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Liu P, Wilson P, Redquest B, Keobouasone S, Manseau M. Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data. Mol Ecol Resour 2024; 24:e13929. [PMID: 38289068 DOI: 10.1111/1755-0998.13929] [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: 09/11/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024]
Abstract
Accurate and efficient microsatellite loci genotyping is an essential process in population genetics that is also used in various demographic analyses. Protocols for next-generation sequencing of microsatellite loci enable high-throughput and cross-compatible allele scoring, common issues that are not addressed by conventional capillary-based approaches. To improve this process, we have developed an all-in-one software, called Seq2Sat (sequence to microsatellite), in C++ to support automated microsatellite genotyping. It directly takes raw reads of microsatellite amplicons and conducts read quality control before inferring genotypes based on depth-of-read, read ratio, sequence composition and length. We have also developed a module for sex identification based on sex chromosome-specific locus amplicons. To allow for greater user access and complement autoscoring, we developed SatAnalyzer (microsatellite analyzer), a user-friendly web-based platform that conducts reads-to-report analyses by calling Seq2Sat for genotype autoscoring and produces interactive genotype graphs for manual editing. SatAnalyzer also allows users to troubleshoot multiplex optimization by analysing read quality and distribution across loci and samples in support of high-quality library preparation. To evaluate its performance, we benchmarked our toolkit Seq2Sat/SatAnalyzer against a conventional capillary gel method and existing microsatellite genotyping software, MEGASAT, using two datasets. Results showed that SatAnalyzer can achieve >99.70% genotyping accuracy and Seq2Sat is ~5 times faster than MEGASAT despite many more informative tables and figures being generated. Seq2Sat and SatAnalyzer are freely available on github (https://github.com/ecogenomicscanada/Seq2Sat) and dockerhub (https://hub.docker.com/r/rocpengliu/satanalyzer).
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Affiliation(s)
- Peng Liu
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Paul Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | | | - Sonesinh Keobouasone
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Micheline Manseau
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
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Račka K, Bártová E, Hamidović A, Plault N, Kočišová A, Camacho G, Mercier A, Halajian A. First detection of Toxoplasma gondii Africa 4 lineage in a population of carnivores from South Africa. Front Cell Infect Microbiol 2024; 14:1274577. [PMID: 38352059 PMCID: PMC10861644 DOI: 10.3389/fcimb.2024.1274577] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction There have only been a few molecular studies conducted on the detection of T. gondii in tissues of carnivores in South Africa, with no data on the genetic diversity of this parasite. That is why the aim of this study was to detect and genotype T. gondii DNA in tissues of selected wild and domestic carnivores in South Africa. Methods Samples were collected from 80 animals of 20 species (mainly road-killed) in the four provinces of Limpopo (n=57), Mpumalanga (n=21), Gauteng (n=1) and Free State (n=1) during the period 2014-2018. Samples of brain (n=31), heart (n=4), liver (n=40), spleen (n=2) and lung (n=3) were used to detect T. gondii by real-time PCR targeting a 529 bp repeating fragment of T. gondii DNA. Samples that were positive in real-time PCR were genotyped using 15 microsatellite markers. Results T. gondii DNA was detected in 4 (5 %) samples: in the brain from a Black-backed Jackal (Canis mesomelas), in the liver from a African Wildcat (Felis silvestris lybica) and in the liver and heart of two Rusty-spotted Genets (Genetta maculata) respectively. The DNA sample from Black-backed Jackal was genotyped and characterized as belonging to the type Africa 4 lineage (equivalent to RFLP genotype ToxoDB#20), that is a widespread lineage in Africa. Discussion This is the first genetic characterization of T. gondii isolated from a wild carnivore on the African continent and the first report of T. gondii in Black-backed Jackal. The Africa 4 lineage was also confirmed in the region of Southern Africa for the first time.
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Affiliation(s)
- Karol Račka
- Department of Epizootology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Eva Bártová
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Azra Hamidović
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Nicolas Plault
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Alica Kočišová
- Department of Epizootology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Gerrie Camacho
- Department of Scientific Services, Mpumalanga Tourism & Parks Agency (MTPA), Nelspruit, South Africa
| | - Aurelién Mercier
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Ali Halajian
- Research Administration and Development, University of Limpopo, Sovenga, South Africa
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Khalifa HO, Watanabe A, Kamei K. Antifungal Resistance and Genotyping of Clinical Candida parapsilosis Complex in Japan. J Fungi (Basel) 2023; 10:4. [PMID: 38276020 PMCID: PMC10816931 DOI: 10.3390/jof10010004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Non-albicans Candida infections have recently gained worldwide attention due to their intrinsic resistance to different antifungal agents and the limited therapeutic options for treating them. Although the Candida parapsilosis complex is reported to be the second or third most prevalent Candida spp., little information is available on the prevalence of antifungal resistance along with genotyping of the C. parapsilosis complex. In this study, we aimed to evaluate the prevalence of antifungal resistance, the genetic basis of such resistance, and the genotyping of C. parapsilosis complex isolates that were recovered from hospitalized patients in Japan from 2005 to 2019. Our results indicated that, with the exception of one single C. metapsilosis isolate that was dose-dependently susceptible to fluconazole, all other isolates were susceptible or showed wild phenotypes to all tested antifungals, including azoles, echinocandins, amphotericin B, and flucytosine. Molecular analyses for azole and echinocandin resistance via evaluating ERG11 mutation and FKS1 hotspot one (HS1) and hotspot two (HS2) mutations, respectively, confirmed the phenotypic results. Genotyping of our isolates confirmed that they belong to 53 different but closely related genotypes, with a similarity percentage of up to 90%. Our results are of significant concern, since understanding the genetic basis of echinocandin resistance in the C. parapsilosis complex as well their genotyping is essential for directing targeted therapy, identifying probable infection sources, and developing strategies for overcoming epidemic spread.
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Affiliation(s)
- Hazim O. Khalifa
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates
- Medical Mycology Research Centre, Division of Clinical Research, Chiba University, Chiba 260-8673, Japan; (A.W.); (K.K.)
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Akira Watanabe
- Medical Mycology Research Centre, Division of Clinical Research, Chiba University, Chiba 260-8673, Japan; (A.W.); (K.K.)
| | - Katsuhiko Kamei
- Medical Mycology Research Centre, Division of Clinical Research, Chiba University, Chiba 260-8673, Japan; (A.W.); (K.K.)
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De Carolis E, Posteraro B, Falasca B, Spruijtenburg B, Meis JF, Sanguinetti M. The Fourier-transform infrared spectroscopy-based method as a new typing tool for Candida parapsilosis clinical isolates. Microbiol Spectr 2023; 11:e0238823. [PMID: 37695061 PMCID: PMC10580913 DOI: 10.1128/spectrum.02388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/21/2023] [Indexed: 09/12/2023] Open
Abstract
The Fourier-transform infrared spectroscopy-based IR Biotyper is a straightforward typing tool for bacterial species, but its use with Candida species is limited. We applied IR Biotyper to Candida parapsilosis, a common cause of nosocomial bloodstream infection (BSI), which is aggravated by the intra-hospital spread of fluconazole-resistant isolates. Of 59 C. parapsilosis isolates studied, n = 56 (48 fluconazole-resistant and 8 fluconazole-susceptible) and n = 3 (2 fluconazole-resistant and 1 fluconazole-susceptible) isolates, respectively, had been recovered from BSI episodes in 2 spatially distant Italian hospitals. The latter isolates served as an outgroup. Of fluconazole-resistant isolates, n = 40 (including one outgroup) harbored the Y132F mutation alone and n = 10 (including one outgroup) harbored both Y132F and R398I mutations in the ERG11-encoded azole-target enzyme. Using a microsatellite typing method, which relies on the amplification of genomic short tandem repeats (STR), two major clusters were obtained based on the mutation(s) (Y132F or Y132F/R398I) present in the isolates. Regarding IR Biotyper, each isolate was analyzed in quintuplicate using an automatic (i.e., proposed by the manufacturer's software) or tentative (i.e., proposed by us) cutoff value. In the first case, four clusters were identified, with clusters I and II formed by Y132F or Y132F/R398I isolates, respectively. In the second case, six subclusters (derived by the split of clusters I and II) were identified. This allowed to separate the outgroup isolates from other isolates and to increase the IR Biotyper typeability. The agreement of IR Biotyper with STR ranged from 47% to 74%, depending on type of cutoff value used in the analysis. IMPORTANCE Establishing relatedness between clinical isolates of Candida parapsilosis is important for implementing rapid measures to control and prevent nosocomial transmission of this Candida species. We evaluated the FTIR-based IR Biotyper, a new typing method in the Candida field, using a collection of fluconazole-resistant C. parapsilosis isolates supposed to be genetically related due to the presence of the Y132F mutation. We showed that IR Biotyper was discriminatory but not as much as the STR method, which is still considered the method of choice. Further studies on larger series of C. parapsilosis isolates or closely related Candida species will be necessary to confirm and/or extend the results from this study.
