Imperial College London

Professor Matthew Fisher

Faculty of MedicineSchool of Public Health

Professor of Fungal Disease Epidemiology
 
 
 
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Contact

 

matthew.fisher Website

 
 
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Location

 

1113Sir Michael Uren HubWhite City Campus

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Summary

 

Publications

Publication Type
Year
to

247 results found

Schelenz S, Hagen F, Rhodes JL, Abdolrasouli A, Chowdhary A, Hall A, Ryan L, Shackleton J, Trimlett R, Meis JF, Armstrong-James DPH, Fisher MCet al., 2016, First hospital outbreak of the globally emerging Candida auris in a European hospital, Antimicrobial Resistance and Infection Control, Vol: 5, ISSN: 2047-2994

Background: Candida auris is a globally emerging multidrug resistant fungal pathogen causing nosocomial transmission.We report an ongoing outbreak of C. auris in a London cardio-thoracic center between April 2015 and July 2016. This isthe first report of C. auris in Europe and the largest outbreak so far. We describe the identification, investigation andimplementation of control measures.Methods: Data on C. auris case demographics, environmental screening, implementation of infection prevention/controlmeasures, and antifungal susceptibility of patient isolates were prospectively recorded then analysed retrospectively.Speciation of C. auris was performed by MALDI-TOF and typing of outbreak isolates performed by amplified fragmentlength polymorphism (AFLP).Results: This report describes an ongoing outbreak of 50 C. auris cases over the first 16 month (April 2015 to July 2016)within a single Hospital Trust in London. A total of 44 % (n = 22/50) patients developed possible or proven C. aurisinfection with a candidaemia rate of 18 % (n = 9/50). Environmental sampling showed persistent presence of the yeastaround bed space areas. Implementation of strict infection and prevention control measures included: isolationof cases and their contacts, wearing of personal protective clothing by health care workers, screening ofpatients on affected wards, skin decontamination with chlorhexidine, environmental cleaning with chorinebased reagents and hydrogen peroxide vapour. Genotyping with AFLP demonstrated that C. auris isolates fromthe same geographic region clustered.Conclusion: This ongoing outbreak with genotypically closely related C. auris highlights the importance ofappropriate species identification and rapid detection of cases in order to contain hospital acquired transmission.

Journal article

Auliya M, Garcia-Moreno J, Schmidt BR, Schmeller DS, Hoogmoed MS, Fisher MC, Pasmans F, Henle K, Bickford D, Martel Aet al., 2016, The global amphibian trade flows through Europe: the need for enforcing and improving legislation, BIODIVERSITY AND CONSERVATION, Vol: 25, Pages: 2581-2595, ISSN: 0960-3115

Journal article

Armstrong-James DPH, 2016, Calcineurin Orchestrates Lateral Transfer of Aspergillus fumigatus during Macrophage Cell Death, American Journal of Respiratory and Critical Care Medicine, Vol: 194, Pages: 1127-1139, ISSN: 1535-4970

Rationale: Pulmonary aspergillosis is a lethal mold infection in the immunocompromised host. Understanding initial control of infection and how this is altered in the immunocompromised host are key goals for comprehension of the pathogenesis of pulmonary aspergillosis.Objectives: To characterize the outcome of human macrophage infection with Aspergillus fumigatus and how this is altered in transplant recipients on calcineurin inhibitor immunosuppressants.Methods: We defined the outcome of human macrophage infection with A. fumigatus, as well as the impact of calcineurin inhibitors, through a combination of single-cell fluorescence imaging, transcriptomics, proteomics, and in vivo studies.Measurements and Main Results: Macrophage phagocytosis of A. fumigatus enabled control of 90% of fungal germination. However, fungal germination in the late phagosome led to macrophage necrosis. During programmed necroptosis, we observed frequent cell–cell transfer of A. fumigatus between macrophages, which assists subsequent control of germination in recipient macrophages. Lateral transfer occurred through actin-dependent exocytosis of the late endosome in a vasodilator-stimulated phosphoprotein envelope. Its relevance to the control of fungal germination was also shown by direct visualization in our zebrafish aspergillosis model in vivo. The calcineurin inhibitor FK506 (tacrolimus) reduced cell death and lateral transfer in vitro by 50%. This resulted in uncontrolled fungal germination in macrophages and also resulted in hyphal escape.Conclusions: These observations identify programmed, necrosis-dependent lateral transfer of A. fumigatus between macrophages as an important host strategy for controlling fungal germination. This process is critically dependent on calcineurin. Our studies provide fundamental insights into the pathogenesis of pulmonary aspergillosis in the immunocompromised host.

