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Dai R, Jin C, Xiao M. The influence of urban environmental effects on the orchard soil microbial community structure and function: a case study in Zhejiang, China. Front Microbiol 2024; 15:1403443. [PMID: 39314879 PMCID: PMC11417026 DOI: 10.3389/fmicb.2024.1403443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/08/2024] [Indexed: 09/25/2024] Open
Abstract
The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture.
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Affiliation(s)
- Rongchen Dai
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Cuixiang Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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2
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Chen L, Xie Z, Jian J. Epidemiology and Risk Factors of Candidemia a 8-Year Retrospective Study from a Teaching Hospital in China. Infect Drug Resist 2024; 17:3415-3423. [PMID: 39131515 PMCID: PMC11317046 DOI: 10.2147/idr.s471171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Purpose We investigated the Epidemiology, risk factors and outcomes of Candida bloodstream infection. Methods The electronic laboratory records data of patients with candidemia (2015-2022) were collected. We used univariate and multivariate logistic regression to determine the risk factors of candidemia. Results Of the 134 patients with candidemia, the most prevalent species were Candida albicans (37.2%), followed by Candida glabrata (27.7%), Candida parapsilosis (18.9%), and others. The mean annual incidence was 0.33/1000 admissions. The overall resistance rate of Candida spp. against fluconazole and voriconazole were 4.9% (7/142) and 5.9% (6/101), while Candida tropicalis showed high resistance to fluconazole (38.8%) and voriconazole (27.8%). The 30-day mortality rate was 32.8%. On multivariate analysis, age ≥ 65 (odds ratio [OR] = 3.874, 95% confidence interval [CI]: 1.146, 13.092; P = 0.029), high Acute Physiology and Chronic Health Evaluation II (APACHE II) score (OR = 12.384, 95% CI: 2.963, 51.762; P = 0.001), shock (OR = 3.428, 95% CI: 1.097, 10.719; P = 0.034), initial antifungal therapy (OR = 0.057, 95% CI: 0.011, 0.306; P = 0.001) and White blood cells (OR = 1.129, 95% CI: 1.016, 1.255; P = 0.024) were the independent risk factors with mortality within 30 day in patients with candidemia. Conclusion The incidence rate and the mortality rate of candidemia are high, and lower azole susceptibility was found in Candida tropicalis. Age≥65 years, Shock, high APACHE II score, Antifungal therapy and White blood cells count were independently associated with 30-day mortality.
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Affiliation(s)
- Liang Chen
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, People’s Republic of China
| | - Zeqiang Xie
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, People’s Republic of China
| | - Jiyong Jian
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, People’s Republic of China
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3
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Keighley C, Kim HY, Kidd S, Chen SCA, Alastruey A, Dao A, Bongomin F, Chiller T, Wahyuningsih R, Forastiero A, Al-Nuseirat A, Beyer P, Gigante V, Beardsley J, Sati H, Morrissey CO, Alffenaar JW. Candida tropicalis-A systematic review to inform the World Health Organization of a fungal priority pathogens list. Med Mycol 2024; 62:myae040. [PMID: 38935905 PMCID: PMC11210624 DOI: 10.1093/mmy/myae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/14/2024] [Accepted: 04/29/2024] [Indexed: 06/29/2024] Open
Abstract
In response to the growing global burden of fungal infections with uncertain impact, the World Health Organization (WHO) established an Expert Group to identify priority fungal pathogens and establish the WHO Fungal Priority Pathogens List for future research. This systematic review aimed to evaluate the features and global impact of invasive candidiasis caused by Candida tropicalis. PubMed and Web of Science were searched for studies reporting on criteria of mortality, morbidity (defined as hospitalization and disability), drug resistance, preventability, yearly incidence, diagnostics, treatability, and distribution/emergence from 2011 to 2021. Thirty studies, encompassing 436 patients from 25 countries were included in the analysis. All-cause mortality due to invasive C. tropicalis infections was 55%-60%. Resistance rates to fluconazole, itraconazole, voriconazole and posaconazole up to 40%-80% were observed but C. tropicalis isolates showed low resistance rates to the echinocandins (0%-1%), amphotericin B (0%), and flucytosine (0%-4%). Leukaemia (odds ratio (OR) = 4.77) and chronic lung disease (OR = 2.62) were identified as risk factors for invasive infections. Incidence rates highlight the geographic variability and provide valuable context for understanding the global burden of C. tropicalis infections. C. tropicalis candidiasis is associated with high mortality rates and high rates of resistance to triazoles. To address this emerging threat, concerted efforts are needed to develop novel antifungal agents and therapeutic approaches tailored to C. tropicalis infections. Global surveillance studies could better inform the annual incidence rates, distribution and trends and allow informed evaluation of the global impact of C. tropicalis infections.
