2017 Publications

Selected publications of CREID investigators

Moso MA, Woolnough E, Langham F, Hoy JF, Cheng AC, Walker RG, Chrysostomou A, Woolley I, Weeraratne A, Trevillyan JM. Increasing prevalence and risk of chronic kidney disease in HIV-positive individuals: changing demographics over a six-year period. Journal of Infectious Diseases. 2017 Dec 22. doi: 10.1093/infdis/jix676.


Heriot GS, Cronin K, Tong SYC, Cheng AC, Liew D. Criteria for identifying patients with Staphylococcus aureus bacteremia who are at low risk of endocarditis: a systematic review. Open Forum Infectious Diseases. 2017 Nov 24;4(4):ofx261.


Shetty AL, Thompson K, Byth K, Macaskill P, Green M, Fullick M, Lander H, Iredell J. Serum lactate cut-offs as a risk stratification tool for in-hospital adverse outcomes in emergency department patients screened for suspected sepsis. BMJ Open. 2018 Jan 5;8(1):e015492.


Maali Y, Perez-Concha O, Coiera E, Roffe D, Day RO, Gallego B. Predicting 7-day, 30-day and 60-day all-cause unplanned readmission: a case study of a Sydney hospital. BMC Med Informatics and Decision Making. 2018 Jan 4;18(1):1.


Dunn AG, Coiera E, Bourgeois FT. Unreported links between trial registrations and published articles were identified using document similarity measures in a cross-sectional analysis of ClinicalTrials.gov. Journal of Clinical Epidemiology. 2017 Dec 19. pii: S0895-4356(17)30596-6.


Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens. 2018 Jan 4;14(1):e1006750.


Wang Y, Coiera E, Runciman W, Magrabi F. Automating the identification of patient safety incident reports using multi-label classification. Studies in Health Technology and Informatics. 2017;245:609-613.

Townsi N, Simpson SJ, Sikazwe CT, Chidlow GR, Hall GL, Pillow JJ, Wilson AC, Smith DW, Laing IA. Environmental exposure and parental collection does not affect detection or semi-quantitative load assessment of bacteria in nasal swab specimens from children. Infectious Diseases (London). 2017 Dec 13:1-4.


Lin YW, Zhou QT, Han ML, Chen K, Onufrak NJ, Wang J, Turnidge JD, Howden BP, Forrest A, Chan HK, Li J. Elucidating the pharmacokinetics/pharmacodynamics of aerosolized colistin against multidrug-resistant Acinetobacter baumannii and Klebsiella pneumoniae in a mouse lung infection model. Antimicrobial Agents and Chemotherapy. 2017 Dec 11. pii: AAC.01790-17.


Carter GP, Schultz MB, Baines SL, Goncalves da Silva A, Heffernan H, Tiong A, Pham PH, Monk IR, Stinear TP, Howden BP, Williamson DA. Topical antibiotic use co-selects for the carriage of mobile genetic elements conferring resistance to unrelated antimicrobials in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy. 2017 Dec 11. pii: AAC.02000-17


Gao W, Howden BP, Stinear TP. Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen. Current Opinion in Microbiology. 2017 Dec 8;41:76-82.


Lau AY, Piper K, Bokor D, Martin P, Lau VS, Coiera E. Challenges during implementation of a patient-facing mobile app for surgical rehabilitation: feasibility study. JMIR Human Factors. 2017 Dec 7;4(4):e31.


Rodríguez-Nevado C, Lam TT, Holmes EC, Pagán I. The impact of host genetic diversity on virus evolution and emergence. Ecology Letters. 2017 Dec 5. doi: 10.1111/ele.12890.


Shane AL, Mody RK, Crump JA, Tarr PI, Steiner TS, Kotloff K, Langley JM, Wanke C, Warren CA, Cheng AC, Cantey J, Pickering LK. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clinical Infectious Diseases. 2017 Nov 29;65(12):1963-1973.


Mitchell BG, Fasugba O, Gardner A, Koerner J, Collignon P, Cheng AC, Graves N, Morey P, Gregory V. Reducing catheter-associated urinary tract infections in hospitals: study protocol for a multi-site randomised controlled study. BMJ Open. 2017 Nov 28;7(11):e018871.


Lee RS, Seemann T, Heffernan H, Kwong JC, Gonçalves da Silva A, Carter GP, Woodhouse R, Dyet KH, Bulach DM, Stinear TP, Howden BP, Williamson DA. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. Journal of Antimicrobial Chemotherapy. 2017 Nov 22. doi: 10.1093/jac/dkx405.