Journal article

Clare F, Daniel O, Garner T, Fisher Met al., 2016, Assessing the ability of swab data to determine the true burden of infection for the amphibian pathogen Batrachochytrium dendrobatidis, Ecohealth, Vol: 13, Pages: 360-367, ISSN: 1612-9210

Batrachochytrium dendrobatidis (Bd) is a pathogenic fungus which causes the disease chytridiomycosisin amphibians by infecting the animals’ epidermis. The most commonly applied method for the detectionof Bd is the use of a sterile swab, rubbed over the keratinized areas of an amphibian and then processed to yieldDNA for detection by qPCR. This method has been used to infer a threshold of lethal infection in some species;however, how reliable and reproducible the swabbing method is at detecting the true burden of infectionsuffered by individuals is not known. European midwife toads, Alytes obstetricans, are susceptible to chytridiomycosisand are highly parasitised by Bd across Europe. By quantifying Bd-load throughout the entire skinand comparing this to swab results taken from the same individual, we determined whether epidermal swabsprovide a quantifiable and accurate indication of the true fungal burden suffered. Further, we examinedwhether we could infer a threshold for lethal infection based on comparison of swab data taken from infectedA. obstetricans exhibiting different clinical states. From swab data, we detected significantly higher fungalburdens from moribund metamorphs compared to visually healthy individuals; however, the ability of theseswab data to provide an accurate indication of the true fungal burden was not reliable. These data suggest thatfungal load dynamics play an important role in disease-induced mortality in A. obstetricans at these sites, butthat using swab data to infer an exact threshold for Bd-associated mortality might be inappropriate andmisleading.

Journal article

Ghosh P, Fisher MC, 2016, Dr Jekyll and Mrs Hyde: Risky hybrid sex by amphibian-parasitizing chytrids in the Brazilian Atlantic Forests, Molecular Ecology, Vol: 25, Pages: 2961-2963, ISSN: 1365-294X

Journal article

Bosch J, Sanchez-Tome E, Fernandez-Loras A, Oliver JA, Fisher MC, Garner TWJet al., 2015, Successful elimination of a lethal wildlife infectious disease in nature, Biology Letters, Vol: 11, ISSN: 1744-957X

Methods to mitigate the impacts of emerging infectious diseases affecting wildlife are urgently needed to combat loss of biodiversity. However, the successful mitigation of wildlife pathogens in situ has rarely occurred. Indeed, most strategies for combating wildlife diseases remain theoretical, despite the wealth of information available for combating infections in livestock and crops. Here, we report the outcome of a 5-year effort to eliminate infection with Batrachochytrium dendrobatidis affecting an island system with a single amphibian host. Our initial efforts to eliminate infection in the larval reservoir using a direct application of an antifungal were successful ex situ but infection returned to previous levels when tadpoles with cleared infections were returned to their natal sites. We subsequently combined antifungal treatment of tadpoles with environmental chemical disinfection. Infection at four of the five pools where infection had previously been recorded was eradicated, and remained so for 2 years post-application.

Journal article

Bletz MC, Rosa GM, Andreone F, Courtois EA, Schmeller DS, Rabibisoa NHC, Rabemananjara FCE, Raharivololoniaina L, Vences M, Weldon C, Edmonds D, Raxworthy CJ, Harris RN, Fisher MC, Crottini Aet al., 2015, Consistency of Published Results on the Pathogen Batrachochytrium dendrobatidis in Madagascar: Formal Comment on Kolby et al. Rapid Response to Evaluate the Presence of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) and Ranavirus in Wild Amphibian Populations in Madagascar, PLOS One, Vol: 10, ISSN: 1932-6203

Journal article

Farret RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, Fisher MC, Cuomo CAet al., 2015, Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii, mBio, Vol: 6, ISSN: 2161-2129

Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. Tocharacterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, andcompared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenicregions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages.Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all fourlineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress,mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought tobe important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to theother lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV,which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. Through inclusion ofpopulation-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrialrecombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur proteinaconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positiveselection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex.

