreover, the Eurasian population could be the source of the NA population. Our study indicates the existence of cryptic diversity in this pathogen species, and strongly suggests that the NA and Eurasian populations represent two lineages, which have progressively diverged from each other in allopatry.
Collapse
Affiliation(s)
- I Leal
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - M-J Bergeron
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - N Feau
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - C K M Tsui
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - B Foord
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - K Pellow
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R C Hamelin
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R N Sturrock
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| |
Collapse
|
32
|
Xu W, Peng J, Li D, Tsui CKM, Long Z, Wang Q, Mei H, Liu W. Transcriptional profile of the human skin pathogenic fungus Mucor irregularis in response to low oxygen. Med Mycol 2018; 56:631-644. [PMID: 29420826 DOI: 10.1093/mmy/myx081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Mucormycosis is one of the most invasive mycosis and has caused global concern in public health. Cutaneous mucormycosis caused by Mucor irregularis (formerly Rhizomucor variabilis) is an emerging disease in China. To survive in the human body, M. irregularis must overcome the hypoxic (low oxygen) host microenvironment. However, the exact molecular mechanism of its pathogenicity and adaptation to low oxygen stress environment is relatively unexplored. In this study, we used Illumina HiSeq technology (RNA-Seq) to determine and compare the transcriptome profile of M. irregularis CBS103.93 under normal growth condition and hypoxic stress. Our analyses demonstrated a series of genes involved in TCA, glyoxylate cycle, pentose phosphate pathway, and GABA shunt were down-regulated under hypoxic condition, while certain genes in the lipid/fatty acid metabolism and endocytosis were up-regulated, indicating that lipid metabolism was more active under hypoxia. Comparing the data with other important human pathogenic fungi such as Aspergillus spp., we found that the gene expression pattern and metabolism in responses to hypoxia in M. irregularis were unique and different. We proposed that these metabolic changes can represent a species-specific hypoxic adaptation in M. irregularis, and we hypothesized that M. irregularis could use the intra-lipid pool and lipid secreted in the infection region, as an extracellular nutrient source to support its hypoxic growth. Characterizing the significant differential gene expression in this species could be beneficial to uncover their role in hypoxia adaptation and fungalpathogenesis and further facilitate the development of novel targets in disease diagnosis and treatment against mucormycosis.
Collapse
Affiliation(s)
- Wenqi Xu
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Jingwen Peng
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Clement K M Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Zhimin Long
- Demo Lab, Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, IBP, Shanghai, 200335, People's Republic of China
| | - Qiong Wang
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Huan Mei
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| | - Weida Liu
- Department of Mycology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, Jiangsu, People's Republic of China
| |
Collapse
|
33
|
Ojeda Alayon DI, Tsui CKM, Feau N, Capron A, Dhillon B, Zhang Y, Massoumi Alamouti S, Boone CK, Carroll AL, Cooke JEK, Roe AD, Sperling FAH, Hamelin RC. Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts. Mol Ecol 2017; 26:2077-2091. [PMID: 28231417 DOI: 10.1111/mec.14074] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 12/08/2016] [Accepted: 02/09/2017] [Indexed: 12/19/2022]
Abstract
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defences and modifying host tissues to favour brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype-environment association analysis and phenotypic characterization of growth rate under different temperatures. We found that genetic variation and population structure within each species is best explained by distinct spatial and environmental variables. We observed both common (temperature seasonality and the host species) and distinct (drought, cold stress, precipitation) environmental and spatial factors that shaped the genomes of these fungi resulting in contrasting outcomes. Phenotypic intraspecific variations in Grosmannia clavigera and Leptographium longiclavatum, together with high heritability, suggest potential for adaptive selection in these species. By contrast, Ophiostoma montium displayed narrower intraspecific variation but greater tolerance to extreme high temperatures. Our study highlights unique phenotypic and genotypic characteristics in these symbionts that are consistent with our hypothesis. By maintaining this multipartite relationship, the bark beetles have a greater likelihood of obtaining the benefits afforded by the fungi and reduce the risk of being left aposymbiotic. Complementarity among species could facilitate colonization of new habitats and survival under adverse conditions.