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Affiliation(s)
- Caitlin Keighley
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW, Australia
- Southern IML Pathology, 3 Bridge St, Coniston, NSW, Australia
| | - Hannah Yejin Kim
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital, Westmead, NSW, Australia
| | - Sarah Kidd
- National Mycology Reference Centre, Microbiology & Infectious Diseases, SA Pathology, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Sharon C-A Chen
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW, Australia
| | - Ana Alastruey
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Aiken Dao
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital, Westmead, NSW, Australia
| | - Felix Bongomin
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GE, USA
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Agustina Forastiero
- Servicio de Micologia, Laboratorio de Microbiologia, Hospital Britanico, Buenos Aires, Argentina
| | - Adi Al-Nuseirat
- World Health Organization Regional Office for the Eastern Mediterranean, Cairo 11371, Egypt
| | - Peter Beyer
- AMR Division, World Health Organization, Geneva
| | | | - Justin Beardsley
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital, Westmead, NSW, Australia
| | - Hatim Sati
- AMR Division, World Health Organization, Geneva
| | - C Orla Morrissey
- The Alfred Hospital, Department of Infectious Diseases, Melbourne, Victoria, Australia
- Monash University, Department of Infectious Diseases, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Jan-Willem Alffenaar
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital, Westmead, NSW, Australia
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Álvarez-Pérez S, Quevedo-Caraballo S, García ME, Blanco JL. Prevalence and genetic diversity of azole-resistant Malassezia pachydermatis isolates from canine otitis and dermatitis: A 2-year study. Med Mycol 2024; 62:myae053. [PMID: 38734886 DOI: 10.1093/mmy/myae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
Despite previous reports on the emergence of Malassezia pachydermatis strains with decreased susceptibility to azoles, there is limited information on the actual prevalence and genetic diversity of azole-resistant isolates of this yeast species. We assessed the prevalence of azole resistance in M. pachydermatis isolates from cases of dog otitis or skin disease attended in a veterinary teaching hospital during a 2-year period and analyzed the ERG11 (encoding a lanosterol 14-α demethylase, the primary target of azoles) and whole genome sequence diversity of a group of isolates that displayed reduced azole susceptibility. Susceptibility testing of 89 M. pachydermatis isolates from 54 clinical episodes (1-6 isolates/episode) revealed low minimum inhibitory concentrations (MICs) to most azoles and other antifungals, but 11 isolates from six different episodes (i.e., 12.4% of isolates and 11.1% of episodes) had decreased susceptibility to multiple azoles (fluconazole, itraconazole, ketoconazole, posaconazole, ravuconazole, and/or voriconazole). ERG11 sequencing of these 11 azole-resistant isolates identified eight DNA sequence profiles, most of which contained amino acid substitutions also found in some azole-susceptible isolates. Analysis of whole genome sequencing (WGS) results revealed that the azole-resistant isolates from the same episode of otitis, or even different episodes affecting the same animal, were more genetically related to each other than to isolates from other dogs. In conclusion, our results confirmed the remarkable ERG11 sequence variability in M. pachydermatis isolates of animal origin observed in previous studies and demonstrated the value of WGS for disentangling the epidemiology of this yeast species.