Williamson DA, Lane CR, Easton M, Valcanis M, Strachan J, Veitch MG, Kirk MD, Howden BP. Increasing antimicrobial resistance in non-typhoidal Salmonella in Australia, 1979 - 2015. Antimicrobial Agents and Chemotherapy. 2017 Nov 27. pii: AAC.02012-17.


Shetty A, MacDonald SP, Williams JM, van Bockxmeer J, de Groot B, Esteve Cuevas LM, Ansems A, Green M, Thompson K, Lander H, Greenslade J, Finfer S, Iredell J. Lactate ≥2 mmol/L plus qSOFA improves utility over qSOFA alone in emergency department patients presenting with suspected sepsis. Emerging Medicine Australasia. 2017 Dec;29(6):626-634.


Yong MK, Cameron PU, Slavin MA, Cheng AC, Morrissey CO, Bergin K, Spencer A, Ritchie D, Lewin SR. Low T-cell responses to mitogen stimulation predicts poor survival in recipients of allogeneic hematopoietic stem cell transplantation. Frontiers in Immunology. 2017 Nov 9;8:1506.

Nie FY, Lin XD, Hao ZY, Chen XN, Wang ZX, Wang MR, Wu J, Wang HW, Zhao G, Ma RZ, Holmes EC, Zhang YZ. Extensive diversity and evolution of hepadnaviruses in bats in China. Virology. 2017 Nov 16;514:88-97.


Shi M, Zhang YZ, Holmes EC. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Research. 2017 Oct 27


Mahar JE, Hall RN, Peacock D, Kovaliski J, Piper M, Mourant R, Huang N, Campbell S, Gu X, Read A, Urakova N, Cox T, Holmes EC, Strive T. Rabbit haemorrhagic disease virus 2 (GI.2) is replacing endemic strains of RHDV in the Australian landscape within 18 months of its arrival. Journal of Virology. 2017 Nov 1. pii: JVI.01374-17.


Knight KW, Stephenson SE, West S, Delatycki MB, Jones CA, Little MH, Patton GC, Sawyer SM, Skinner SR, Telfer MM, Wake M, North KN, Oberklaid F. The kids are OK: it is discrimination not same-sex parents that harms children. Medical Journal of Australia. 2017 Nov 6;207(9):374-375.

Qi W, Jia W, Liu D, Li J, Bi Y, Xie S, Li B, Hu T, Du Y, Xing L, Zhang J, Zhang F, Wei X, Eden JS, Li H, Tian H, Li W, Su G, Lao G, Xu C, Xu B, Liu W, Zhang G, Ren T, Holmes EC, Cui J, Shi W, Gao GF, Liao M. Emergence and adaptation of a novel highly pathogenic H7N9 influenza virus in birds and humans from a 2013-human-infecting low pathogenic ancestor. Journal of Virology. 2017 Oct 25. pii: JVI.00921-17.


Geoghegan JL, Holmes EC. Predicting virus emergence amid evolutionary noise. Open Biology. 2017 Oct;7(10). pii: 170189.


Mowlaboccus S, Mullally CA, Richmond PC, Howden BP, Stevens K, Speers DJ, Keil AD, Bjørnstad ON, Perkins TT, Kahler CM. Differences in the population structure of Neisseria meningitidis in two Australian states: Victoria and Western Australia. PLoS One. 2017 Oct 24;12(10):e0186839.


Shane AL, Mody RK, Crump JA, Tarr PI, Steiner TS, Kotloff K, Langley JM, Wanke C, Warren CA, Cheng AC, Cantey J, Pickering LK. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clinical Infectious Diseases. 2017 Oct 19. doi: 10.1093/cid/cix669.


Mackenzie JS, Lindsay MDA, Smith DW, Imrie A. The ecology and epidemiology of Ross River and Murray Valley encephalitis viruses in Western Australia: examples of One Health in Action. Transactions of the Royal Society of Tropical Medicine and Hygiene. 2017 Jun 1;111(6):248-254.


Day RO, Frensham LJ, Nguyen AD, Baysari MT, Aung E, Lau AYS, Zwar N, Reath J, Laba T, Li L, McLachlan A, Runciman WB, Buchbinder R, Clay-Williams R, Coiera E, Braithwaite J, McNeil HP, Hunter DJ, Pile KJ, Portek I, WIlliams KM, Westbrook JI. Effectiveness of an electronic patient-centred self-management tool for gout sufferers: a cluster randomised controlled trail protocol. BMJ Open. 2017 Oct 16;7(10):e017281.