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Affiliation(s)
- Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Roma, Italy
- Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Benedetta Falasca
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Bram Spruijtenburg
- Radboudumc/Canisius Wilhelmina Hospital Center of Expertise for Mycology, Nijmegen, the Netherlands
| | - Jacques F. Meis
- Radboudumc/Canisius Wilhelmina Hospital Center of Expertise for Mycology, Nijmegen, the Netherlands
- Department I of Internal Medicine and ECMM Excellence Center for Medical Mycology, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Roma, Italy
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Korfanty G, Heifetz E, Xu J. Assessing thermal adaptation of a global sample of Aspergillus fumigatus: Implications for climate change effects. Front Public Health 2023; 11:1059238. [PMID: 36875405 PMCID: PMC9978374 DOI: 10.3389/fpubh.2023.1059238] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Aspergillus fumigatus is a common environmental mold and a major cause of opportunistic infections in humans. It's distributed among many ecological niches across the globe. A major virulence factor of A. fumigatus is its ability to grow at high temperature. However, at present, little is known about variations among strains in their growth at different temperatures and how their geographic origins may impact such variations. In this study, we analyzed 89 strains from 12 countries (Cameroon, Canada, China, Costa Rica, France, India, Iceland, Ireland, New Zealand, Peru, Saudi Arabia, and USA) representing diverse geographic locations and temperature environments. Each strain was grown at four temperatures and genotyped at nine microsatellite loci. Our analyses revealed a range of growth profiles, with significant variations among strains within individual geographic populations in their growths across the temperatures. No statistically significant association was observed between strain genotypes and their thermal growth profiles. Similarly geographic separation contributed little to differences in thermal adaptations among strains and populations. The combined analyses among genotypes and growth rates at different temperatures in the global sample suggest that most natural populations of A. fumigatus are capable of rapid adaptation to temperature changes. We discuss the implications of our results to the evolution and epidemiology of A. fumigatus under increasing climate change.
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Affiliation(s)
- Greg Korfanty
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Erin Heifetz
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Díaz-García J, Gómez A, Machado M, Alcalá L, Reigadas E, Sánchez-Carrillo C, Pérez-Ayala A, de la Pedrosa EGG, González-Romo F, Cuétara MS, García-Esteban C, Quiles-Melero I, Zurita ND, Algarra MM, Durán-Valle MT, Sánchez-García A, Muñoz P, Escribano P, Guinea J. Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis. J Fungi (Basel) 2022; 8:jof8111228. [PMID: 36422050 PMCID: PMC9698610 DOI: 10.3390/jof8111228] [Citation(s) in RCA: 4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Candidaemia and invasive candidiasis are typically hospital-acquired. Genotyping isolates from patients admitted to different hospitals may be helpful in tracking clones spreading across hospitals, especially those showing antifungal resistance. METHODS We characterized Candida clusters by studying Candida isolates (C. albicans, n = 1041; C. parapsilosis, n = 354, and C. tropicalis, n = 125) from blood cultures (53.8%) and intra-abdominal samples (46.2%) collected as part of the CANDIMAD (Candida in Madrid) study in Madrid (2019-2021). Species-specific microsatellite markers were used to define the genotypes of Candida spp. found in a single patient (singleton) or several patients (cluster) from a single hospital (intra-hospital cluster) or different hospitals (widespread cluster). RESULTS We found 83 clusters, of which 20 were intra-hospital, 49 were widespread, and 14 were intra-hospital and widespread. Some intra-hospital clusters were first detected before the onset of the COVID-19 pandemic, but the number of clusters increased during the pandemic, especially for C. parapsilosis. The proportion of widespread clusters was significantly higher for genotypes found in both compartments than those exclusively found in either the blood cultures or intra-abdominal samples. Most C. albicans- and C. tropicalis-resistant genotypes were singleton and presented exclusively in either blood cultures or intra-abdominal samples. Fluconazole-resistant C. parapsilosis isolates belonged to intra-hospital clusters harboring either the Y132F or G458S ERG11p substitutions; the dominant genotype was also widespread. CONCLUSIONS the number of clusters-and patients involved-increased during the COVID-19 pandemic mainly due to the emergence of fluconazole-resistant C. parapsilosis genotypes.
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Affiliation(s)
- Judith Díaz-García
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Ana Gómez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Marina Machado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Elena Reigadas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Ana Pérez-Ayala
- Clinical Microbiology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital 12 de Octubre, 28041 Madrid, Spain
| | - Elia Gómez-García de la Pedrosa
- Clinical Microbiology Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fernando González-Romo
- Clinical Microbiology Department, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos IdISSC, 28040 Madrid, Spain
| | - María Soledad Cuétara
- Clinical Microbiology Department, Hospital Universitario Severo Ochoa, 28914 Leganés, Spain
| | - Coral García-Esteban
- Clinical Microbiology Department, Hospital Universitario de Getafe, 28901 Madrid, Spain
| | | | - Nelly Daniela Zurita
- Clinical Microbiology Department, Hospital Universitario de La Princesa, 28006 Madrid, Spain
| | - María Muñoz Algarra
- Clinical Microbiology Department, Hospital Universitario Puerta de Hierro Majadahonda, 28220 Madrid, Spain
| | - María Teresa Durán-Valle
- Clinical Microbiology Department, Hospital Universitario de Móstoles, Móstoles, 28935 Madrid, Spain
| | - Aída Sánchez-García
- Laboratorio Central de la CAM-URSalud-Hospital Infanta Sofía, San Sebastián de los Reyes, 28703 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-915-868-453; Fax: +34-915-044-906
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Díaz-García J, Gómez A, Alcalá L, Reigadas E, Sánchez-Carrillo C, Pérez-Ayala A, Gómez-García de la Pedrosa E, González-Romo F, Merino-Amador P, Cuétara MS, García-Esteban C, Quiles-Melero I, Zurita ND, Muñoz-Algarra M, Sánchez-Romero I, Durán-Valle MT, Sánchez-García A, Alcoceba E, Muñoz P, Escribano P, Guinea J; CANDIMAD study group. Evidence of Fluconazole-Resistant Candida parapsilosis Genotypes Spreading across Hospitals Located in Madrid, Spain and Harboring the Y132F ERG11p Substitution. Antimicrob Agents Chemother 2022; 66:e0071022. [PMID: 35852369 DOI: 10.1128/aac.00710-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We have been monitoring the antifungal resistance in Candida parapsilosis isolates collected from inpatients at Madrid metropolitan area hospitals for the last 3 years. The study aimed to elucidate the presence of fluconazole-resistant C. parapsilosis genotypes in Madrid. From January 2019 to December 2021, a total of 354 C. parapsilosis isolates (n = 346 patients) from blood (76.6%) or intraabdominal samples were collected and genotyped using species-specific microsatellite markers. Antifungal susceptibilities to amphotericin B, the triazoles, micafungin, anidulafungin, and ibrexafungerp were performed according to EUCAST E.Def 7.3.2; the ERG11 gene was sequenced in fluconazole-resistant isolates. A total of 13.6% (n = 48/354) isolates (one per patient) were found to be resistant to fluconazole and non-wild-type to voriconazole but fully susceptible to ibrexafungerp. Resistant isolates were mostly sourced from blood (n = 45/48, 93.8%) and were detected in five hospitals. Two hospitals accounted for a high proportion of resistant isolates (n = 41/48). Resistant isolates harbored either the Y132F ERG11p amino acid substitution (n = 43) or the G458S substitution (n = 5). Isolates harboring the Y132F substitution clustered into a clonal complex involving three genotypes (one genotype accounted for n = 39/43 isolates) that were found in four hospitals. Isolates harboring the G458S substitution clustered into another genotype found in a fifth hospital. C. parapsilosis genotypes demonstrating resistance to fluconazole have been spreading across hospitals in Madrid, Spain. Over the last 3 years, the frequency of isolation of such isolates and the number of hospitals affected is on the rise.
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Cateau E, Leclerc A, Cartier N, Valsechi I, Bailly É, Senechal RL, Becerra M, Gallou BL, Lavergne RA, Chesnay A, Robin JP, Cray C, Goddard N, Thorel M, Guillot J, Mulot B, Desoubeaux G. pAspergillosis in a colony of Humboldt penguins (Spheniscus humboldti) under managed care: a clinical and environmental investigation in a French zoological park. Med Mycol 2022; 60:6609783. [PMID: 35713494 DOI: 10.1093/mmy/myac046] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/27/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillosis is pervasive in bird populations, especially those under human care. Its management can be critically impacted by exposure to high levels of conidia and by resistance to azole drugs. The fungal contamination in the environment of a Humboldt penguin (Spheniscus humboldti) group, housed in a French zoological park next to numerous large crop fields, was assessed through three serial sessions of surface sampling in nests, in 2018-20: all isolates were counted and characterized by sequencing. When identified as A. fumigatus, they were systematically screened for resistance mutations in the cyp51A gene and tested for MICs determination. In the same time, the clinical incidence of aspergillosis was evaluated in the penguin population by the means of systematic necropsy and mycological investigations. A microsatellite-based analysis tracked the circulation of A. fumigatus strains. Environmental investigations highlighted substantial increase of the fungal load during the summer season (>12-fold vs. the other timepoints) and large overrepresentation of species belonging to the Aspergillus section Fumigati, ranging from 22.7 to 94.6% relative prevalence. Only one cryptic species was detected (A. nishimurae), and one isolate exhibited G138S resistance mutation with elevated MICs. The overall incidence of aspergillosis was measured at ∼3.4% case-years, and mostly in juveniles. The analysis of microsatellite polymorphism revealed a high level of genetic diversity among A. fumigatus clinical isolates. In contrast, one environmental strain appeared largely overrepresented during the summer sampling session. In all, the rural location of the zoo did not influence the emergence of resistant strains.
