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Pitarch A, Diéguez-Uribeondo J, Martín-Torrijos L, Sergio F, Blanco G. Fungal signatures of oral disease reflect environmental degradation in a facultative avian scavenger. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155397. [PMID: 35460785 DOI: 10.1016/j.scitotenv.2022.155397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Degradation of natural ecosystems increases the risk of infections in wildlife due to microbiota dysbiosis. However, little is known about its influence on the development of fungal communities in predators and facultative avian scavengers. We evaluated the incidence of oral disease in wild nestling black kites (Milvus migrans) under contrasting environmental degradation conditions, and explored their oral fungal patterns using molecular methods and multivariate analysis. Oral lesions were found in 36.8% of the 38 nestlings examined in an anthropogenically altered habitat (southeastern Madrid, Spain), but in none of the 105 nestlings examined in a well-conserved natural area (Doñana National Park, Spain). In a subsample of 48 black kites, the composition of the oral fungal community differed among symptomatic nestlings from Madrid (SM) and asymptomatic nestlings from Madrid (AM) and Doñana (AD). Opportunistic fungal pathogens (e.g., Fusarium incarnatum-equiseti species complex, Mucor spp., Rhizopus oryzae) were more prevalent in SM and AM than in AD. Hierarchical clustering and principal component analyses revealed that fungal patterns were distinct between both study areas, and that anthropogenic and natural environmental factors had a greater impact on them than oral disease. Fungal signatures associated with anthropogenic and natural stresses harbored some taxa that could be used to flag oral infection (F. incarnatum-equiseti species complex and Alternaria), indicate environmental degradation (Alternaria) or provide protective benefits in degraded environments (Trichoderma, Epicoccum nigrum and Sordaria). Co-occurrence associations between potentially beneficial and pathogenic fungi were typical of AM and AD, hinting at a possible role in host health. This study shows that early-life exposure to highly degraded environments induces a shift towards a higher prevalence of pathogenic species in the oral cavity of black kites, favoring oral disease. Furthermore, our findings suggest potential ecological applications of the monitoring of oral mycobiome as a bioindication of oral disease and environmental degradation.
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Affiliation(s)
- Aida Pitarch
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM) and Ramón y Cajal Institute of Health Research (IRYCIS), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain; Teaching Unit of Microbiology and Parasitology, Faculty of Optics and Optometry, Complutense University of Madrid (UCM), Arcos de Jalón, 118, 28037 Madrid, Spain.
| | | | - Laura Martín-Torrijos
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza Murillo 2, 28014 Madrid, Spain
| | - Fabrizio Sergio
- Department of Conservation Biology, Estacion Biologica de Doñana-CSIC, Americo Vespucio 26, 41092 Sevilla, Spain
| | - Guillermo Blanco
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales-CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Sirag B, Khidir ES, Dumyati M, Sindi B, Alsinnari M, Faidah H, Ahmed A. Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing. Front Microbiol 2021; 12:726203. [PMID: 34707582 PMCID: PMC8544600 DOI: 10.3389/fmicb.2021.726203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022] Open
Abstract
The prevalent variants of Cryptococcus neoformans, and other Cryptococcus species in pigeon excreta in Western Region of Saudi Arabia were studied. Ninety pigeon dropping samples were plated directly on Niger seed agar, and suspected colonies were sequenced using Illumina MiSeq. Species identification was determined using sequence read mapping to reference genomes of the two C. neoformans variants. In addition, sequence reads were identified using the KmerFinder tool. internal transcribed spacer 2 in the rDNA was also used for fungal barcoding of none of the C. neoformans species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The C. neoformans var. grubii mitochondrion and chromosome 1 reference sequences (accession numbers NC_004336.1 and CP022321.1, respectively) were used for sequence comparison and variant calling. Fifteen Cryptococcus isolates were isolated, 11 were identified as C. neoformans var. grubii, and 4 were found to be other opportunistic Cryptococcus species. Phylogeny analysis of C. neoformans var. grubii isolates showed a high degree of similarity between the C. neoformans isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic Cryptococcus species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.
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Affiliation(s)
- Bashir Sirag
- Department of Microbiology, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - El-Shiekh Khidir
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammed Dumyati
- Department of Medicine, National Guard Health Affairs, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Basam Sindi
- Department of Medicine, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Mahir Alsinnari
- Department of Anesthesia, Al Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abdalla Ahmed
- Department of Microbiology, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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Chen M, Wang Y, Li Y, Hong N, Zhu X, Pan W, Liao W, Xu J, Du J, Chen J. Genotypic diversity and antifungal susceptibility of environmental isolates of Cryptococcus neoformans from the Yangtze River Delta region of East China. Med Mycol 2020; 59:653-663. [PMID: 33269400 DOI: 10.1093/mmy/myaa096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Although cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources, information concerning the characteristics of environmental isolates of C. neoformans s. l. and how they are related to clinical isolates is very limited, especially in East China. In this study, 61 environmental isolates of C. neoformans were recovered from pigeon (Columba livia) droppings from the Yangtze River Delta region of East China. These isolates were genotyped using the ISHAM-MLST consensus scheme and their antifungal drug susceptibilities were determined following the CLSI M27-A3 guidelines. The 61 isolates were found belonging to 13 sequence types (STs), including several novel STs such as ST254 and ST194. The dominant ST in this environmental sample was ST31, different from that of clinical strains (ST5) in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, population genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for further comparative analysis the potential mechanisms for the observed differences between environmental and clinical populations of C. neoformans in China. LAY SUMMARY Cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources. However, there is currently limited information about the genetic diversity and antifungal susceptibility of environmental C. neoformans s. l. isolates, including how they may differ from clinical samples. In this study, we collected 61 environmental C. neoformans isolates from domestic pigeon droppings from the Yangtze River Delta region of East China. These isolates were genotyped using multi-locus sequencing. We found a high genotypic diversity in this population of C. neoformans, with several novel genotypes and a distribution of genotypes different from that of clinical strains in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for phylogenomic analysis investigating why and how disparate population structures of C. neoformans isolates formed between environmental and clinical sources in the region.
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Affiliation(s)
- Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yan Wang
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yingfang Li
- Department of Skin & Cosmetic Research, Shanghai Skin Diseases Hospital, Shanghai, China
| | - Nan Hong
- Department of Dermatology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xinlin Zhu
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Weihua Pan
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wanqing Liao
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Canada
| | - Jingxia Du
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianghan Chen
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
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Osman M, Al Bikai A, Rafei R, Mallat H, Dabboussi F, Hamze M. Update on invasive fungal infections in the Middle Eastern and North African region. Braz J Microbiol 2020; 51:1771-1789. [PMID: 32623654 PMCID: PMC7335363 DOI: 10.1007/s42770-020-00325-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/22/2020] [Indexed: 12/18/2022] Open
Abstract
In the recent years, the epidemiology of invasive fungal infections (IFIs) has changed worldwide. This is remarkably noticed with the significant increase in high-risk populations. Although surveillance of such infections is essential, data in the Middle Eastern and North African (MENA) region remain scarce. In this paper, we reviewed the existing data on the epidemiology of different IFIs in the MENA region. Epidemiological surveillance is crucial to guide optimal healthcare practices. This study can help to guide appropriate interventions and to implement antimicrobial stewardship and infection prevention and control programs in countries.
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Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Aisha Al Bikai
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
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