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Affiliation(s)
- Sergio Álvarez-Pérez
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Sergio Quevedo-Caraballo
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - Marta E García
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
| | - José L Blanco
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040 Madrid, Spain
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Fan X, Dai RC, Zhang S, Geng YY, Kang M, Guo DW, Mei YN, Pan YH, Sun ZY, Xu YC, Gong J, Xiao M. Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population. Nat Commun 2023; 14:8369. [PMID: 38102133 PMCID: PMC10724272 DOI: 10.1038/s41467-023-43380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
Invasive diseases caused by the globally distributed commensal yeast Candida tropicalis are associated with mortality rates of greater than 50%. Notable increases of azole resistance have been observed in this species, particularly within Asia-Pacific regions. Here, we carried out a genetic population study on 1571 global C. tropicalis isolates using multilocus sequence typing (MLST). In addition, whole-genome sequencing (WGS) analysis was conducted on 629 of these strains, comprising 448 clinical invasive strains obtained in this study and 181 genomes sourced from public databases. We found that MLST clade 4 is the predominant azole-resistant clone. WGS analyses demonstrated that dramatically increasing rates of azole resistance are associated with a rapid expansion of cluster AZR, a sublineage of clade 4. Cluster AZR isolates exhibited a distinct high-level azole resistance, which was induced by tandem duplications of the ERG11A395T gene allele. Ty3/gypsy-like retrotransposons were found to be highly enriched in this population. The alarming expansion of C. tropicalis cluster AZR population underscores the urgent need for strategies against growing threats of antifungal resistance.
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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, 100020, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Rong-Chen Dai
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shu Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Peking University First Hospital - National Institute for Communicable Disease Control and Prevention Joint Laboratory of Pathogenic Fungi, Beijing, 102206, China
| | - Yuan-Yuan Geng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Peking University First Hospital - National Institute for Communicable Disease Control and Prevention Joint Laboratory of Pathogenic Fungi, Beijing, 102206, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Da-Wen Guo
- Department of Clinical Laboratory, First Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Ya-Ning Mei
- Department of Clinical Laboratory, Jiangsu Province Hospital, Nanjing, 210029, Jiangsu, China
| | - Yu-Hong Pan
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Zi-Yong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ying-Chun Xu
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Jie Gong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Peking University First Hospital - National Institute for Communicable Disease Control and Prevention Joint Laboratory of Pathogenic Fungi, Beijing, 102206, China.
| | - Meng Xiao
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Hu T, Wang S, Bing J, Zheng Q, Du H, Li C, Guan Z, Bai FY, Nobile CJ, Chu H, Huang G. Hotspot mutations and genomic expansion of ERG11 are major mechanisms of azole resistance in environmental and human commensal isolates of Candida tropicalis. Int J Antimicrob Agents 2023; 62:107010. [PMID: 37863341 DOI: 10.1016/j.ijantimicag.2023.107010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 10/11/2023] [Accepted: 10/14/2023] [Indexed: 10/22/2023]
Abstract
OBJECTIVES Infections caused by azole-resistant Candida tropicalis strains are increasing in clinical settings. The reason for this epidemical change and the mechanisms of C. tropicalis azole resistance are not fully understood. METHODS In this study, we performed biological and genomic analyses of 239 C. tropicalis strains, including 115 environmental and 124 human commensal isolates. RESULTS Most (99.2%) of the isolates had a baseline diploid genome. The strains from both environmental and human niches exhibit similar abilities to survive under stressful conditions and produce secreted aspartic proteases. However, the human commensal isolates exhibited a stronger ability to filament than the environmental strains. We found that 19 environmental isolates (16.5%) and 24 human commensal isolates (19.4%) were resistant to fluconazole. Of the fluconazole-resistant strains, 37 isolates (86.0%) also exhibited cross-resistance to voriconazole. Whole-genome sequencing and phylogenetic analyses revealed that both environmental and commensal isolates were widely distributed in a number of genetic clusters, but the two populations exhibited a close genetic association. The majority of fluconazole-resistant isolates were clustered within a single clade (X). CONCLUSIONS The combination of hotspot mutations (Y132F and S154F) and genomic expansion of ERG11, which encodes the azole target lanosterol 14-α-demethylase and represents a major target of azole drugs, was a major mechanism for the development of azole resistance. The isolates carrying both hotspot mutations and genomic expansion of ERG11 exhibited cross-resistance to fluconazole and voriconazole. Moreover, the azole-resistant isolates from both the environmental and human commensal niches showed similar genotypes.