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Affiliation(s)
- Estelle Cateau
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France.,Parasitologie - Mycologie, Hôpital de la Milétrie, 86021 CHU Poitiers, France
| | - Antoine Leclerc
- ZooParc de Beauval & Beauval Nature, 41110 Saint-Aignan-sur-Cher, France
| | - Noémie Cartier
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France
| | - Isabel Valsechi
- Dynamyc - Université Paris-Est Créteil-Val de Marne (UPEC), Ecole nationale vétérinaire d'Alfort (EnvA), USC Anses, 94000 Créteil, France
| | - Éric Bailly
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France
| | - Ronan Le Senechal
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France
| | - Margaux Becerra
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France
| | - Brice Le Gallou
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France
| | - Rose-Anne Lavergne
- Parasitologie - Mycologie, Hôtel Dieu, 44093 CHU Nantes, France.,Institute de Recherche en Santé 2, EA1155-IICiMed, 44200 Université de Nantes Atlantique, France
| | - Adélaïde Chesnay
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France.,Centre d'Etude des Pathologies Respiratoires - Inserm U100, Faculté de médecine, 37032 Université de Tours, France
| | - Jean-Patrice Robin
- Institut pluridisciplinaire Hubert Curien, CNRS - UMR 7178, 67037 Université de Strasbourg, France
| | - Carolyn Cray
- Miami University, Comparative pathology, Miller school of medicien, 33136 Miami - Florida, U.S.A
| | - Nicolas Goddard
- ZooParc de Beauval & Beauval Nature, 41110 Saint-Aignan-sur-Cher, France
| | - Milan Thorel
- ZooParc de Beauval & Beauval Nature, 41110 Saint-Aignan-sur-Cher, France
| | - Jacques Guillot
- Dynamyc - Université Paris-Est Créteil-Val de Marne (UPEC), Ecole nationale vétérinaire d'Alfort (EnvA), USC Anses, 94000 Créteil, France.,Oniris, Ecole nationale vétérinaire de Nantes, 44307 Nantes, France
| | - Baptiste Mulot
- ZooParc de Beauval & Beauval Nature, 41110 Saint-Aignan-sur-Cher, France
| | - Guillaume Desoubeaux
- Parasitologie - Mycologie - Médecine tropicale, Hôpital Bretonneau, 37044 CHRU Tours, France.,Centre d'Etude des Pathologies Respiratoires - Inserm U100, Faculté de médecine, 37032 Université de Tours, France
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9
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Bose APH, Dabernig-Heinz J, Koch L, Grimm J, Lang S, Hegedűs B, Banda T, Makasa L, Jordan A, Sefc KM. Parentage analysis across age cohorts reveals sex differences in reproductive skew in a group-living cichlid fish, Neolamprologus multifasciatus. Mol Ecol 2022; 31:2418-2434. [PMID: 35170123 DOI: 10.1111/mec.16401] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
Abstract
Group-living animals are often faced with complex reproductive decisions, namely how to partition within-group reproduction, how to obtain extra-group reproduction, and how these two means of reproduction should be balanced. The solutions to these questions can be difficult to predict because ecological conditions can affect the scopes for within-group and extra-group reproduction in complex ways. For example, individuals that are restricted from moving freely around their habitats may have limited extra-group reproductive opportunities, but at the same time, groups may live in close proximities to one another, which could potentially have the opposite effect. The group-living cichlid fish, Neolamprologus multifasciatus, experiences such ecological conditions, and we conducted an intensive genetic parentage analysis to investigate how reproduction is distributed within and among groups for both males and females. We found that cohabiting males live in 'high-skew' societies, where dominant males monopolize the majority of within-group reproduction, while females live in 'low-skew' societies, where multiple females can produce offspring concurrently. Despite extremely short distances separating groups, we inferred only very low levels of extra-group reproduction suggesting that subordinate males have very limited reproductive opportunities. A strength of our parentage analysis lies in its inclusion of individuals that spanned a wide age range, from young fry to adults. We outline the logistical circumstances when very young offspring may not always be accessible to parentage researchers, and present strategies to overcome the challenges of inferring mating patterns from a wide age range of offspring.
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Affiliation(s)
- Aneesh P H Bose
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Lukas Koch
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | | | | | | | - Taylor Banda
- Lake Tanganyika Research Unit, Department of Fisheries, Ministry of Fisheries and Livestock, Mpulungu, Zambia
| | - Lawrence Makasa
- Lake Tanganyika Research Unit, Department of Fisheries, Ministry of Fisheries and Livestock, Mpulungu, Zambia
| | - Alex Jordan
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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10
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Korfanty GA, Dixon M, Jia H, Yoell H, Xu J. Genetic Diversity and Dispersal of Aspergillus fumigatus in Arctic Soils. Genes (Basel) 2021; 13:19. [PMID: 35052359 DOI: 10.3390/genes13010019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
Aspergillus fumigatus is a saprophytic mold and an opportunistic pathogen with a broad geographic and ecological distribution. A. fumigatus is the most common etiological agent of aspergillosis, affecting over 8,000,000 individuals worldwide. Due to the rising number of infections and increasing reports of resistance to antifungal therapy, there is an urgent need to understand A. fumigatus populations from local to global levels. However, many geographic locations and ecological niches remain understudied, including soil environments from arctic regions. In this study, we isolated 32 and 52 A. fumigatus strains from soils in Iceland and the Northwest Territories of Canada (NWT), respectively. These isolates were genotyped at nine microsatellite loci and the genotypes were compared with each other and with those in other parts of the world. Though significantly differentiated from each other, our analyses revealed that A. fumigatus populations from Iceland and NWT contained evidence for both clonal and sexual reproductions, and shared many alleles with each other and with those collected from across Europe, Asia, and the Americas. Interestingly, we found one triazole-resistant strain containing the TR34 /L98H mutation in the cyp51A gene from NWT. This strain is closely related to a triazole-resistant genotype broadly distributed in India. Together, our results suggest that the northern soil populations of A. fumigatus are significantly influenced by those from other geographic regions.
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11
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Majima H, Arai T, Kusuya Y, Takahashi H, Watanabe A, Miyazaki Y, Kamei K. Genetic differences between Japan and other countries in cyp51A polymorphisms of Aspergillus fumigatus. Mycoses 2021; 64:1354-1365. [PMID: 34558115 DOI: 10.1111/myc.13370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/26/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Mutations in cyp51A gene are known as main mechanisms of azole resistance in Aspergillus fumigatus, whereas azole-susceptible strains also carry cyp51A mutations (polymorphisms). The polymorphisms found in Europe mainly consist of two combinations of mutations, that is combinations of five single-nucleotide polymorphisms (SNPs) of cyp51A, referred to as cyp51A-5SNPs, and combinations of three SNPs of cyp51A, referred to as cyp51A-3SNPs. Few studies have compared the distributions of cyp51A polymorphisms between different regions. OBJECTIVES The aim of this study was to investigate the regional differences of cyp51A polymorphisms. METHODS We compared the proportions of cyp51A polymorphisms in clinical and environmental strains isolated in various countries, and analysed the strains phylogenetically using short tandem repeats (STRs) and whole-genome sequence (WGS). RESULTS Among the Japanese strains, 15 out of 98 (15.3%) clinical strains and 8 out of 95 (8.4%) environmental strains had cyp51A polymorphisms. A mutation of cyp51AN248K was the most prevalent polymorphism in both clinical (n = 14, 14.3%) and environmental strains (n = 3, 3.2%). Only one environmental strain harboured cyp51A-5SNPs, which was reported to be the most prevalent in Europe. For phylogenetic analyses using STRs and WGS, 183 and 134 strains, respectively, were employed. They showed that most of the strains with cyp51AN248K clustered in the clades different from those of the strains with cyp51A-5SNPs and cyp51A-3SNPs as well as from those with TR34 /L98H mutations. CONCLUSIONS This study suggests that there are genetic differences between cyp51A polymorphisms of A. fumigatus in Japan and Europe.
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Affiliation(s)
- Hidetaka Majima
- Division of Clinical Research, Medical Mycology Research Center, Chiba University, Chiba, Japan.,Department of Respiratory Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Teppei Arai
- Division of Clinical Research, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Yoko Kusuya
- Division of Bioresources, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Hiroki Takahashi
- Division of Bioresources, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Akira Watanabe
- Division of Clinical Research, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Katsuhiko Kamei
- Division of Clinical Research, Medical Mycology Research Center, Chiba University, Chiba, Japan
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12
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Argyropoulos DC, Ruybal‐Pesántez S, Deed SL, Oduro AR, Dadzie SK, Appawu MA, Asoala V, Pascual M, Koram KA, Day KP, Tiedje KE. The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Mol Ecol 2021; 30:3974-3992. [PMID: 34143538 PMCID: PMC8456823 DOI: 10.1111/mec.16029] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 01/16/2023]
Abstract
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.
