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The use of taxon-specific reference databases compromises metagenomic classification.

R Marcelino V, Holmes EC, Sorrell TC.

BMC Genomics. 2020 Feb 27;21(1):184. doi: 10.1186/s12864-020-6592-2.


Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium.

Donnelly JP, Chen SC, Kauffman CA, Steinbach WJ, Baddley JW, Verweij PE, Clancy CJ, Wingard JR, Lockhart SR, Groll AH, Sorrell TC, Bassetti M, Akan H, Alexander BD, Andes D, Azoulay E, Bialek R, Bradsher RW, Bretagne S, Calandra T, Caliendo AM, Castagnola E, Cruciani M, Cuenca-Estrella M, Decker CF, Desai SR, Fisher B, Harrison T, Heussel CP, Jensen HE, Kibbler CC, Kontoyiannis DP, Kullberg BJ, Lagrou K, Lamoth F, Lehrnbecher T, Loeffler J, Lortholary O, Maertens J, Marchetti O, Marr KA, Masur H, Meis JF, Morrisey CO, Nucci M, Ostrosky-Zeichner L, Pagano L, Patterson TF, Perfect JR, Racil Z, Roilides E, Ruhnke M, Prokop CS, Shoham S, Slavin MA, Stevens DA, Thompson GR, Vazquez JA, Viscoli C, Walsh TJ, Warris A, Wheat LJ, White PL, Zaoutis TE, Pappas PG.

Clin Infect Dis. 2019 Dec 5. pii: ciz1008. doi: 10.1093/cid/ciz1008. [Epub ahead of print]


Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics.

Irinyi L, Hu Y, Hoang MTV, Pasic L, Halliday C, Jayawardena M, Basu I, McKinney W, Morris AJ, Rathjen J, Stone E, Chen S, Sorrell TC, Schwessinger B, Meyer W.

Med Mycol. 2019 Nov 23. pii: myz109. doi: 10.1093/mmy/myz109. [Epub ahead of print]


Corrigendum: Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types.

Biswas C, Marcelino VR, Van Hal S, Halliday C, Martinez E, Wang Q, Kidd S, Kennedy K, Marriott D, Morrissey CO, Arthur I, Weeks K, Slavin MA, Sorrell TC, Sintchenko V, Meyer W, Chen SC.

Front Microbiol. 2019 Sep 27;10:2218. doi: 10.3389/fmicb.2019.02218. eCollection 2019.


Central Nervous System Cryptococcal Infections in Non-HIV Infected Patients.

Beardsley J, Sorrell TC, Chen SC.

J Fungi (Basel). 2019 Aug 2;5(3). pii: E71. doi: 10.3390/jof5030071. Review.


Fungal Kinases With a Sweet Tooth: Pleiotropic Roles of Their Phosphorylated Inositol Sugar Products in the Pathogenicity of Cryptococcus neoformans Present Novel Drug Targeting Opportunities.

Lev S, Li C, Desmarini D, Sorrell TC, Saiardi A, Djordjevic JT.

Front Cell Infect Microbiol. 2019 Jul 15;9:248. doi: 10.3389/fcimb.2019.00248. eCollection 2019. Review.


Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections.

Hoang MTV, Irinyi L, Chen SCA, Sorrell TC; ISHAM Barcoding of Medical Fungi Working Group, Meyer W.

Front Microbiol. 2019 Jul 18;10:1647. doi: 10.3389/fmicb.2019.01647. eCollection 2019.


Advancing Planetary Health in Australia: focus on emerging infections and antimicrobial resistance.

Hill-Cawthorne G, Negin J, Capon T, Gilbert GL, Nind L, Nunn M, Ridgway P, Schipp M, Firman J, Sorrell TC, Marais BJ.

BMJ Glob Health. 2019 Apr 22;4(2):e001283. doi: 10.1136/bmjgh-2018-001283. eCollection 2019. Review.


Candidaemia and a risk predictive model for overall mortality: a prospective multicentre study.

Keighley C, Chen SC, Marriott D, Pope A, Chapman B, Kennedy K, Bak N, Underwood N, Wilson HL, McDonald K, Darvall J, Halliday C, Kidd S, Nguyen Q, Hajkowicz K, Sorrell TC, Van Hal S, Slavin MA.

BMC Infect Dis. 2019 May 21;19(1):445. doi: 10.1186/s12879-019-4065-5.


Network properties of salmonella epidemics.