Collapse
Affiliation(s)
- Dario I Ojeda Alayon
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Clement K M Tsui
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Arnaud Capron
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Yiyuan Zhang
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Sepideh Massoumi Alamouti
- Department of Wood Science, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Celia K Boone
- Ecosystem Science and Management Program, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada, V2N 4Z9
| | - Allan L Carroll
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2R3
| | - Amanda D Roe
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2R3.,Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen St E, Sault Ste. Marie, ON, Canada, P6A 2E5
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2R3
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4.,Institut de Biologie Intégrative des Systèmes, Université Laval, 1030 Avenue de la Médecine, Québec City, QC, Canada, G1V 0A6
| |
Collapse
|
34
|
Deng S, Tsui CKM, Gerrits van den Ende AHG, Yang L, Najafzadeh MJ, Badali H, Li R, Hagen F, Meis JF, Sun J, Dolatabadi S, Papierok B, Pan W, de Hoog GS, Liao W. Global Spread of Human Chromoblastomycosis Is Driven by Recombinant Cladophialophora carrionii and Predominantly Clonal Fonsecaea Species. PLoS Negl Trop Dis 2015; 9:e0004004. [PMID: 26496430 PMCID: PMC4619687 DOI: 10.1371/journal.pntd.0004004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/22/2015] [Indexed: 12/20/2022] Open
Abstract
Global distribution patterns of Cladophialophora carrionii, agent of human chromoblastomycosis in arid climates of Africa, Asia, Australia, Central-and South-America, were compared with similar data of the vicarious Fonsecaea spp., agents of the disease in tropical rain forests. Population diversities among 73 C. carrionii strains and 60 strains of three Fonsecaea species were analyzed for rDNA ITS, partial β-tubulin, and amplified fragment-length polymorphism (AFLP) fingerprints. Populations differed significantly between continents. Lowest haplotype diversity was found in South American populations, while African strains were the most diverse. Gene flow was noted between the African population and all other continents. The general pattern of Fonsecaea agents of chromoblastomycosis differed significantly from that of C. carrionii and revealed deeper divergence among three differentiated species with smaller numbers of haplotypes, indicating a longer evolutionary history.
Collapse
Affiliation(s)
- Shuwen Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Shanghai, China
- First Hospital of Xinjiang Medical University, Xinjiang, China
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Clement K. M. Tsui
- British Columbia Public Health Microbiology & Reference Laboratory at BCCDC site, Provincial Health Services Authority, Vancouver, Canada
| | | | - Liyue Yang
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Mohammad Javad Najafzadeh
- Department of Parasitology and Mycology & Cancer Molecular Pathology Research Center, Ghaem Hospital, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Badali
- Department of Medical Mycology and Parasitology / Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ruoyu Li
- Research Center for Medical Mycology, Beijing Medical University, Beijing, China
| | - Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Somayeh Dolatabadi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | | | - Weihua Pan
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Shanghai, China
| | - G. S. de Hoog
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Shanghai, China
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Research Center for Medical Mycology, Beijing Medical University, Beijing, China
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
- King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (GSdH); (WL)
| | - Wanqing Liao
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Shanghai, China
- * E-mail: (GSdH); (WL)
| |
Collapse
|
35
|
Brar S, Tsui CKM, Dhillon B, Bergeron MJ, Joly DL, Zambino PJ, El-Kassaby YA, Hamelin RC. Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen. PLoS One 2015; 10:e0127916. [PMID: 26010250 PMCID: PMC4444259 DOI: 10.1371/journal.pone.0127916] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/20/2015] [Indexed: 11/19/2022] Open
Abstract
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.