Journal article

Voyles J, Kilpatrick AM, Collins JP, Fisher MC, Frick WF, McCallum H, Willis CKR, Blehert DS, Murray KA, Puschendorf R, Rosenblum EB, Bolker BM, Cheng TL, Langwig KE, Lindner DL, Toothman M, Wilber MQ, Briggs CJet al., 2015, Moving Beyond Too Little, Too Late: Managing Emerging Infectious Diseases in Wild Populations Requires International Policy and Partnerships, ECOHEALTH, Vol: 12, Pages: 404-407, ISSN: 1612-9202

Journal article

Hamlyn E, Stoehr W, Cooper DA, Fisher M, Tambussi G, Schechter M, Miro JM, Vanobberghen F, Babiker A, Weber J, Mcclure M, Porter K, Fidler Set al., 2015, The effect of short-course antiretroviral therapy initiated in primary HIV-1 infection on interleukin-6 and D-dimer levels, AIDS, Vol: 29, Pages: 1355-1361, ISSN: 0269-9370

Objective: Interruption of antiretroviral therapy (ART) in chronic HIV disease is associated with increased mortality, predicted by elevations in interleukin-6 (IL-6) and D-dimer. The effect of ART interruption in primary HIV-1 infection on these biomarkers is unknown.Methods: Plasma samples from 200 HIV seroconverters enrolled in the Short Pulse Anti-Retroviral Therapy At HIV Seroconversion trial of deferred ART (standard of care) – 12 or 48 week ART (ART12 or ART48, respectively) – were analysed for IL-6 and D-dimer at weeks 0, 12, 16, 48, 52, 60 and 108 after randomization. Changes in log10 levels from weeks 0 to 12 were analysed using linear regression, as were changes from baseline to 4 weeks after stopping ART. Areas under the biomarker–time curves (AUC) to week 108 were adjusted for baseline values, and compared across all arms.Results: Median (inter-quartile range) baseline IL-6 and D-dimer were 1.45 (0.88, 2.41) pg/ml and 0.34 (0.20, 0.50) mg/l, respectively. At week 12, D-dimer levels were significantly lower among treated compared to untreated individuals (P < 0.001), whereas IL-6 levels were similar (P = 0.23). Within 4 weeks from stopping ART, IL-6 and D-dimer levels rose by 22 and 18%, reaching pre-ART levels. Over 108-week follow-up, there was no difference between arms in IL-6 AUC (P = 0.53), but D-dimer AUC was significantly lower for ART12 and ART48 compared to standard of care (overall P = 0.008).Conclusion: Stopping ART in primary HIV-1 infection leads to inflammatory biomarker rebound to pre-treatment levels. However, over 108-week follow-up, we found no evidence that biomarker levels were higher for those interrupting ART, compared to those remaining ART-naïve, and D-dimer levels were significantly lower.

Journal article

Abdolrasouli A, Rhodes J, Beale MA, Hagen F, Rogers TR, Chowdhary A, Meis JF, Armstrong-James D, Fisher MCet al., 2015, Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing (vol 6, e00536, 2015), MBIO, Vol: 6, ISSN: 2150-7511

Journal article

Jarrin I, Pantazis N, Dalmau J, Phillips AN, Olson A, Mussini C, Boufassa F, Costagliola D, Porter K, Blanco J, Del Amo J, Martinez-Picado J, Chene G, Sabin C, Walker S, Fisher M, Kelleher T, Cooper D, Finlayson R, Bloch M, Ramacciotti T, Gelgor L, Smith D, Zangerle R, Gill J, Lutsar I, Dabis F, Thiebaut R, Guiguet M, Vanhems P, Chaix ML, Ghosn J, Meyer L, Hamouda O, Kucherer C, Bartmeyer B, Antoniadou A, Chrysos G, Daikos GL, Touloumi G, Katsarou O, Rezza G, Dorrucci M, Monforte ADA, De Luca A, Prins M, Geskus R, Van Der Helm J, Schuitemaker H, Sannes M, Brubakk O, Kran AMB, Rosinska M, Muga R, Tor J, De Olalla PG, Cayla J, Moreno S, Monge S, Del Romero J, Perez-Hoyos S, Sonnerborg A, Bucher HC, Gunthard H, Rickenbach M, Malyuta R, Murphy G, Johnson A, Babiker A, Pillay D, Morrison C, Salata R, Mugerwa R, Chipato T, Amornkul PN, Gilmour J, Kamali Aet al., 2015, Does rapid HIV disease progression prior to combination antiretroviral therapy hinder optimal CD4 + T-cell recovery once HIV-1 suppression is achieved?, AIDS, Vol: 29, Pages: 2323-2333, ISSN: 0269-9370