Lee RS, Howden BP. The critical importance of sampling fraction to inferences of Mycobacterium tuberculosis transmission. Clinical Infectious Diseases. 2017 Oct 13. doi: 10.1093/cid/cix750.


Marais BJ, Walker TM, Cirillo DM, Raviglione M, Abubakar I, van der Werf MJ, Boehme C, Niemann S, Castro KG, Zumla A, Sintchenko V, Crook DW. Aiming for zero tuberculosis transmission in low-burden countries. Lancet Respiratory Medicine. 2017 Oct 12. pii: S2213-2600(17)30382-X.


Heriot GS, Cheng AC, Tong SYC, Liew D. Clinical prediction rules used to rule out endocarditis must be assessed against a sensitive reference standard. Clinical Microbiology and Infection. 2017 Oct 10. pii: S1198-743X(17)30536-0.


Wiles LK, Hibbert PD, Stephens JH, Coiera E, Westbrook J, Braithwaite J, Day RO, Hillman KM, Runciman WB. STANDING Collaboration: a study protocol for developing clinical standards. BMJ Open. 2017 Oct 11;7(10):e014048.


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. Influenza A virus as a predisposing factor for cryptococcosis. Frontiers in Cellular and Infection Microbiology. 2017 Sep 26;7:419.


Britton PN, Blyth CC, Macartney K, Dale RC, Li-Kim-Moy J, Khandaker G, Crawford NW, Marshall H, Clark JE, Elliott EJ, Booy R, Cheng AC, Jones CA; Australian Childhood Encephalitis (ACE) Study Investigators, Influenza Complications Alert Network (FluCAN) Investigators, and Paediatric Active Enhanced Disease Surveillance (PAEDS) Network. The spectrum and burden of influenza-associated neurological disease in children: combined encephalitis and influenza sentinel site surveillance from Australia, 2013-2015. Clinical Infectious Diseases. 2017 Aug 15;65(4):653-660.


Hodgson T, Magrabi F, Coiera E. Efficiency and safety of speech recognition for documentation in the electronic health record. The Journal of the American Medical Informatics Association. 2017 Nov 1;24(6):1127-1133.


Smibert OC, Hall AJ, Varma D, Cheng AC. Painful loss of vision after an episode of herpes simplex encephalitis. Internal Medicine Journal. 2017 Oct;47(10):1210-1211.


Li C, Lev S, Desmarini D, Kaufman-Francis K, Saiardi A, Silva APG, Mackay JP, Thompson PE, Sorrell TC, Djordjevic JT. IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model. Virulence. 2017 Oct 4:0. doi: 10.


Britton PN, Khandaker G, Khatami A, Teutsch S, Francis S, McMullan BJ, Jones CA. High prevalence of developmental concern amongst infants at 12 months following hospitalised parechovirus infection. Journal of Paediatrics and Child Health. 2017 Sep 28. doi: 10.1111/jpc.13728.


Srikhanta YN, Fung KY, Pollock GL, Bennett-Wood V, Howden BP, Hartland EL. Phasevarion regulated virulence in the emerging paediatric pathogen Kingella kingae. Infection and Immunity. 2017 Sep 25. pii: IAI.00319-17.


Porter AF, Duggan AT, Poinar HN, Holmes EC. Comment: Characterization of two historic smallpox specimens from a Czech museum. Viruses. 2017 Sep 28;9(10). pii: E276.


Bowden T, Coiera E. The role and benefits of accessing primary care patient records during unscheduled care: a systematic review. BMC Medical Informatics and Decision Making. 2017 Sep 22;17(1):138.


Pettersson JH, Shi M, Bohlin J, Eldholm V, Brynildsrud OB, Paulsen KM, Andreassen Å, Holmes EC. Characterizing the virome of Ixodes ricinus ticks from northern Europe. Scientific Reports. 2017 Sep 7;7(1):10870.


Spelman T, Pilcher DV, Cheng AC, Bull AL, Richards MJ, Worth LJ. Central line-associated bloodstream infections in Australian ICUs: evaluating modifiable and non-modifiable risks in Victorian healthcare facilities. Epidemiology and Infection. 2017 Sep 4:1-9.