Collapse
Affiliation(s)
- Simren Brar
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Clement K. M. Tsui
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marie-Josée Bergeron
- Natural Resources Canada, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| | - David L. Joly
- Département de Biologie, Université de Moncton, Moncton, New Brunswick, Canada
| | - P. J. Zambino
- USDA Forest Service, Coeur d'Alene Field Office, Coeur d'Alene, Idaho, United States of America
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Natural Resources Canada, Laurentian Forestry Centre, Quebec City, Quebec, Canada
| |
Collapse
|
36
|
Ojeda DI, Dhillon B, Tsui CKM, Hamelin RC. Single-nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing. Mol Ecol Resour 2013; 14:401-10. [PMID: 24152017 DOI: 10.1111/1755-0998.12191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are rapidly becoming the standard markers in population genomics studies; however, their use in nonmodel organisms is limited due to the lack of cost-effective approaches to uncover genome-wide variation, and the large number of individuals needed in the screening process to reduce ascertainment bias. To discover SNPs for population genomics studies in the fungal symbionts of the mountain pine beetle (MPB), we developed a road map to discover SNPs and to produce a genotyping platform. We undertook a whole-genome sequencing approach of Leptographium longiclavatum in combination with available genomics resources of another MPB symbiont, Grosmannia clavigera. We sequenced 71 individuals pooled into four groups using the Illumina sequencing technology. We generated between 27 and 30 million reads of 75 bp that resulted in a total of 1, 181 contigs longer than 2 kb and an assembled genome size of 28.9 Mb (N50 = 48 kb, average depth = 125x). A total of 9052 proteins were annotated, and between 9531 and 17,266 SNPs were identified in the four pools. A subset of 206 genes (containing 574 SNPs, 11% false positives) was used to develop a genotyping platform for this species. Using this roadmap, we developed a genotyping assay with a total of 147 SNPs located in 121 genes using the Illumina(®) Sequenom iPLEX Gold. Our preliminary genotyping (success rate = 85%) of 304 individuals from 36 populations supports the utility of this approach for population genomics studies in other MPB fungal symbionts and other fungal nonmodel species.
Collapse
Affiliation(s)
- Dario I Ojeda
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | | | | | | |
Collapse
|
37
|
Tsui CKM, Roe AD, El-Kassaby YA, Rice AV, Alamouti SM, Sperling FAH, Cooke JEK, Bohlmann J, Hamelin RC. Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle. Mol Ecol 2011; 21:71-86. [PMID: 22118059 DOI: 10.1111/j.1365-294x.2011.05366.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect-fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north-south differentiation of MPB and G. clavigera populations points to the fungal pathogen's dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus-beetle association is important for the modelling and prediction of MPB epidemics.
Collapse
Affiliation(s)
- Clement K M Tsui
- Department of Forest Sciences, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Tsui CKM, Wang B, Khadempour L, Alamouti SM, Bohlmann J, Murray BW, Hamelin RC. Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes. J Microbiol Methods 2010; 83:26-33. [PMID: 20650291 DOI: 10.1016/j.mimet.2010.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/10/2010] [Accepted: 07/10/2010] [Indexed: 11/16/2022]
Abstract
Fifteen million hectares of pine forests in western Canada have been attacked by the mountain pine beetle (Dendroctonus ponderosae; MPB), leading to devastating economic losses. Grosmannia clavigera and Leptographium longiclavatum, are two fungi intimately associated with the beetles, and are crucial components of the epidemic. To detect and discriminate these two closely related pathogens, we utilized a method based on ligase-mediated nucleotide discrimination with padlock probe technology, and signal amplification by hyperbranched rolling circle amplification (HRCA). Two padlock probes were designed to target species-specific single nucleotide polymorphisms (SNPs) located at the inter-generic spacer 2 region and large subunit of the rRNA respectively, which allows discrimination between the two species. Thirty-four strains of G. clavigera and twenty-five strains of L. longiclavatum representing a broad geographic origin were tested with this assay. The HRCA results were largely in agreement with the conventional identification based on morphology or DNA-based methods. Both probes can also efficiently distinguish the two MPB-associated fungi from other fungi in the MPB, as well as other related fungi in the order Ophiostomatales. We also tested this diagnostic method for the direct detection of these fungi from the DNA of MPB. A nested PCR approach was used to enrich amplicons for signal detection. The results confirmed the presence of these two fungi in MPB. Thus, the padlock probe assay coupled with HRCA is a rapid, sensitive and reproducible method for the identification and detection of these ophiostomatoid fungi.