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Affiliation(s)
- Dionne C. Argyropoulos
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Shazia Ruybal‐Pesántez
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical ResearchMelbourneVic.Australia
- Present address:
Department of Medical Biology and Bio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Burnet InstituteMelbourneVic.Australia
| | - Samantha L. Deed
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Abraham R. Oduro
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Samuel K. Dadzie
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Maxwell A. Appawu
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Victor Asoala
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Mercedes Pascual
- Department of Ecology and EvolutionUniversity of ChicagoChicagoUSA
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Karen P. Day
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Kathryn E. Tiedje
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
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13
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Laczi M, Kopena R, Sarkadi F, Kötél D, Török J, Rosivall B, Hegyi G. Triparental care in the collared flycatcher ( Ficedula albicollis): Cooperation of two females with a cuckolded male in rearing a brood. Ecol Evol 2021; 11:10754-10760. [PMID: 34429878 PMCID: PMC8366852 DOI: 10.1002/ece3.7923] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Certain predominant forms of mating and parental care systems are assumed in several model species among birds, but the opportunistic and apparently infrequent variations of "family structures" may often remain hidden due to methodological limitations with regard to genetic or behavioral observations. One of the intensively studied model species, the collared flycatcher (Ficedula albicollis), is usually characterized by social monogamy with polyterritorial, facultative social polygyny, and frequent extrapair mating and extrapair paternity. During a brood-size manipulation experiment, we observed two females and a male delivering food at an enlarged brood. A combination of breeding phenology data (egg laying and hatching date), behavioral data (feeding rates) from video recordings at 10 days of nestling age, and microsatellite genotyping for maternity and paternity suggests a situation of an unrelated female helping a pair in chick rearing. Such observations highlight the relevance of using traditional techniques and genetic analyses together to assess the parental roles within a population, which becomes more important where individuals may dynamically switch from their main and presupposed roles according to the actual environmental conditions.
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Affiliation(s)
- Miklós Laczi
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- The Barn Owl FoundationOrosztonyHungary
| | - Renáta Kopena
- Centre for Ecological ResearchInstitute of Ecology and BotanyVácrátótHungary
| | - Fanni Sarkadi
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Dóra Kötél
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - János Török
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
- Ecology Research Group of the Hungarian Academy of SciencesBudapestHungary
| | - Balázs Rosivall
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Gergely Hegyi
- Behavioural Ecology GroupDepartment of Systematic Zoology and EcologyInstitute of BiologyELTE Eötvös Loránd UniversityBudapestHungary
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14
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Stroheker S, Dubach V, Vögtli I, Sieber TN. Investigating Host Preference of Root Endophytes of Three European Tree Species, with a Focus on Members of the Phialocephala fortinii- Acephala applanata Species Complex (PAC). J Fungi (Basel) 2021; 7:jof7040317. [PMID: 33921799 PMCID: PMC8073920 DOI: 10.3390/jof7040317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 10/29/2022] Open
Abstract
Host preference of root endophytes of the three European tree species of Norway spruce (Picea abies), common ash (Fraxinus excelsior), and sycamore maple (Acer pseudoplatanus) were investigated in two forest stands near Zurich, Switzerland. The focus was placed on members of the Phialocephala fortinii s.l. (sensu lato)-Acephala applanata species complex (PAC), as well as other dark septate endopyhtes (DSE). PAC species were identified based on 13 microsatellite loci. Eleven PAC species were found, with Phialocephala helvetica, P. europaea being the most frequent. All but cryptic species 12 (CSP12) preferred Norway spruce as a host. Though very rare in general, CSP12 was most frequently isolated from maple roots. Regarding the abundant PAC species, P. helvetica and P. europaea, the preference of spruce as a host was least pronounced in P. europaea, as it was also often isolated from ash and maple. It is the first record of PAC found on common ash (Fraxinus excelsior). Cadophora orchidicola, a close relative of PAC, has frequently been isolated from ash. Various species of the Nectriaceae (Cylindrocarpon spp.) have often been isolated, particularly from maple roots. By comparison, Pezicula spp. (Cryptosporiopsis spp.) was found to be abundant on all three hosts. Phomopsis phaseoli exhibits a clear preference for spruce.
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Affiliation(s)
- Sophie Stroheker
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Swiss Forest Protection, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland; (V.D.); (I.V.)
- Correspondence: ; Tel.: +41-447-392-368
| | - Vivanne Dubach
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Swiss Forest Protection, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland; (V.D.); (I.V.)
| | - Irina Vögtli
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Swiss Forest Protection, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland; (V.D.); (I.V.)
| | - Thomas N. Sieber
- ETH Zurich, Institute of Integrative Biology, Forest Pathology and Dendrology, Universitätstrasse 16, 8092 Zurich, Switzerland;
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15
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Díaz-García J, Mesquida A, Sánchez-Carrillo C, Reigadas E, Muñoz P, Escribano P, Guinea J. Monitoring the Epidemiology and Antifungal Resistance of Yeasts Causing Fungemia in a Tertiary Care Hospital in Madrid, Spain: Any Relevant Changes in the Last 13 Years? Antimicrob Agents Chemother 2021; 65:e01827-20. [PMID: 33468487 PMCID: PMC8097463 DOI: 10.1128/aac.01827-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 08/24/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
We conducted an updated analysis on yeast isolates causing fungemia in patients admitted to a tertiary hospital in Madrid, Spain, over a 13-year period. We studied 896 isolates associated with 872 episodes of fungemia in 857 hospitalized patients between January 2007 and December 2019. Antifungal susceptibility was assessed by EUCAST EDef 7.3.2. Mutations conferring azole and echinocandin resistance were further studied, and genotyping of resistant clones was performed with species-specific microsatellite markers. Candida albicans (45.8%) was the most frequently identified species, followed by the Candida parapsilosis complex (26.4%), Candida glabrata (12.3%), Candida tropicalis (7.3%), Candida krusei (2.3%), other Candida spp. (3.1%), and non-Candida yeasts (2.8%). The rate of fluconazole resistance in Candida spp. was 4.7%, ranging from 0% (C. parapsilosis) to 9.1% (C. glabrata). The overall rate of echinocandin resistance was 3.1%. Resistance was highly influenced by the presence of intrinsically resistant species. Although the number of isolates between 2007 and 2013 was almost 2-fold higher than that in the period from 2014 to 2019 (566 versus 330), fluconazole resistance in Candida spp. was greater in the second period (3.5% versus 6.8%; P < 0.05), while overall resistance to echinocandins remained stable (3.5% versus 2.4%; P > 0.05). Resistant clones were collected from different wards and/or time points, suggesting that there were no epidemiological links. The number of fungemia episodes has been decreasing over the last 13 years, with a slight increase in the rate of fluconazole resistance and stable echinocandin resistance. Antifungal resistance is not the cause of the spread of resistant clones.
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Affiliation(s)
- Judith Díaz-García
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Aina Mesquida
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
| | - Elena Reigadas
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Pilar Escribano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jesús Guinea
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias-CIBERES (CB06/06/0058), Madrid, Spain
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16
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Khan MR, Imtiaz M, Ahmad B, Munir A, Rattu AUR, Facho ZH, Ali S. Diversity in Puccinia striiformis populations causing the 2013 yellow rust epidemics on major wheat cultivars of Pakistan. Mycologia 2020; 112:871-879. [PMID: 32813615 DOI: 10.1080/00275514.2020.1792263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Wheat yellow/stripe rust pathogen Puccinia striiformis is highly diverse and recombinant in the north of Pakistan in the Himalayan region. However, little is known about the role of this diversity in disease epidemics in areas where wheat yellow rust is an important disease in both irrigated and rain-fed wheat (i.e., in the plains of Pakistan). We explored the population diversity in P. striiformis during the rust epidemics of 2013 in the major wheat-growing regions of Pakistan (the Himalayan region, central Khyber Pakhtunkhwa [KP], southern KP, central and northern Punjab). Disease severities among commonly grown cultivars ranged from 5% to 100%. Microsatellite genotyping with 16 simple sequence repeat (SSR) markers revealed a high diversity among 266 isolates collected during the season, with the Simpson diversity index (Simpson 1949) ranging from 0.870 (Himalayan) to 0.955 (southern KP). The recombination signature was stronger in the Himalayan population and central KP compared with wheat-growing regions of Punjab and southern KP. The overall diversity was higher in Pakistan relative to the clonal populations present in Europe, Australia, and the Americas. Analyses of population subdivision revealed no clear evidence of spatial structure for samples from Pakistan, with a maximum fixation index (FST) value of only 0.10. The lack of clear population subdivision could be attributed to migration of pathogen. In turn, the high diversity of P. striiformis in Pakistan represents a potential threat to wheat production in the region and worldwide, as a possible source to found clonal populations in diverse wheat-growing areas.