Cliff OM, Sintchenko V, Sorrell TC, Vadlamudi K, McLean N, Prokopenko M.

Sci Rep. 2019 Apr 16;9(1):6159. doi: 10.1038/s41598-019-42582-3.


Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

Marcelino VR, Wille M, Hurt AC, González-Acuña D, Klaassen M, Schlub TE, Eden JS, Shi M, Iredell JR, Sorrell TC, Holmes EC.

BMC Biol. 2019 Apr 8;17(1):31. doi: 10.1186/s12915-019-0649-1.


The PHO signaling pathway directs lipid remodeling in Cryptococcus neoformans via DGTS synthase to recycle phosphate during phosphate deficiency.

Lev S, Rupasinghe T, Desmarini D, Kaufman-Francis K, Sorrell TC, Roessner U, Djordjevic JT.

PLoS One. 2019 Feb 21;14(2):e0212651. doi: 10.1371/journal.pone.0212651. eCollection 2019.


Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types.

Biswas C, Marcelino VR, Van Hal S, Halliday C, Martinez E, Wang Q, Kidd S, Kennedy K, Marriott D, Morrissey CO, Arthur I, Weeks K, Slavin MA, Sorrell TC, Sintchenko V, Meyer W, Chen SC.

Front Microbiol. 2018 Dec 3;9:2946. doi: 10.3389/fmicb.2018.02946. eCollection 2018. Erratum in: Front Microbiol. 2019 Sep 27;10:2218.


Database establishment for the secondary fungal DNA barcode translational elongation factor 1α (TEF1α) 1.

Meyer W, Irinyi L, Hoang MTV, Robert V, Garcia-Hermoso D, Desnos-Ollivier M, Yurayart C, Tsang CC, Lee CY, Woo PCY, Pchelin IM, Uhrlaß S, Nenoff P, Chindamporn A, Chen S, Hebert PDN, Sorrell TC; ISHAM barcoding of pathogenic fungi working group.

Genome. 2019 Mar;62(3):160-169. doi: 10.1139/gen-2018-0083. Epub 2018 Nov 22.


Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside.

Beardsley J, Halliday CL, Chen SC, Sorrell TC.

Future Microbiol. 2018 Aug;13:1175-1191. doi: 10.2217/fmb-2018-0059. Epub 2018 Aug 16. Review.


The Early Innate Immune Response to, and Phagocyte-Dependent Entry of, Cryptococcus neoformans Map to the Perivascular Space of Cortical Post-Capillary Venules in Neurocryptococcosis.

Kaufman-Francis K, Djordjevic JT, Juillard PG, Lev S, Desmarini D, Grau GER, Sorrell TC.

Am J Pathol. 2018 Jul;188(7):1653-1665. doi: 10.1016/j.ajpath.2018.03.015. Epub 2018 Jun 19.


Surveillance for azole resistance in clinical and environmental isolates of Aspergillus fumigatus in Australia and cyp51A homology modelling of azole-resistant isolates.

Talbot JJ, Subedi S, Halliday CL, Hibbs DE, Lai F, Lopez-Ruiz FJ, Harper L, Park RF, Cuddy WS, Biswas C, Cooley L, Carter D, Sorrell TC, Barrs VR, Chen SC.

J Antimicrob Chemother. 2018 Sep 1;73(9):2347-2351. doi: 10.1093/jac/dky187.


Synthesis and Evaluation of a Series of Bis(pentylpyridinium) Compounds as Antifungal Agents.

Obando D, Koda Y, Pantarat N, Lev S, Zuo X, Bijosono Oei J, Widmer F, Djordjevic JT, Sorrell TC, Jolliffe KA.

ChemMedChem. 2018 Jul 18;13(14):1421-1436. doi: 10.1002/cmdc.201800331. Epub 2018 Jun 19.


Opportunities and challenges to improving antibiotic prescribing practices through a One Health approach: results of a comparative survey of doctors, dentists and veterinarians in Australia.

Zhuo A, Labbate M, Norris JM, Gilbert GL, Ward MP, Bajorek BV, Degeling C, Rowbotham SJ, Dawson A, Nguyen KA, Hill-Cawthorne GA, Sorrell TC, Govendir M, Kesson AM, Iredell JR, Dominey-Howes D.

BMJ Open. 2018 Mar 30;8(3):e020439. doi: 10.1136/bmjopen-2017-020439.