Collapse
Affiliation(s)
- Clement K M Tsui
- Department of Forest Science, University of British Columbia, Vancouver, BC, Canada.
| | | | | | | | | | | | | |
Collapse
|
39
|
Tsui CKM, Marshall W, Yokoyama R, Honda D, Lippmeier JC, Craven KD, Peterson PD, Berbee ML. Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding. Mol Phylogenet Evol 2008; 50:129-40. [PMID: 18977305 DOI: 10.1016/j.ympev.2008.09.027] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 09/23/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
The labyrinthulomycetes, also known as the 'Labyrinthulomycota' are saprotrophic or less frequently parasitic stramenopilan protists, usually in marine ecosystems. Their distinguishing feature is an 'ectoplasmic net,' an external cytoplasmic network secreted by a specialized organelle that attaches the cell to its substrate and secretes digestive enzymes for absorptive nutrition. In this study, one of our aims was to infer the phylogenetic position of the labyrinthulomycetes relative to the non-photosynthetic bicoeceans and oomycetes and the photosynthetic ochrophytes and thereby evaluate patterns of change from photosynthesis to saprotrophism among the stramenopiles. For the labyrinthulomycetes, we determined sequences of the actin, beta-tubulin, and elongation factor 1-alpha gene fragments and where necessary, ribosomal small subunit (SSU) genes. Multilocus analysis using standard tree construction techniques not only strongly supported the oomycetes as the sister group to the phototrophic stramenopiles, but also, for the first time with moderate statistical support, showed that the labyrinthulomycetes and the bicoecean as sister groups. The paraphyly of the non-photosynthetic groups was consistent with independent loss of photosynthesis in labyrinthulomycetes and oomycetes. We also wished to develop a phylogenetically based hypothesis for the origin of the gliding cell bodies and the ectoplasmic net found in some labyrinthulomycetes. The cells of species in Labyrinthula and Aplanochytrium share a specialized form of motility involving gliding on ectoplasmic tracks. Before our study, only ribosomal DNA genes had been determined for these genera and their phylogenetic position in the labyrinthulomycetes was equivocal. Multilocus phylogenies applying our newly determined protein-coding sequences divided the labyrinthulomycetes between sister clades 'A' and 'B' and showed that the monophyletic group containing all of the gliding species was nested among non-gliding species in clade B. This phylogeny suggested that species that glide via an ectoplasm evolved from species that had used the ectoplasm mainly for anchorage and assimilation rather than motility.
Collapse
Affiliation(s)
- Clement K M Tsui
- Department of Botany, #3529-6270 University Blvd., The University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Tsui CKM, Daniel HM, Robert V, Meyer W. Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses. FEMS Yeast Res 2008; 8:651-9. [PMID: 18248416 DOI: 10.1111/j.1567-1364.2007.00342.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not clearly resolved. Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually reproducing genera were therefore selected, and their phylogenetic relationships were investigated using nuclear sequences of the largest subunit and second largest subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the recognition of six major phylogenetic groups (A-F). Group A contains six facultative pathogenic Candida species, which seem to have derived from nonpathogenic species, while Group B contains species of Clavispora, Metschnikowia, and Pichia guilliermondii. Species of Debaryomyces form an independent group C that is related to groups A and B. Pichia fermentans and other environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex.
Collapse
Affiliation(s)
- Clement K M Tsui
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Westmead, NSW, Australia
| | | | | | | |
Collapse
|
41
|
Abstract
Three genera of asexual, helical-spored fungi, Helicoma, Helicomyces and Helicosporium traditionally have been differentiated by the morphology of their conidia and conidiophores. In this paper we assessed their phylogenetic relationships from ribosomal sequences from ITS, 5.8S and partial LSU regions using maximum parsimony, maximum likelihood and Bayesian analysis. Forty-five isolates from the three genera were closely related and were within the teleomorphic genus Tubeufia sensu Barr (Tubeufiaceae, Ascomycota). Most of the species could be placed in one of the seven clades that each received 78% or greater bootstrap support. However none of the anamorphic genera were monophyletic and all but one of the clades contained species from more than one genus. The 15 isolates of Helicoma were scattered through the phylogeny and appeared in five of the clades. None of the four sections within the genus were monophyletic, although species from Helicoma sect. helicoma were concentrated in Clade A. The Helicosporium species also appeared in five clades. The four Helicomyces species were distributed among three clades. Most of the clades supported by sequence data lacked unifying morphological characters. Traditional characters such as the thickness of the conidial filament and whether conidiophores were conspicuous or reduced proved to be poor predictors of phylogenetic relationships. However some combinations of characters including conidium colour and the presence of lateral, tooth-like conidiogenous cells did appear to be predictive of genetic relationships.