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Affiliation(s)
- Muhammad Rameez Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Centre (CIMMYT) , Islamabad, Pakistan
| | - Bashir Ahmad
- Directorate of Agriculture Research, Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Anjum Munir
- Crop Disease Research Institute, National Agricultural Research Centre , Islamabad, Pakistan
| | | | - Zakir Hussain Facho
- Department of Plant Breeding & Genetics, The University of Agriculture , Peshawar, Pakistan
| | - Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
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17
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Wongnikong W, van Brunschot SL, Hereward JP, De Barro PJ, Walter GH. Testing mate recognition through reciprocal crosses of two native populations of the whitefly Bemisia tabaci (Gennadius) in Australia. Bull Entomol Res 2020; 110:328-339. [PMID: 31640818 DOI: 10.1017/s0007485319000683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/10/2023]
Abstract
Bemisia tabaci (Gennadius) represents a relatively large cryptic species complex. Australia has at least two native populations of B. tabaci sensu lato and these were first found on different host plants in different parts of Australia. The species status of these populations has not been resolved, although their mitochondrial sequences differ by 3.82-4.20%. We addressed the question of whether these AUSI and AUSII B. tabaci populations are distinct species. We used reciprocal cross-mating tests to establish whether the insects from these different populations recognize one another as potential mating partners. The results show that the two native Australian populations of B. tabaci have a mating sequence with four phases, each of which is described. Not all pairs in the control crosses mated and the frequency of mating differed across them. Some pairs in the AUSI-M × AUSII-F did mate (15%) and did produce female progeny, but the frequency was extremely low relative to controls. Microsatellite genotyping of the female progeny produced in the crosses showed these matings were successful. None of the AUSII-M × AUSI-F crosses mated although some of the males did search for females. These results demonstrate the critical role of the mate recognition process and the need to assess this directly in cross-mating tests if the species status of different populations is to be tested realistically. In short, AUSI and AUSII B. tabaci populations are distinct species because the individual males and females do not recognize individuals of the alternative population as potential mating partners.
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Affiliation(s)
- W Wongnikong
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
| | - S L van Brunschot
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
- Agriculture, Health & Environment Department, Natural Resources Institute, University of Greenwich, Medway Campus, Central Avenue, Chatham Maritime ME4 4TB, UK
| | - J P Hereward
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
| | - P J De Barro
- CSIRO Health & Biosecurity, GPO Box 2583, Brisbane QLD 4001, Australia
| | - G H Walter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland4072, Australia
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18
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Roh ME, Tessema SK, Murphy M, Nhlabathi N, Mkhonta N, Vilakati S, Ntshalintshali N, Saini M, Maphalala G, Chen A, Wilheim J, Prach L, Gosling R, Kunene S, S Hsiang M, Greenhouse B. High Genetic Diversity of Plasmodium falciparum in the Low-Transmission Setting of the Kingdom of Eswatini. J Infect Dis 2020; 220:1346-1354. [PMID: 31190073 PMCID: PMC6743842 DOI: 10.1093/infdis/jiz305] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 01/07/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To better understand transmission dynamics, we characterized Plasmodium falciparum genetic diversity in Eswatini, where transmission is low and sustained by importation. METHODS Twenty-six P. falciparum microsatellites were genotyped in 66% of confirmed cases (2014-2016; N = 582). Population and within-host diversity were used to characterize differences between imported and locally acquired infections. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone. RESULTS Parasite population in Eswatini was highly diverse (expected heterozygosity [HE] = 0.75) and complex: 67% polyclonal infections, mean multiplicity of infection (MOI) 2.2, and mean within-host infection fixation index (FWS) 0.84. Imported cases had comparable diversity to local cases but exhibited higher MOI (2.4 vs 2.0; P = .004) and lower mean FWS (0.82 vs 0.85; P = .03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections. CONCLUSIONS In contrast to the common perception that P. falciparum diversity declines with decreasing transmission intensity, Eswatini isolates exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.
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Affiliation(s)
- Michelle E Roh
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Sofonias K Tessema
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Maxwell Murphy
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | | | | | | | | | - Manik Saini
- Clinton Health Access Initiative, Mbabane, Eswatini
| | | | - Anna Chen
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Jordan Wilheim
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Lisa Prach
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco
| | - Roly Gosling
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | | | - Michelle S Hsiang
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Pediatrics, University of California, San Francisco.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco.,Chan Zuckerberg Biohub, San Francisco, California
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19
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Martini C, Torelli R, de Groot T, De Carolis E, Morandotti GA, De Angelis G, Posteraro B, Meis JF, Sanguinetti M. Prevalence and Clonal Distribution of Azole-Resistant Candida parapsilosis Isolates Causing Bloodstream Infections in a Large Italian Hospital. Front Cell Infect Microbiol 2020; 10:232. [PMID: 32523896 PMCID: PMC7261875 DOI: 10.3389/fcimb.2020.00232] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 01/12/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
The most prevalent cause of nosocomial bloodstream infection (BSI) among non-C. albicans Candida species, Candida parapsilosis, may not only be resistant to azole antifungal agents but also disseminate to vulnerable patients. In this survey of BSIs occurring at a large Italian hospital between May 2014 and May 2019, C. parapsilosis accounted for 28.5% (241/844) of all Candida isolates causing BSI episodes. The majority of episodes (151/844) occurred in medical wards. Across the 5 yearly periods, the rates of azole non-susceptibility were 11.8% (4/34), 17.8% (8/45), 28.6% (12/42), 32.8% (19/58), and 17.7% (11/62), respectively, using the Sensititre YeastOne® method. Among azole non-susceptible isolates (54/241; 22.4%), 49 were available for further investigation. Using the CLSI reference method, all 49 isolates were resistant to fluconazole and, except one (susceptible dose-dependent), to voriconazole. Forty (81.6%) isolates harbored the Erg11p Y132F substitution and nine (18.4%) isolates the Y132F in combination with the Erg11p R398I substitution. According to their genotypes, as defined using a microsatellite analysis based on six short tandem repeat markers, 87.7% of isolates (43/49) grouped in two major clusters (II and III), whereas 4.1% of isolates (2/49) belonged to a separate cluster (I). Interestingly, all the isolates from cluster II harbored the Y132F substitution, and those from cluster III harbored both Y132F and R398I substitutions. Of 56 non-Italian isolates included as controls, two Indian isolates with the Y132F substitution had a genotype clearly differing from that of the isolates from clusters II and I. In conclusion, these findings show the dominance of clonal Y132F isolates in our hospital and suggest detection of the Y132F substitution as helpful tool to prevent transmission among hospitalized patients at risk of BSI.
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Affiliation(s)
- Cecilia Martini
- Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Torelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands
| | - Elena De Carolis
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Grazia Angela Morandotti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital (CWZ), Nijmegen, Netherlands.,Centre of Expertise in Mycology Radboudumc/Canisius Wilhelmina Hospital, Nijmegen, Netherlands.,Bioprocess Engineering and Biotechnology Graduate Program, Federal University of Paraná, Curitiba, Brazil
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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20
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Kiasat N, Rezaei-Matehkolaei A, Mahmoudabadi AZ. Microsatellite Typing and Antifungal Susceptibility of Candida glabrata Strains Isolated From Patients With Candida Vaginitis. Front Microbiol 2019; 10:1678. [PMID: 31417505 PMCID: PMC6685060 DOI: 10.3389/fmicb.2019.01678] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/08/2019] [Indexed: 01/30/2023] Open
Abstract
Vulvovaginal candidiasis (VVC) is a yeast infection with a global reach and millions of dollars are spent annually for its diagnosis and treatment. Recently, Candida glabrata with different degrees of antifungal resistance has been considered as the second most common cause of vaginal infections. The aim of the present study is to determine the antifungal susceptibility and molecular epidemiology profiles of C. glabrata isolates from patients with VVC. Sixty-one C. glabrata isolates were examined for antifungal susceptibility using the EUCAST broth microdilution method. Moreover, microsatellite length polymorphism (MLP) was used for typing the C. glabrata isolates using six microsatellite markers. Overall, 13, 3.3, and 0% of the isolates were non-wild types to itraconazole, posaconazole, and voriconazole, respectively. Sixty (98.4%) isolates were an intermediate phenotype to fluconazole and only one isolate was fluconazole resistant. Microsatellite length polymorphism with a discriminatory power of 0.964 identified 35 distinct types and 24 singleton genotypes. The assessment of the population genetic structure revealed that the non-wild-type population had a moderate genetic differentiation compared to the wild type population (FST = 0.1457). It was also found that the most common genotypes were G27 (eight strains), G12 (six strains), and G4 (five strains). We found that eight strains were resistant/a non-wild phenotype to itraconazole. Five out of eight (62.5%) resistant/non-wild phenotype strains correlated to a predominant genotype (GT27) and the rest belonged to GT11 (12.5%), GT29 (12.5%), and GT28 (12.5%). The current study is the first molecular epidemiology study in the southwest of Iran and demonstrates the antifungal susceptibility profiles of C. glabrata in it. This study shows a wide range of the genetic diversity of C. glabrata (35 different genotypes) from VVC in the southwest of Iran. The majority of the non-wild isolates had a dominant genotype or genotypes related to this dominant genotype (clonal cluster one).