In vitro activity of the novel antifungal compound F901318 against Australian Scedosporium and Lomentospora fungi.

Biswas C, Law D, Birch M, Halliday C, Sorrell TC, Rex J, Slavin M, Chen SC.

Med Mycol. 2018 Nov 1;56(8):1050-1054. doi: 10.1093/mmy/myx161.


Whole Genome Sequencing of Candida glabrata for Detection of Markers of Antifungal Drug Resistance.

Biswas C, Chen SC, Halliday C, Martinez E, Rockett RJ, Wang Q, Timms VJ, Dhakal R, Sadsad R, Kennedy KJ, Playford G, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V.

J Vis Exp. 2017 Dec 28;(130). doi: 10.3791/56714.


Influenza A Virus as a Predisposing Factor for Cryptococcosis.

Oliveira LVN, Costa MC, Magalhães TFF, Bastos RW, Santos PC, Carneiro HCS, Ribeiro NQ, Ferreira GF, Ribeiro LS, Gonçalves APF, Fagundes CT, Pascoal-Xavier MA, Djordjevic JT, Sorrell TC, Souza DG, Machado AMV, Santos DA.

Front Cell Infect Microbiol. 2017 Sep 26;7:419. doi: 10.3389/fcimb.2017.00419. eCollection 2017.


IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model.

Li C, Lev S, Desmarini D, Kaufman-Francis K, Saiardi A, Silva APG, Mackay JP, Thompson PE, Sorrell TC, Djordjevic JT.

Virulence. 2017 Nov 17;8(8):1833-1848. doi: 10.1080/21505594.2017.1385692. Epub 2017 Dec 8.


Candida and invasive mould diseases in non-neutropenic critically ill patients and patients with haematological cancer.

Colombo AL, de Almeida Júnior JN, Slavin MA, Chen SC, Sorrell TC.

Lancet Infect Dis. 2017 Nov;17(11):e344-e356. doi: 10.1016/S1473-3099(17)30304-3. Epub 2017 Jul 31. Review.


Pseudomonas aeruginosa Inhibits the Growth of Scedosporium and Lomentospora In Vitro.

Chen SC, Patel S, Meyer W, Chapman B, Yu H, Byth K, Middleton PG, Nevalainen H, Sorrell TC.

Mycopathologia. 2018 Feb;183(1):251-261. doi: 10.1007/s11046-017-0140-x. Epub 2017 May 16.


Is Australia prepared for the next pandemic?

McVernon J, Sorrell TC, Firman J, Murphy B, Lewin SR.

Med J Aust. 2017 Apr 17;206(7):284-286. No abstract available.


Developing research priorities for Australia's response to infectious disease emergencies.

Lewin SR, Andrews RM, McVernon J, Milland J, Smith MZ, Sorrell TC; investigators of the Australian Partnership for Preparedness Research on Infectious Disease Emergencies

Commun Dis Intell Q Rep. 2017 Mar 31;41(1):E1-E3. No abstract available.


A planetary health approach to emerging infections in Australia.

Hill-Cawthorne GA, Capon AG, Sorrell TC, Marais BJ.

Lancet. 2017 Apr 1;389(10076):1293. doi: 10.1016/S0140-6736(17)30830-9. No abstract available.


Changing epidemiology of candidaemia in Australia.

Chapman B, Slavin M, Marriott D, Halliday C, Kidd S, Arthur I, Bak N, Heath CH, Kennedy K, Morrissey CO, Sorrell TC, van Hal S, Keighley C, Goeman E, Underwood N, Hajkowicz K, Hofmeyr A, Leung M, Macesic N, Botes J, Blyth C, Cooley L, George CR, Kalukottege P, Kesson A, McMullan B, Baird R, Robson J, Korman TM, Pendle S, Weeks K, Liu E, Cheong E, Chen S; Australian and New Zealand Mycoses Interest Group.

J Antimicrob Chemother. 2017 Apr 1;72(4):1103-1108. doi: 10.1093/jac/dkw422. Erratum in: J Antimicrob Chemother. 2017 Apr 1;72 (4):1270.


Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata by next-generation sequencing: a feasibility study.

Biswas C, Chen SC, Halliday C, Kennedy K, Playford EG, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V.

Clin Microbiol Infect. 2017 Sep;23(9):676.e7-676.e10. doi: 10.1016/j.cmi.2017.03.014. Epub 2017 Mar 23.