Objective: This article compares trends in CD4+ T-cell recovery and proportions achieving optimal restoration (>=500 cells/µl) after viral suppression following combination antiretroviral therapy (cART) initiation between rapid and nonrapid progressors.Methods: We included HIV-1 seroconverters achieving viral suppression within 6 months of cART. Rapid progressors were individuals experiencing at least one CD4+ less than 200 cells/µl within 12 months of seroconverters before cART. We used piecewise linear mixed models and logistic regression for optimal restoration.Results: Of 4024 individuals, 294 (7.3%) were classified as rapid progressors. At the same CD4+ T-cell count at cART start (baseline), rapid progressors experienced faster CD4+ T-cell increases than nonrapid progressors in first month [difference (95% confidence interval) in mean increase/month (square root scale): 1.82 (1.61; 2.04)], which reversed to slightly slower increases in months 1–18 [-0.05 (-0.06; -0.03)] and no significant differences in 18–60 months [-0.003 (-0.01; 0.01)]. Percentage achieving optimal restoration was significantly lower for rapid progressors than nonrapid progressors at months 12 (29.2 vs. 62.5%) and 36 (47.1 vs. 72.4%) but not at month 60 (70.4 vs. 71.8%). These differences disappeared after adjusting for baseline CD4+ T-cell count: odds ratio (95% confidence interval) 0.86 (0.61; 1.20), 0.90 (0.38; 2.17) and 1.56 (0.55; 4.46) at months 12, 36 and 60, respectively.Conclusion: Among people on suppressive antiretroviral therapy, rapid progressors experience faster initial increases of CD4+ T-cell counts than nonrapid progressors, but are less likely to achieve optimal restoration during the first 36 months after cART, mainly because of lower CD4+ T-cell counts at cART initiation.

Journal article

Fisher M, 2015, Genotypic diversity is associated with clinical outcome and phenotype in Cryptococcal meningitis across Southern Africa, PLOS Neglected Tropical Diseases, Vol: 9, ISSN: 1935-2735

Cryptococcal meningitis is a major cause of mortality throughout the developing world, yet little is known about the genetic markers underlying Cryptococcal virulence and patient outcome. We studied a cohort of 230 Cryptococcus neoformans (Cn) isolates from HIV-positive South African clinical trial patients with detailed clinical follow-up using multi-locus sequence typing and in vitro phenotypic virulence assays, correlating these data with clinical and fungal markers of disease in the patient. South African Cn displayed high levels of genetic diversity and locus variability compared to globally distributed types, and we identified 50 sequence types grouped within the main molecular types VNI, VNII and VNB, with 72% of isolates typed into one of seven 'high frequency' sequence types. Spatial analysis of patients’ cryptococcal genotype was not shown to be clustered geographically, which might argue against recent local acquisition and in favour of reactivation of latent infection. Through comparison of MLST genotyping data with clinical parameters, we found a relationship between genetic lineage and clinical outcome, with patients infected with the VNB lineage having significantly worse survival (n=8, HR 3.35, CI 1.51-7.20, p=0.003), and this was maintained even after adjustment for known prognostic indicators and treatment regimen. Comparison of fungal genotype with in vitro phenotype (phagocytosis, laccase activity and CSF survival) performed on a subset of 89 isolates revealed evidence of lineage-associated virulence phenotype, with the VNII lineage displaying increased laccase activity (p=0.001) and ex vivo CSF survival (p=0.0001). These findings show that Cryptococcus neoformans is a phenotypically heterogeneous pathogen, and that lineage plays an important role in cryptococcal virulence during human infection. Furthermore, a detailed understanding of the genetic diversity in Southern Africa will support further investigation into how genetic diversity is

Journal article

Abdolrasouli A, Rhodes J, Beale M, Hagen F, Rogers TR, Chowdhary A, Meis JF, Armstrong-James, Fisher MCet al., 2015, Genomic context of Azole-resistance mutations in Aspergillus fumigatus using whole-genome sequencing, mBio, Vol: 6, ISSN: 2161-2129

A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance. WGS analysis confirmed that TR34/L98H (a mutation comprising a tandem repeat [TR] of 34 bases in the promoter of the cyp51A gene and a leucine-to-histidine change at codon 98) is the sole mechanism of azole resistance among the isolates tested in this panel of isolates. We used population genomic analysis and showed that A. fumigatus was panmictic, with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where isolates are highly related despite being isolated from both clinical and environmental sources across >1,000 km; this broad occurrence suggests a recent selective sweep of a highly fit genotype that is associated with the TR34/L98H allele. We found that these sequenced isolates are all recombining, showing that azole-resistant alleles are segregating into diverse genetic backgrounds. Our analysis delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP diversity to the generation and spread of azole resistance in this medically important fungus.