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Affiliation(s)
- Neda Kiasat
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Rezaei-Matehkolaei
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Zarei Mahmoudabadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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21
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Baudrin LG, Deleuze JF, How-Kit A. Molecular and Computational Methods for the Detection of Microsatellite Instability in Cancer. Front Oncol 2018; 8:621. [PMID: 30631754 PMCID: PMC6315116 DOI: 10.3389/fonc.2018.00621] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Microsatellite instability (MSI) is a genomic alteration in which microsatellites, usually of one to four nucleotide repeats, accumulate mutations corresponding to deletions/insertions of a few nucleotides. The MSI phenotype has been extensively characterized in colorectal cancer and is due to a deficiency of the DNA mismatch repair system. MSI has recently been shown to be present in most types of cancer with variable frequencies (from <1 to 30%). It correlates positively to survival outcome and predicts the response to immune checkpoint blockade therapy. The different methods developed for MSI detection in cancer require taking into consideration two critical parameters which influence method performance. First, the microsatellite markers used should be chosen carefully to ensure they are highly sensitive and specific for MSI detection. Second, the analytical method used should be highly resolute to allow clear identification of MSI and of the mutant allele genotype, and should present the lowest limit of detection possible for application in samples with low mutant allele frequency. In this review, we describe all the different molecular and computational methods developed to date for the detection of MSI in cancer, how they have evolved and improved over the years, and their advantages and drawbacks.
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Affiliation(s)
- Laura G Baudrin
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France.,Laboratoire d'Excellence GenMed Paris, Paris, France
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France.,Centre National de Recherche en Génomique Humaine, CEA-Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France
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22
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Shink KG, Sutton TM, Murphy JM, López JA. Genetic variation and population structure among larval Lethenteron spp. within the Yukon River drainage, Alaska. J Fish Biol 2018; 93:1130-1140. [PMID: 30306562 DOI: 10.1111/jfb.13833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The absence of information on genetic variation and population structure of lampreys Lethenteron spp. in the eastern part of their distribution limits our understanding of the migration ecology and spatial population genetic structure of the species. We examined genetic variation within and among three aggregations of Lethenteron spp. larvae in the Yukon River drainage, Alaska, using microsatellite genotypes. A total of 120 larval lampreys were genotyped at eight microsatellite loci. Global FST was 0.053 (95% CI 0.021-0.086), while pairwise FST values ranged from 0.048-0.057. Model-based Bayesian clustering analyses with sample locality priors (LOCPRIOR) identified three distinct, but admixed, genetic clusters that corresponded with the three aggregations. Estimates of contemporary gene flow indicate substantial reciprocal migration among sites consistent with no or low-fidelity natal homing. These results are largely in agreement with previous reports of historic and contemporary gene flow among Lethenteron spp. in other parts of their geographic distribution.
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Affiliation(s)
- Katie G Shink
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
| | - Trent M Sutton
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
| | - James M Murphy
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA Fisheries, Juneau, Alaska
| | - J Andrés López
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska
- University of Alaska Museum of the North, Fairbanks, Alaska
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23
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Gómez R, Méndez-Vigo B, Marcer A, Alonso-Blanco C, Picó FX. Quantifying temporal change in plant population attributes: insights from a resurrection approach. AoB Plants 2018; 10:ply063. [PMID: 30370042 PMCID: PMC6198925 DOI: 10.1093/aobpla/ply063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/05/2018] [Indexed: 05/11/2023]
Abstract
Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to rapid environmental shifts, such as the ones imposed by global climate change. To that end, we undertook a resurrection approach in Spanish populations of the annual plant Arabidopsis thaliana that were sampled twice over a decade. Annual weather records were compared to their historical records to extract patterns of climatic shifts over time. We evaluated the differences between samplings in flowering time, a key life-history trait with adaptive significance, with a field experiment. We also estimated genetic diversity and differentiation based on neutral nuclear markers and nucleotide diversity in candidate flowering time (FRI and FLC) and seed dormancy (DOG1) genes. The role of genetic drift was estimated by computing effective population sizes with the temporal method. Overall, two climatic scenarios were detected: intense warming with increased precipitation and moderate warming with decreased precipitation. The average flowering time varied little between samplings. Instead, within-population variation in flowering time exhibited a decreasing trend over time. Substantial temporal changes in genetic diversity and differentiation were observed with both nuclear microsatellites and candidate genes in all populations, which were interpreted as the result of natural demographic fluctuations. We conclude that drought stress caused by moderate warming with decreased precipitation may have the potential to reduce within-population variation in key life-cycle traits, perhaps as a result of stabilizing selection on them, and to constrain the genetic differentiation over time. Besides, the demographic behaviour of populations probably accounts for the substantial temporal patterns of genetic variation, while keeping rather constant those of phenotypic variation.
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Affiliation(s)
- Rocío Gómez
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Arnald Marcer
- CREAF, Cerdanyola del Vallès, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Corresponding author’s e-mail address:
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24
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Bose APH, Zimmermann H, Henshaw JM, Fritzsche K, Sefc KM. Brood-tending males in a biparental fish suffer high paternity losses but rarely cuckold. Mol Ecol 2018; 27:4309-4321. [PMID: 30182504 PMCID: PMC6221093 DOI: 10.1111/mec.14857] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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] [Received: 02/22/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022]
Abstract
Extra‐pair paternity within socially monogamous mating systems is well studied in birds and mammals but rather neglected in other animal taxa. In fishes, social monogamy has evolved several times but few studies have investigated the extent to which pair‐bonded male fish lose fertilizations to cuckolders and gain extra‐pair fertilizations themselves. We address this gap and present genetic paternity data collected from a wild population of Variabilichromis moorii, a socially monogamous African cichlid with biparental care of offspring. We show that brood‐tending, pair‐bonded males suffer exceptionally high paternity losses, siring only 63% of the offspring produced by their female partners on average. The number of cuckolders per brood ranged up to nine and yet, surprisingly, brood‐tending males in the population were rarely the culprits. Brood‐tending males sired very few extra‐pair offspring, despite breeding in close proximity to one another. While unpaired males were largely responsible for the cuckoldry, pair‐bonded males still enjoyed higher fertilization success than individual unpaired males. We discuss these results in the context of ecological and phenotypic constraints on cuckoldry and the fitness payoffs of alternative male tactics. Our study provides new insights into how pair‐bonded males handle the trade‐off between securing within‐pair and extra‐pair reproduction.
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25
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Vallant S, Niederstätter H, Berger B, Lentner R, Parson W. Increased DNA typing success for feces and feathers of capercaillie ( Tetrao urogallus) and black grouse ( Tetrao tetrix). Ecol Evol 2018; 8:3941-3951. [PMID: 29721270 PMCID: PMC5916295 DOI: 10.1002/ece3.3951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 09/29/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/02/2022] Open
Abstract
Noninvasive sampling, for example, of droppings or feathers, is a promising approach for molecular genetic studies on endangered and elusive animal species. Yet, such specimens are known for containing only minute amounts of DNA, resulting in lower typing success rates relative to analyses on fresh tissues such as muscle or blood. Furthermore, artefactual signals as well as contamination are more likely to occur when DNA is limited. To increase the reliability of DNA typing from noninvasive samples, optimized DNA extraction and polymerase chain reaction protocols were developed, taking advantage of developments in the forensic field aiming at successful molecular genetic analysis of DNA templates being low in quality and quantity. In the framework of an extensive monitoring project on population dynamics of capercaillie and black grouse in the Tyrolean Alps, feces samples and molted feathers from both species were collected. On a subset comprising about 200 specimens of either species, eight polymorphic short tandem repeat (STR) markers were analyzed to test these improved protocols. Besides optimizing DNA yields, both lowered sample consumption and reduced hands‐on time were achieved, and the rates of informative profiles amounted to 90.7% for capercaillie and 92.4% for black grouse. Similarly, high success rates had not been achieved in earlier studies and demonstrate the benefit of the improved methodology, which should be easily adaptable for use on animal species other than those studied here. The STR genotypes were not only powerful enough to discriminate among unrelated birds but also appeared fit for telling apart closely related animals, as indicated by Pi and Pisib values. The software package allelematch aided analysis of genotypes featuring possible dropout and drop‐in effects. Finally, a comparison between molecular genetic and morphology‐based species‐of‐origin determination revealed a high degree of concordance.