Collapse
Affiliation(s)
- Clement K M Tsui
- Department of Botany, University of British Columbia, Vancouver, Canada.
| | | | | |
Collapse
|
42
|
Tsui CKM, Berbee ML. Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences. Mol Phylogenet Evol 2006; 39:587-97. [PMID: 16529956 DOI: 10.1016/j.ympev.2006.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 09/21/2005] [Accepted: 01/23/2006] [Indexed: 11/28/2022]
Abstract
Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.
Collapse
Affiliation(s)
- C K M Tsui
- Department of Botany, The University of British Columbia, #3529-6270 University Blvd., Vancouver, BC, Canada V6T 1Z4.
| | | |
Collapse
|
43
|
Schoch CL, Kohlmeyer J, Volkmann-Kohlmeyer B, Tsui CKM, Spatafora JW. The halotolerant fungus Glomerobolus gelineus is a member of the Ostropales. ACTA ACUST UNITED AC 2006; 110:257-63. [PMID: 16431093 DOI: 10.1016/j.mycres.2005.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 10/24/2005] [Accepted: 10/26/2005] [Indexed: 11/25/2022]
Abstract
Glomerobolus gelineus is a halotolerant species with a unique method of ballistic propagation. The absence of both sexual and asexual spores made reliable placement of this species, based on morphology alone, within the current fungal classification problematical. A phylogenetic analysis of the large and small nuclear ribosomal subunit and the second largest subunit of RNA polymerase II placed this fungus within the Ostropales, an order comprising lichenized and saprobic species, with good statistical support. Subsequently, a more detailed analysis that combined the nuc LSU rDNA and the mt SSU rDNA confirmed a close relationship to the Stictidaceae. The phylogenetic placement of G. gelineus is also supported by morphological characters. We postulate that the hyphoma lobes of Glomerobolus correspond to the periphysoidal layer in the apothecium of Stictis, and the propagule to the hymenium. Moreover, the presence of crystals in the outer lobes of G. gelineus is another indication of its relationship with Ostropales, which have characteristic crystalliferous hyphae. The placement of Glomerobolus within the Ostropales further expands the ecological diversity exhibited by this order. It also provides a phylogenetic hypothesis for assessing the homology of the enigmatic hyphomal morphology with apothecia-forming Ascomycota.
Collapse
Affiliation(s)
- Conrad L Schoch
- Department of Botany and Plant Pathology, University of Oregon State, Corvallis, 97333, USA.
| | | | | | | | | |
Collapse
|
44
|
|
45
|
Abstract
The genus Vanakripa (hyphomycetes) is reviewed based on the examination of type specimens, and V. ellipsoidea sp. nov. is described on submerged wood from Hong Kong. Vanakripa is characterized by punctiform sporodochial colonies, micronematous conidiogenous cells and pigmented conidia with vermiform separating cells. Vanakripa is compared with similar genera, and a synopsis of its morphological characters is provided.
Collapse
Affiliation(s)
- Clement K M Tsui
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | | | | |
Collapse
|
46
|
Tsui CKM, Hyde KD, Hodgkiss IJ. Longitudinal and temporal distribution of freshwater ascomycetes and dematiaceous hyphomycetes on submerged wood in the Lam Tsuen River, Hong Kong. ACTA ACUST UNITED AC 2001. [DOI: 10.2307/1468086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Clement K. M. Tsui
- Center for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Kevin D. Hyde
- Center for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - I. John Hodgkiss
- Center for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong
| |
Collapse
|
47
|
Tsui CKM, Hyde KD, Hodgkiss IJ. Paraniesslia tuberculata gen. et sp. nov., and New Records or Species of Clypeosphaeria, Leptosphaeria and Astrosphaeriella in Hong Kong Freshwater Habitats. Mycologia 2001. [DOI: 10.2307/3761763] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
48
|
Tsui CKM, Goh TK, Hyde KD, Hodgkiss IJ. New Species or Records of Cacumisporium, Helicosporium, Monotosporella and Bahusutrabeeja on Submerged Wood in Hong Kong Streams. Mycologia 2001. [DOI: 10.2307/3761660] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
49
|
Ranghoo VM, Hyde KD, Wong SW, Tsui CKM, Jones EBG. Vertexicola caudatus gen. et sp. nov., and a New Species of Rivulicola from Submerged Wood in Freshwater Habitats. Mycologia 2000. [DOI: 10.2307/3761596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|