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Affiliation(s)
- Tianren Hu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Sijia Wang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian Bing
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiushi Zheng
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Du
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chao Li
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhangyue Guan
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, Merced, California; Health Sciences Research Institute, University of California, Merced, California
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.
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Wang Y, Wan X, Zhao L, Jin P, Zhang J, Zhou X, Ye N, Wang X, Pan Y, Xu L. Clonal aggregation of fluconazole-resistant Candida tropicalis isolated from sterile body fluid specimens from patients in Hefei, China. Med Mycol 2023; 61:myad097. [PMID: 37777835 DOI: 10.1093/mmy/myad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/28/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023] Open
Abstract
Candida tropicalis, a human conditionally pathogenic yeast, is distributed globally, especially in Asia-Pacific. The increasing morbidity and azole resistance of C. tropicalis have made clinical treatment difficult. The correlation between clonality and antifungal susceptibility of clinical C. tropicalis isolates has been reported. To study the putative correlation in C. tropicalis isolated from normally sterile body fluid specimens and explore the distinct clonal complex (CC) in Hefei, 256 clinical C. tropicalis isolates were collected from four teaching hospitals during 2016-2019, of which 30 were fluconazole-resistant (FR). Genetic profiles of 63 isolates, including 30 FR isolates and 33 fluconazole-susceptible (FS) isolates, were characterized using multilocus sequence typing (MLST). Phylogenetic analysis of the data was conducted using UPGMA (unweighted pair group method with arithmetic averages) and the minimum spanning tree algorithm. MLST clonal complexes (CCs) were analyzed using the goeBURST package. Among 35 differentiated diploid sequence types (DSTs), 16 DSTs and 1 genotype were identified as novel. A total of 35 DSTs were assigned to five major CCs based on goeBURST analysis. CC1 (containing DST376, 505, 507, 1221, 1222, 1223, 1226, and 1229) accounted for 86.7% (26/30) of the FR isolates. However, the genetic relationships among the FS isolates were relatively decentralized. The local FR CC1 belongs to a large fluconazole non-susceptible CC8 in global isolates, of which the putative founder genotype was DST225. The putative correlation between MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Hefei showed that DSTs are closely related to FR clones.