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Affiliation(s)
| | | | - Burkhard Berger
- Institute of Legal Medicine Medical University of Innsbruck Innsbruck Austria
| | - Reinhard Lentner
- Institute of Zoology University of Innsbruck Innsbruck Austria.,Department of Environmental Protection Provincial Government of Tyrol Innsbruck Austria
| | - Walther Parson
- Institute of Legal Medicine Medical University of Innsbruck Innsbruck Austria.,Forensic Science Program Pennsylvania State University University Park PA USA
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26
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Luan J, Sun X, Fei Z, Douglas AE. Maternal Inheritance of a Single Somatic Animal Cell Displayed by the Bacteriocyte in the Whitefly Bemisia tabaci. Curr Biol 2018; 28:459-465.e3. [PMID: 29395925 PMCID: PMC5807091 DOI: 10.1016/j.cub.2017.12.041] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 10/17/2017] [Revised: 11/18/2017] [Accepted: 12/18/2017] [Indexed: 11/21/2022]
Abstract
Bacteriocytes are insect cells harboring symbiotic bacteria that are required by their insect host and are transmitted vertically via the female ovary [1]. In most insect groups, the bacteria are released from the bacteriocytes and transferred to the ovary [2, 3], but in whiteflies, maternal bacteriocytes migrate to each egg [4, 5, 6], where they have been reported to lyse, releasing the symbionts [1]. To investigate bacteriocyte inheritance in whiteflies further, we applied microsatellite genotyping and genomic analysis to a genetically diverse population of Bemisia tabaci, and we observed the fate of the bacteriocyte in embryos. Surprisingly, the microsatellite profile of the bacteriocytes was uniform, and insect cross experiments demonstrated that the bacteriocytes have a stable genotype that differs from the genotype of the insect head (which lacks bacteriocytes). Comparative genomic analysis indicates that genomes of the bacteriocyte and whitefly head are distinct. Interestingly, the bacterioyte genome contains the canonical arthropod telomere repeats TTAGG, and the bacteriocytes express telomere maintenance genes that may underlie cellular immortality in animal cells [7]. Microscopy observations confirmed that a single bacteriocyte transmitted to each egg is retained and divides once just before egg hatch, yielding two bacteriocytes in the neonate insect. These data demonstrate the maternal inheritance of an absolutely required somatic insect cell, violating the developmental separation of germline and soma [8, 9]. Future investigation on the mechanism and phylogenetic distribution of maternally inherited bacteriocytes will shed light on the developmental origins and evolutionary diversification of bacteriocytes [10] and the processes underlying cellular immortality [11]. Whitefly bacteriocytes have different microsatellite alleles from other somatic cells The bacteriocyte genotype is stable over three sexual generations of the insect Bacteriocyte genomes in different insects are genetically very similar The single bacteriocyte transmitted to the sexual egg persists through embryogenesis
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Affiliation(s)
- Junbo Luan
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Xuepeng Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA; USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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27
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Hou X, Xiao M, Chen SCA, Kong F, Wang H, Chu YZ, Kang M, Sun ZY, Hu ZD, Li RY, Lu J, Liao K, Hu TS, Ni YX, Zou GL, Zhang G, Fan X, Zhao YP, Xu YC. Molecular Epidemiology and Antifungal Susceptibility of Candida glabrata in China (August 2009 to July 2014): A Multi-Center Study. Front Microbiol 2017; 8:880. [PMID: 28588560 PMCID: PMC5440528 DOI: 10.3389/fmicb.2017.00880] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 03/04/2017] [Accepted: 05/02/2017] [Indexed: 02/05/2023] Open
Abstract
Candida glabrata is an increasingly important cause of invasive candidiasis. In China, relatively little is known of the molecular epidemiology of C. glabrata and of its antifungal susceptibility patterns. Here we studied 411 non-duplicate C. glabrata isolates from 411 patients at 11 hospitals participating in the National China Hospital Invasive Fungal Surveillance Net program (CHIF-NET; 2010-2014). Genotyping was performed using multilocus sequence typing (MLST) employing six genetic loci and by microsatellite analysis. Antifungal susceptibility testing was performed using Sensititre YeastOne™ YO10 methodology. Of 411 isolates, 35 sequence types (ST) were identified by MLST and 79 different genotypes by microsatellite typing; the latter had higher discriminatory power than MLST in the molecular typing of C. glabrata. Using MLST, ST7 and ST3 were the most common STs (66.4 and 9.5% of all isolates, respectively) with 24 novel STs identified; the most common microsatellite types were T25 (30.4% of all isolates) and T31 (12.4%). Resistance to fluconazole (MIC > 32 μg/mL) was seen in 16.5% (68/411) of isolates whilst MICs of >0.5 μg/mL for voriconazole, >2 μg/mL for itraconazole and >2 μg/mL for posaconazole were seen for 28.7, 6.8, and 7.3% of isolates, respectively; 14.8% of all isolates cross-resistant/non-wide-type to fluconazole and voriconazole. Fluconazole resistant rates increased 3-fold over the 5-year period whilst that of isolates with non-WT MICs to voriconazole, 7-fold. All echinocandins exhibited >99% susceptibility rates against all isolates but notably one isolate exhibited multi-drug resistance to the azoles and echinocandins. The study has provided a global picture of the molecular epidemiology and drug resistance rates of C. glabrata in China during the period of the study.
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Affiliation(s)
- Xin Hou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, University of SydneySydney, NSW, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, University of SydneySydney, NSW, Australia
| | - He Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
| | - Yun-Zhuo Chu
- Department of Clinical Laboratory, The First Hospital of China Medical UniversityShenyang, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan UniversityChengdu, China
| | - Zi-Yong Sun
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Zhi-Dong Hu
- Department of Clinical Laboratory, Tianjin Medical University General HospitalTianjin, China
| | - Ruo-Yu Li
- Department of Clinical Laboratory, Peking University First HospitalBeijing, China
| | - Juan Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Harbin Medical UniversityHarbin, China
| | - Kang Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-Sen UniversityGuangzhou, China
| | - Tie-Shi Hu
- Department of Clinical Laboratory, The People's Hospital of Liaoning ProvinceShenyang, China
| | - Yu-Xing Ni
- Department of Clinical Microbiology and Infection Control, Ruijin Hospital Affiliated to School of Medicine, Shanghai Jiaotong UniversityShanghai, China
| | - Gui-Ling Zou
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Harbin Medical UniversityHarbin, China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
| | - Xin Fan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal DiseasesBeijing, China
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Morgado-Santos M, Carona S, Vicente L, Collares-Pereira MJ. First empirical evidence of naturally occurring androgenesis in vertebrates. R Soc Open Sci 2017; 4:170200. [PMID: 28573029 PMCID: PMC5451830 DOI: 10.1098/rsos.170200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Androgenesis among vertebrates is considered a rare phenomenon, with some cases reported so far, but linked to experiments involving gamete manipulation (artificial androgenesis). Herein, we report the first empirical evidence of the natural occurrence of spontaneous androgenesis in a vertebrate, the Squalius alburnoides allopolyploid complex. A genetically screened random sample of a natural population was allowed to reproduce in an isolated pond without any human interference, and the viable offspring obtained was later analysed for paternity. Both nuclear and mitochondrial markers showed that the only allodiploid fish found among all the allotriploid offspring was androgenetically produced by an allodiploid male. This specimen had no female nuclear genomic input, and the sequence of the mitochondrial fragment examined differed from that of the male progenitor, matching one of the parental females available in the pond, probably the mother. The possible role of androgenesis in the reproductive dynamics of this highly successful vertebrate complex is discussed.
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Affiliation(s)
- Miguel Morgado-Santos
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sara Carona
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Luís Vicente
- Centro de Filosofia das Ciências da Universidade de Lisboa (CFCUL), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Maria João Collares-Pereira
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Wang Y, Schwartz LE, Anderson D, Lin MT, Haley L, Wu RC, Vang R, Shih IM, Kurman RJ. Molecular analysis of ovarian mucinous carcinoma reveals different cell of origins. Oncotarget 2016; 6:22949-58. [PMID: 26355245 PMCID: PMC4673211 DOI: 10.18632/oncotarget.5146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 07/14/2015] [Accepted: 08/20/2015] [Indexed: 11/25/2022] Open
Abstract
It is believed that a subset of primary ovarian mucinous tumors is derived from mature teratomas [1–5]. To confirm this, we performed microsatellite genotyping using a variety of short tandem repeat makers and analyzed allelotypes of 8 mucinous tumors (4 mucinous carcinomas, 3 atypical proliferative mucinous tumors and 1 mucinous cystadenoma) associated with a teratoma to determine whether they were clonally related. 7 of the 8 mucinous tumors showed complete or a high degree of homozygosity. Among the 6 pairs of tumors with teratoma tissue available for comparison, 5 of 6 showed a high or complete degree of allelotypes matching, which differed from the somatic allelotypes of the normal control tissue. A discrepancy was detected between carcinoma and teratoma in one pair at several loci, with different X-chromosome inactivation patterns revealed by the HUMARA clonality assay. We also investigated the allelotypes of 16 ovarian mucinous carcinomas without a teratoma in young patients (range 13–30) and in 6 older patients (range 40–67) using the same method. None of these tumors showed pure homozygosity. The number of homozygous loci in this cohort was significantly lower than that in the first. Our results suggest first, that most mucinous tumors associated with a teratoma are derived from the teratoma but occasionally they could be collision tumors and second that the majority of pure mucinous tumors in young women in whom a teratoma is not present are not derived from a teratoma.