Journal article

Bielby J, Fisher MC, Clare FC, Rosa GM, Garner TWJet al., 2015, Host species vary in infection probability, sub-lethal effects, and costs of immune response when exposed to an amphibian parasite, Scientific Reports, Vol: 5, ISSN: 2045-2322

The amphibian parasite Batrachochytrium dendrobatidis (Bd) is regarded as an extreme generalist,infecting over 500 species, but amongst these hosts there exists a great deal of variation in thesusceptibility to and the costs of parasite exposure. We use two infection experiments to determinewhether inter-specific variation in the sublethal and lethal effects of parasite exposure exist in twohost species. We then tested the relative roles of host density and diversity on infection probabilityof a focal susceptible host. Our results show significant heterogeneity in host species response toparasite exposure, and that both lethal and sub-lethal costs exist in individuals that are able toresist infection, indicating that successful immune response to infection comes at a cost. Further,we show that increasing host density significantly increased the likelihood of susceptible individualsbecoming infected with Bd irrespective of host diversity and variation in host susceptibility. Theseresults suggest that populations of resistant species are likely to suffer ill-effects of exposure to Bdregardless of their infection status, and that at the stage of initial infection there was no supportfor the dilution of transmission events, in contrast to other studies that focus on subsequenttransmission of infection.

Journal article

Cunningham AA, Beckmann K, Perkins M, Fitzpatrick L, Cromie R, Redbond J, O'Brien MF, Ghosh P, Shelton J, Fisher MCet al., 2015, SURVEILLANCE Emerging disease in UK amphibians, VETERINARY RECORD, Vol: 176, Pages: 468-468, ISSN: 0042-4900

Journal article

Langwig KE, Voyles J, Wilber MQ, Frick WF, Murray KA, Bolker BM, Collins JP, Cheng TL, Fisher MC, Hoyt JR, Lindner DL, McCallum HI, Puschendorf R, Rosenblum EB, Toothman M, Willis CKR, Briggs CJ, Kilpatrick AMet al., 2015, Context-dependent conservation responses to emerging wildlife diseases, FRONTIERS IN ECOLOGY AND THE ENVIRONMENT, Vol: 13, Pages: 195-202, ISSN: 1540-9295

Journal article

Fernández-Beaskoetxea S, Carrascal LM, Fernández-Loras A, Fisher MC, Bosch Jet al., 2015, Short Term Minimum Water Temperatures Determine Levels of Infection by the Amphibian Chytrid Fungus in Alytes obstetricans Tadpoles, PLOS ONE, Vol: 10, Pages: e0120237-e0120237

Journal article

Bletz MC, Rosa GM, Andreone F, Courtois EA, Schmeller DS, Rabibisoa NHC, Rabemananjara FCE, Raharivololoniaina L, Vences M, Weldon C, Edmonds D, Raxworthy CJ, Harris RN, Fisher MC, Crottini Aet al., 2015, Widespread presence of the pathogenic fungus <i>Batrachochytrium dendrobatidis</i> in wild amphibian communities in Madagascar, SCIENTIFIC REPORTS, Vol: 5, ISSN: 2045-2322

Journal article

Solís R, Penna M, De la Riva I, Fisher MC, Bosch Jet al., 2015, Presence of Batrachochytrium dendrobatidis in anurans from the Andes highlands of northern Chile, Herpetological Journal, Vol: 25, Pages: 55-59, ISSN: 0268-0130

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a causal agent of infectious disease and decline of anuran populations inhabiting mountain systems in Central and South America. The chytrid is believed to have spread from Ecuador southward, as has recently been detected in the Andean cordilleras of Peru, Bolivia and Argentina. However, since the status of anuran populations from the Chilean Altiplano is unknown, we undertook an intensive survey of amphibian populations inhabiting high elevations in northern Chile. Bd-infected individuals were detected only in the northernmost localities sampled suggesting an ongoing process of Bd spread southward along the Andes.

Journal article

Solis R, Penna M, De la Riva I, Fisher MC, Bosch Jet al., 2015, Presence of <i>Batrachochytrium</i> <i>dendrobatidis</i> in anurans from the Andes highlands of northern Chile, HERPETOLOGICAL JOURNAL, Vol: 25, Pages: 55-59, ISSN: 0268-0130

Journal article

Rhodes J, Beale MA, Fisher MC, 2014, Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq, PLOS ONE, Vol: 9, ISSN: 1932-6203

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use.