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Affiliation(s)
- Ying Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
| | - Xin Wan
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
| | - Li Zhao
- Department of Urology, Anhui Zhongke Gengjiu Hospital, Hefei, China
| | - Peipei Jin
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
| | - Ju Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
| | - Xin Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
| | - Naifang Ye
- Department of Clinical Laboratory Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Xiaowei Wang
- Department of Clinical Laboratory Medicine, The First Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Yaping Pan
- Department of Clinical Laboratory Medicine, High Tech Branch of The First Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Liangfei Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Hefei, China
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Domán M, Makrai L, Vásárhelyi B, Balka G, Bányai K. Molecular epidemiology of Candida albicans infections revealed dominant genotypes in waterfowls diagnosed with esophageal mycosis. Front Vet Sci 2023; 10:1215624. [PMID: 37456960 PMCID: PMC10344593 DOI: 10.3389/fvets.2023.1215624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Fungal infections of animals could yield significant economic losses, especially in the poultry industry, due to their adverse effects on growth, feed intake, digestion, and reproduction. Previous investigations showed that Candida albicans plays the main etiological role in the esophageal mycosis of birds. In this study, we used multilocus sequence typing (MLST) to determine the population structure and molecular epidemiology of C. albicans isolated from geese and ducks in Hungary. Interestingly, only three known genotypes were identified among investigated flocks, namely, diploid sequence type (DST) 840, DST 656, and DST 605, suggesting the intra-species transmission of these genotypes. Additionally, two novel allele combinations (new DSTs) were found that have not been previously submitted to the MLST database. Phylogenetic analysis of isolates revealed a close relationship between DST 656 and DST 605 as well as between the two newly identified genotypes (designated DST 3670 and DST 3671). Although isolates from birds belonged to minor clades in contrast with most human isolates, no species-specificity was observed. Poultry-derived isolates were group founders or closely related to group founders of clonal complexes, suggesting that C. albicans is exposed to lesser selective pressure in animal hosts. The increasing number of genetic information in the C. albicans MLST database could help to reveal the epidemiological characteristics and evolutionary pathways that are essential for disease prevention strategies.
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Affiliation(s)
- Marianna Domán
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - László Makrai
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Balázs Vásárhelyi
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Gyula Balka
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pathology, University of Veterinary Medicine, Budapest, Hungary
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
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9
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Genetic Diversity of Human Fungal Pathogens. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023. [DOI: 10.1007/s40588-023-00188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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Spruijtenburg B, Baqueiro CCSZ, Colombo AL, Meijer EFJ, de Almeida JN, Berrio I, Fernández NB, Chaves GM, Meis JF, de Groot T. Short Tandem Repeat Genotyping and Antifungal Susceptibility Testing of Latin American Candida tropicalis Isolates. J Fungi (Basel) 2023; 9:207. [PMID: 36836321 PMCID: PMC9958743 DOI: 10.3390/jof9020207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Candida tropicalis is emerging as one of the most common Candida species causing opportunistic infections in Latin America. Outbreak events caused by C. tropicalis were reported, and antifungal resistant isolates are on the rise. In order to investigate population genomics and look into antifungal resistance, we applied a short tandem repeat (STR) genotyping scheme and antifungal susceptibility testing (AFST) to 230 clinical and environmental C. tropicalis isolates from Latin American countries. STR genotyping identified 164 genotypes, including 11 clusters comprised of three to seven isolates, indicating outbreak events. AFST identified one isolate as anidulafungin-resistant and harboring a FKS1 S659P substitution. Moreover, we identified 24 clinical and environmental isolates with intermediate susceptibility or resistance to one or more azoles. ERG11 sequencing revealed each of these isolates harboring a Y132F and/or Y257H/N substitution. All of these isolates, except one, were clustered together in two groups of closely related STR genotypes, with each group harboring distinct ERG11 substitutions. The ancestral C. tropicalis strain of these isolates likely acquired the azole resistance-associated substitutions and subsequently spread across vast distances within Brazil. Altogether, this STR genotyping scheme for C. tropicalis proved to be useful for identifying unrecognized outbreak events and better understanding population genomics, including the spread of antifungal-resistant isolates.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Cynthea C. S. Z. Baqueiro
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Arnaldo L. Colombo
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
| | - Eelco F. J. Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - João N. de Almeida
- Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04021-001, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo 05652-900, SP, Brazil
| | - Indira Berrio
- Hospital General de Medellín Luz Castro de Gutiérrez ESE, Medellín 050015, Colombia
- Medical and Experimental Mycology Group, Corporación para Investigaciones Biológicas (CIB), Medellín 050015, Colombia
| | - Norma B. Fernández
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires 2351, Argentina
| | - Guilherme M. Chaves
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba 80060-000, PR, Brazil
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Excellence Center for Medical Mycology, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology, Radboud University Medical Center, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
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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] [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.
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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,
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