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Affiliation(s)
- Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Lauren Ende Schwartz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Derek Anderson
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Lisa Haley
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Ren-Chin Wu
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Pathology, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 33378, Taiwan
| | - Russell Vang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Robert J Kurman
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
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Sabino R, Sampaio P, Rosado L, Videira Z, Grenouillet F, Pais C. Analysis of clinical and environmental Candida parapsilosis isolates by microsatellite genotyping--a tool for hospital infection surveillance. Clin Microbiol Infect 2015; 21:954.e1-8. [PMID: 26070962 DOI: 10.1016/j.cmi.2015.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/18/2015] [Accepted: 06/01/2015] [Indexed: 11/21/2022]
Abstract
Candida parapsilosis emerged as an important opportunistic pathogen, causing candidaemia worldwide. Nosocomial outbreaks triggered by this species have been frequently described, particularly in cancer patients. For a better understanding of its epidemiology, several typing methods are used and microsatellite analysis has been reported as highly discriminant. The main objective of this work was to study C. parapsilosis isolates by application of microsatellite genotyping to distinguish epidemiologically related strains, compare clinical and environmental isolates and determine possible routes of dispersion of the isolates in the hospital setting. A total of 129 C. parapsilosis isolates from different origins, including hospital environment and hands of healthcare workers, were genotyped using four microsatellite markers. The isolates were recovered from different health institutions. Analysis of C. parapsilosis isolates from hospital environment showed great genotypic diversity; however, the same or very similar genotypes were also found. The same multilocus genotype was shared by isolates recovered from the hand of a healthcare worker, from the hospital environment and from patients of the same healthcare institution, suggesting that these could be possible routes of transmission and that infections due to C. parapsilosis may be mainly related with exogenous transmission to the patient. Examination of sequential isolates from the same patients showed that colonizing and bloodstream isolates had the same multilocus genotype in the majority of cases. We demonstrate that this typing method is able to distinguish clonal clusters from genetically unrelated genotypes and can be a valuable tool to support epidemiologic investigations in the hospital setting.
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Chen CP, Ko TM, Chen CY, Wang TY, Chern SR, Kuo YL, Wang W. First-trimester molecular diagnosis of complete hydatidiform mole associated with dizygotic twin pregnancy conceived by intrauterine insemination. Taiwan J Obstet Gynecol 2014; 53:572-8. [PMID: 25510703 DOI: 10.1016/j.tjog.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE To present first-trimester molecular diagnosis of complete hydatidiform mole (CHM) associated with dizygotic twin pregnancy conceived by intrauterine insemination. MATERIALS AND METHODS A 32-year-old woman presented to the hospital with a huge complex cystic mass measuring about 8.5 cm × 4.1 cm in the uterine cavity and a living co-existing fetus with fetal biometry equivalent to 9 weeks. She underwent chorionic villus sampling at 13 weeks of gestation, and microsatellite genotyping for molar pregnancy test was applied. A molar pregnancy test was performed by a short tandem repeat (STR) identifier polymerase chain reaction (PCR) polymorphic marker analysis. The pregnancy was terminated at 14 weeks of gestation. Postnatal polymorphic DNA marker analysis of the placenta by quantitative fluorescent PCR (QF-PCR) was performed. Analysis of maternal blood total β-human chorionic gonadotropin revealed a high level of 551,600 mIU/mL at 10 weeks of gestation and a level of 1.0 mIU/mL at 15 weeks postpartum. The woman was doing well at 4 months after delivery. RESULTS The results of STR identifier PCR polymorphic marker analysis showed androgenic conception in the complex cystic mass and biparental conception in the living fetus. Pathological analysis of the cystic mass confirmed the diagnosis of CHM. The results of QF-PCR showed biparental inheritance in the normal fetus and complete paternal homozygosity in the CHM of the abnormal fetus in all STRs, indicating dizygotic twinning and CHM of monospermy. CONCLUSION Prenatal sonographic diagnosis of placentomegaly with many grape-like vesicles should include a differential diagnosis of CHM, partial hydatidiform mole (PHM), placental mesenchymal dysplasia (PMD), and recurrent hydatidiform mole. Microsatellite genotyping for molar pregnancy testing and zygosity testing is useful in cases of prenatal diagnosis of placentomegaly associated with many grape-like vesicles and a twin pregnancy with a living fetus in the first trimester.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Chen-Yu Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Tao-Yeuan Wang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City, Taiwan; Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yu-Ling Kuo
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wayseen Wang
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Delfino D, Scordino F, Pernice I, Lo Passo C, Galbo R, David A, Barberi I, Criseo G, Cascio A, Romeo O. Potential association of specific Candida parapsilosis genotypes, bloodstream infections and colonization of health workers' hands. Clin Microbiol Infect 2014; 20:O946-51. [PMID: 24845557 DOI: 10.1111/1469-0691.12685] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 01/12/2023]
Abstract
Fungal nosocomial infections continue to be a serious problem among hospitalized patients, decreasing quality of life and adding millions of euros to healthcare costs. The aim of this study was to describe the pattern of fungi associated with the hands of healthcare workers and to genotype Candida parapsilosis isolates in order to understand whether their high clinical prevalence stems from endemic nosocomial genotypes or from the real emergence of epidemiologically-unrelated strains. Approximately 39% (50/129) of healthcare workers were positive for yeasts and among 77 different fungal isolates recovered, C. parapsilosis was the most frequent (44/77; 57%). Twenty-seven diverse genotypes were obtained by microsatellite analysis of 42 selected blood and hand isolates. Most of the isolates from hands showed a new, unrelated, genotype, whereas a particular group of closely related genotypes prevailed in blood samples. Some of the latter genotypes were also found on the hands of healthcare workers, indicating a persistence of these clones within our hospital. C. parapsilosis genotypes from the hands were much more heterogeneous than clinical ones, thus reflecting a high genetic diversity among isolates, which is notably unusual and unexpected for this species.
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Affiliation(s)
- D Delfino
- Department of Human Pathology, University of Messina, Messina, Italy
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Xu H, Tremblay F, Bergeron Y, Paul V, Chen C. Genetic consequences of fragmentation in "arbor vitae," eastern white cedar (Thuja occidentalis L.), toward the northern limit of its distribution range. Ecol Evol 2012; 2:2506-20. [PMID: 23145335 PMCID: PMC3492776 DOI: 10.1002/ece3.371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 05/07/2012] [Revised: 07/31/2012] [Accepted: 08/08/2012] [Indexed: 11/29/2022] Open
Abstract
We tested the hypothesis that marginal fragmented populations of eastern white cedar (EWC) are genetically isolated due to reduced pollen and gene flow. In accordance with the central-marginal model, we predicted a decrease in population genetic diversity and an increase in differentiation along the latitudinal gradient from the boreal mixed-wood to northern coniferous forest. A total of 24 eastern white cedar populations were sampled along the north-south latitudinal gradient for microsatellite genotyping analysis. Positive Fis values and heterozygote deficiency were observed in populations from the marginal (Fis = 0.244; PHW = 0.0042) and discontinuous zones (Fis = 0.166; PHW = 0.0042). However, populations from the continuous zone were in HW equilibrium (Fis = −0.007; PHW = 0.3625). There were no significant latitudinal effects on gene diversity (Hs), allelic richness (AR), or population differentiation (Fst). Bayesian and NJT (neighbor-joining tree) analyses demonstrated the presence of a population structure that was partly consistent with the geographic origins of the populations. The impact of population fragmentation on the genetic structure of EWC is to create a positive inbreeding coefficient, which was two to three times higher on average than that of a population from the continuous zone. This result indicated a higher occurrence of selfing within fragmented EWC populations coupled with a higher degree of gene exchange among near-neighbor relatives, thereby leading to significant inbreeding. Increased population isolation was apparently not correlated with a detectable effect on genetic diversity. Overall, the fragmented populations of EWC appear well-buffered against effects of inbreeding on genetic erosion.
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Affiliation(s)
- Huaitong Xu
- Northwest A&F University Shaanxi, 712100, China ; Chaire Industrielle CRSNG-UQAT-UQAM en Aménagement Forestier Durable, Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue Québec, J9X 5E4, Canada
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Freedberg S, Ewert MA, Ridenhour BJ, Neiman M, Nelson CE. Nesting fidelity and molecular evidence for natal homing in the freshwater turtle, Graptemys kohnii. Proc Biol Sci 2005; 272:1345-50. [PMID: 16006324 PMCID: PMC1560332 DOI: 10.1098/rspb.2005.3080] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [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: 12/21/2004] [Accepted: 02/27/2005] [Indexed: 11/12/2022] Open
Abstract
Numerous studies of sea turtle nesting ecology have revealed that females exhibit natal homing, whereby they imprint on the nesting area from which they hatch and subsequently return there to nest as adults. Because freshwater turtles comprise the majority of reptiles known to display environmental sex determination (ESD), the study of natal homing in this group may shed light on recent evolutionary models of sex allocation that are predicated on natal homing in reptiles with ESD. We examined natal homing in Graptemys kohnii, a freshwater turtle with ESD, using mitochondrial sequencing, microsatellite genotyping and mark and recapture of 290 nesting females. Females showed high fidelity to nesting areas, even after being transplanted several kilometres away. A Mantel test revealed significant genetic isolation by distance with respect to nesting locations (r=0.147; p<0.05), suggesting that related females nest in close proximity to one another. The patterns of fidelity and genotype distributions are consistent with homing at a scale that may affect population sex ratios.
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Affiliation(s)
- Steven Freedberg
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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