Journal article

Martel A, Blooi M, Adriaensen C, Van Rooij P, Beukema W, Fisher MC, Farrer RA, Schmidt BR, Tobler U, Goka K, Lips KR, Muletz C, Zamudio KR, Bosch J, Loetters S, Wombwell E, Garner TWJ, Cunningham AA, Spitzen-van der Sluijs A, Salvidio S, Ducatelle R, Nishikawa K, Nguyen TT, Kolby JE, Van Bocxlaer I, Bossuyt F, Pasmans Fet al., 2014, Recent introduction of a chytrid fungus endangers Western Palearctic salamanders, SCIENCE, Vol: 346, Pages: 630-631, ISSN: 0036-8075

Journal article

Engelthaler DM, Hicks ND, Gillece JD, Roe CC, Schupp JM, Driebe EM, Gilgado F, Carriconde F, Trilles L, Firacative C, Ngamskulrungroj P, Castaneda E, Lazera MDS, Melhem MSC, Perez-Bercoff A, Huttley G, Sorrell TC, Voelz K, May RC, Fisher MC, Thompson GR, Lockhart SR, Keim P, Meyer Wet al., 2014, <i>Cryptococcus gattii</i> in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal, MBIO, Vol: 5, ISSN: 2150-7511

Journal article

Sabiiti W, Robertson E, Beale MA, Johnston SA, Brouwer AE, Loyse A, Jarvis JN, Gilbert AS, Fisher MC, Harrison TS, May RC, Bicanic Tet al., 2014, Efficient phagocytosis and laccase activity affect the outcome of HIV-associated cryptococcosis, JOURNAL OF CLINICAL INVESTIGATION, Vol: 124, Pages: 2000-2008, ISSN: 0021-9738

Journal article

Vanittanakom N, Szekely J, Khanthawong S, Sawutdeechaikul P, Vanittanakom P, Fisher MCet al., 2014, Molecular detection of <i>Pythium insidiosum</i> from soil in Thai agricultural areas, INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY, Vol: 304, Pages: 321-326, ISSN: 1438-4221

Journal article

Schmeller DS, Blooi M, Martel A, Garner TWJ, Fisher MC, Azemar F, Clare FC, Leclerc C, Jaeger L, Guevara-Nieto M, Loyau A, Pasmans Fet al., 2014, Microscopic Aquatic Predators Strongly Affect Infection Dynamics of a Globally Emerged Pathogen, CURRENT BIOLOGY, Vol: 24, Pages: 176-180, ISSN: 0960-9822

Journal article

Baláž V, Vörös J, Civiš P, Vojar J, Hettyey A, Sós E, Dankovics R, Jehle R, Christiansen DG, Clare F, Fisher MC, Garner TWJ, Bielby Jet al., 2014, Assessing Risk and Guidance on Monitoring of Batrachochytrium dendrobatidis in Europe through Identification of Taxonomic Selectivity of Infection, Conservation Biology, Vol: 28, Pages: 213-223, ISSN: 0888-8892

Amphibians are globally threatened, but not all species are affected equally by different threatening processes. This is true for the threat posed by the chytridiomycete fungus (Batrachochytrium dendrobatidis). We compiled a European data set for B. dendrobatidis to analyze the trends of infection in European amphibians. The risk of infection was not randomly distributed geographically or taxonomically across Europe. Within countries with different prevalence, infection was nonrandom in certain amphibian taxa. Brown frogs of the genus Rana were unlikely to be infected, whereas frogs in the families Alytidae and Bombinatoridae were significantly more likely to be infected than predicted by chance. Frogs in the 2 families susceptible to B. dendrobatidis should form the core of attempts to develop spatial surveillance studies of chytridiomycosis in Europe. Ideally, surveys for B. dendrobatidis should be augmented by sampling the widespread genus Pelophylax because this taxon exhibits geographically inconsistent overinfection with B. dendrobatidis and surveillance of it may facilitate recognition of factors causing spatial variability of infection intensity. Several European amphibian taxa were not represented in our data set; however, surveillance of unsampled species should also occur when warranted. © 2013 Society for Conservation Biology.

Journal article

Fisher MC, Stajich JE, Farrer RA, 2013, Emergence of the Chytrid Fungus Batrachochytrium Dendrobatidis and Global Amphibian Declines, Evolution of Virulence in Eukaryotic Microbes, Pages: 461-472, ISBN: 9781118038185

Book chapter

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