Changing epidemiology of candidaemia in Australia.

Chapman B, Slavin M, Marriott D, Halliday C, Kidd S, Arthur I, Bak N, Heath CH, Kennedy K, Morrissey CO, Sorrell TC, van Hal S, Keighley C, Goeman E, Underwood N, Hajkowicz K, Hofmeyr A, Leung M, Macesic N, Botes J, Blyth C, Cooley L, George CR, Kalukottege P, Kesson A, McMullan B, Baird R, Robson J, Korman TM, Pendle S, Weeks K, Liu E, Cheong E, Chen S; Australian and New Zealand Mycoses Interest Group.

J Antimicrob Chemother. 2017 Apr 1;72(4):1270. doi: 10.1093/jac/dkx047. No abstract available.


Pho4 Is Essential for Dissemination of Cryptococcus neoformans to the Host Brain by Promoting Phosphate Uptake and Growth at Alkaline pH.

Lev S, Kaufman-Francis K, Desmarini D, Juillard PG, Li C, Stifter SA, Feng CG, Sorrell TC, Grau GE, Bahn YS, Djordjevic JT.

mSphere. 2017 Jan 25;2(1). pii: e00381-16. doi: 10.1128/mSphere.00381-16. eCollection 2017 Jan-Feb.


The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.

Kwon-Chung KJ, Bennett JE, Wickes BL, Meyer W, Cuomo CA, Wollenburg KR, Bicanic TA, Castañeda E, Chang YC, Chen J, Cogliati M, Dromer F, Ellis D, Filler SG, Fisher MC, Harrison TS, Holland SM, Kohno S, Kronstad JW, Lazera M, Levitz SM, Lionakis MS, May RC, Ngamskulrongroj P, Pappas PG, Perfect JR, Rickerts V, Sorrell TC, Walsh TJ, Williamson PR, Xu J, Zelazny AM, Casadevall A.

mSphere. 2017 Jan 11;2(1). pii: e00357-16. doi: 10.1128/mSphere.00357-16. eCollection 2017 Jan-Feb.


Future directions for public health research in emerging infectious diseases.

Hill-Cawthorne GA, Sorrell TC.

Public Health Res Pract. 2016 Dec 14;26(5). pii: 2651655. doi: 10.17061/phrp2651655.


Delivering on Antimicrobial Resistance Agenda Not Possible without Improving Fungal Diagnostic Capabilities.

Denning DW, Perlin DS, Muldoon EG, Colombo AL, Chakrabarti A, Richardson MD, Sorrell TC.

Emerg Infect Dis. 2017 Feb;23(2):177-183. doi: 10.3201/eid2302.152042. Epub 2017 Feb 15. Review.


Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast.

Himmelreich U, Sorrell TC, Daniel HM.

Methods Mol Biol. 2017;1508:289-304.


Identification and Characterization of VNI/VNII and Novel VNII/VNIV Hybrids and Impact of Hybridization on Virulence and Antifungal Susceptibility Within the C. neoformans/C. gattii Species Complex.

Aminnejad M, Cogliati M, Duan S, Arabatzis M, Tintelnot K, Castañeda E, Lazéra M, Velegraki A, Ellis D, Sorrell TC, Meyer W.

PLoS One. 2016 Oct 20;11(10):e0163955. doi: 10.1371/journal.pone.0163955. eCollection 2016.


Cathelicidins in the Tasmanian devil (Sarcophilus harrisii).

Peel E, Cheng Y, Djordjevic JT, Fox S, Sorrell TC, Belov K.

Sci Rep. 2016 Oct 11;6:35019. doi: 10.1038/srep35019.


Problematic Dichotomization of Risk for Intensive Care Unit (ICU)-Acquired Invasive Candidiasis: Results Using a Risk-Predictive Model to Categorize 3 Levels of Risk From a Multicenter Prospective Cohort of Australian ICU Patients.

Playford EG, Lipman J, Jones M, Lau AF, Kabir M, Chen SC, Marriott DJ, Seppelt I, Gottlieb T, Cheung W, Iredell JR, McBryde ES, Sorrell TC.

Clin Infect Dis. 2016 Dec 1;63(11):1463-1469. Epub 2016 Sep 6.


Inositol Polyphosphate Kinases, Fungal Virulence and Drug Discovery.

Li C, Lev S, Saiardi A, Desmarini D, Sorrell TC, Djordjevic JT.

J Fungi (Basel). 2016 Sep 6;2(3). pii: E24. doi: 10.3390/jof2030024. Review.


Antifungal susceptibilities of non-Aspergillus filamentous fungi causing invasive infection in Australia: support for current antifungal guideline recommendations.

Halliday CL, Chen SC, Kidd SE, van Hal S, Chapman B, Heath CH, Lee A, Kennedy KJ, Daveson K, Sorrell TC, Morrissey CO, Marriott DJ, Slavin MA.

Int J Antimicrob Agents. 2016 Oct;48(4):453-8. doi: 10.1016/j.ijantimicag.2016.07.005. Epub 2016 Aug 12.


MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors.

Firacative C, Roe CC, Malik R, Ferreira-Paim K, Escandón P, Sykes JE, Castañón-Olivares LR, Contreras-Peres C, Samayoa B, Sorrell TC, Castañeda E, Lockhart SR, Engelthaler DM, Meyer W.

PLoS Negl Trop Dis. 2016 Aug 5;10(8):e0004861. doi: 10.1371/journal.pntd.0004861. eCollection 2016 Aug.


Identification of a major IP5 kinase in Cryptococcus neoformans confirms that PP-IP5/IP7, not IP6, is essential for virulence.

Li C, Lev S, Saiardi A, Desmarini D, Sorrell TC, Djordjevic JT.

Sci Rep. 2016 Apr 1;6:23927. doi: 10.1038/srep23927.


Mucormycosis in Australia: contemporary epidemiology and outcomes.

Kennedy KJ, Daveson K, Slavin MA, van Hal SJ, Sorrell TC, Lee A, Marriott DJ, Chapman B, Halliday CL, Hajkowicz K, Athan E, Bak N, Cheong E, Heath CH, Morrissey CO, Kidd S, Beresford R, Blyth C, Korman TM, Robinson JO, Meyer W, Chen SC; Australia and New Zealand Mycoses Interest Group of the Australasian Society for Infectious Diseases.

Clin Microbiol Infect. 2016 Sep;22(9):775-781. doi: 10.1016/j.cmi.2016.01.005. Epub 2016 Jan 20.


Stimulation with lysates of Aspergillus terreus, Candida krusei and Rhizopus oryzae maximizes cross-reactivity of anti-fungal T cells.

Deo SS, Virassamy B, Halliday C, Clancy L, Chen S, Meyer W, Sorrell TC, Gottlieb DJ.

Cytotherapy. 2016 Jan;18(1):65-79. doi: 10.1016/j.jcyt.2015.09.013. Epub 2015 Nov 6.


Pulmonary Cryptococcosis.

Chang CC, Sorrell TC, Chen SC.

Semin Respir Crit Care Med. 2015 Oct;36(5):681-91. doi: 10.1055/s-0035-1562895. Epub 2015 Sep 23. Review.


Cryptococcal transmigration across a model brain blood-barrier: evidence of the Trojan horse mechanism and differences between Cryptococcus neoformans var. grubii strain H99 and Cryptococcus gattii strain R265.

Sorrell TC, Juillard PG, Djordjevic JT, Kaufman-Francis K, Dietmann A, Milonig A, Combes V, Grau GE.

Microbes Infect. 2016 Jan;18(1):57-67. doi: 10.1016/j.micinf.2015.08.017. Epub 2015 Sep 11.


Modern technology and infectious diseases activity data: how can we use this for service planning?

Keighley C, Hamor P, Chen S, Watts MR, Douglas MW, Kok J, O'Sullivan M, Mitchell DH, Packham D, Sorrell TC, Iredell JR.

Intern Med J. 2015 Jun;45(6):688. doi: 10.1111/imj.12772. No abstract available.


Fungal Inositol Pyrophosphate IP7 Is Crucial for Metabolic Adaptation to the Host Environment and Pathogenicity.

Lev S, Li C, Desmarini D, Saiardi A, Fewings NL, Schibeci SD, Sharma R, Sorrell TC, Djordjevic JT.

mBio. 2015 Jun 2;6(3):e00531-15. doi: 10.1128/mBio.00531-15.


International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castañón-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancopé-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, Dromer F, Ranque S, Guarro J, Cano-Lira JF, Robert V, Velegraki A, Meyer W.

Med Mycol. 2015 May;53(4):313-37. doi: 10.1093/mmy/myv008. Epub 2015 Mar 22.


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