Voorhees IEH, Glaser AL, Toohey-Kurth K, Newbury S, Dalziel BD, Dubovi EJ, Poulsen K, Leutenegger C, Willgert KJE, Brisbane-Cohen L, Richardson-Lopez J, Holmes EC, Parrish CR. Spread of Canine Influenza A(H3N2) Virus, United States. Emerging Infectious Diseases. 2017 Dec 15;23(12).


Fu S, Hiley L, Octavia S, Tanaka MM, Sintchenko V, Lan R. Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles. Scientific Reports. 2017 Aug 29;7(1):9733.

Degeling C, Johnson J, Ward M, Wilson A, Gilbert G. A Delphi survey and analysis of expert perspectives on One Health in Australia. Ecohealth. 2017 Aug 22. doi: 10.1007/s10393-017-1264-7.


Buultjens AH, Chua KYL, Baines SL, Kwong J, Gao W, Cutcher Z, Adcock S, Ballard S, Schultz MB, Tomita T, Subasinghe N, Carter GP, Pidot SJ, Franklin L, Seemann T, Gonçalves Da Silva A, Howden BP, Stinear TP. A supervised statistical learning approach for accurate Legionella pneumophila source attribution during outbreaks. Applied Environmental Microbiology. 2017 Aug 18. pii: AEM.01482-17.


Kerr PJ, Cattadori IM, Liu J, Sim DG, Dodds JW, Brooks JW, Kennett MJ, Holmes EC, Read AF. Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. Proceedings of the National Acadamy of Sciences U S A. 2017 Aug 14;.


Yong MK, Ananda-Rajah M, Cameron PU, Morrissey CO, Spencer A, Ritchie D, Cheng AC, Lewin SR, Slavin M. Cytomegalovirus reactivation is associated with increased risk of late-onset invasive fungal disease following allogeneic hematopoietic stem cell transplantation; a multi-centre study in the current era of viral load monitoring. Biology of Blood and Marrow Transplantation. 2017 Aug 7. pii: S1083-8791(17)30621-3.


Ngo JP, Le B, Khan Z, Kett MM, Gardiner BS, Smith DW, Melhem MM, Maksimenko A, Pearson JT, Evans RG. Micro-computed tomographic analysis of the radial geometry of intrarenal artery-vein pairs in rats and rabbits: comparison with light microscopy. Clinical and Experimental Pharmacology and Physiology. 2017 Aug 10. doi: 10.1111/1440-1681.12842.


Lee JYH, Monk IR, Pidot SJ, Singh S, Chua KYL, Seemann T, Stinear TP, Howden BP. Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis. Microbial Genomics. 2016 Sep 20;2(9):e000077.

Eden JS, Chisholm RH, Bull RA, White PA, Holmes EC, Tanaka MM. Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants. Virus Evolution. 2017 Jul 28;3(2):vex018.


Colombo AL, de Almeida Júnior JN, Slavin MA, Chen SC, Sorrell TC. Candida and invasive mould diseases in non-neutropenic critically ill patients and patients with haematological cancer. Lancet Infectious Diseases. 2017 Jul 31. pii: S1473-3099(17)30304-3. Review.


Krishnaswamy S, Wallace EM, Cheng AC, Buttery J, Giles ML. Protecting newborns from pertussis: The role of partner vaccination in the era of maternal immunization. European Journal of Obstetrics & Gynecology and Reproductive Biology. 2017 Jul 25;216:159-163.


Liu J, Cattadori IM, Sim DG, Eden JS, Holmes EC, Read AF, Kerr PJ. Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or loss of function do not explain virulence changes observed in the field. Journal of Virology. 2017 Aug 2. pii: JVI.01289-17.


Dheilly NM, Bolnick D, Bordenstein S, Brindley PJ, Figuères C, Holmes EC, Martínez Martínez J, Phillips AJ, Poulin R, Rosario K. Parasite Microbiome Project: systematic investigation of microbiome dynamics within and across parasite-host interactions. mSystems. 2017 Jul 18;2(4). pii: e00050-17.


Yeoh HL, Cheng AC, Cherry CL, Weir JM, Meikle PJ, Hoy JF, Crowe SM, Palmer CS. Immunometabolic and lipidomic markers associated with the frailty index and quality of life in aging HIV+ men on antiretroviral therapy. EBioMedicine. 2017 Jul 18. pii: S2352-3964(17)30288-8.


Mai TQ, Van Anh NT, Hien NT, Lan NH, Giang DC, Hang PTT, Lan NTN, Marais BJ, Sintchenko V. Drug resistance and Mycobacterium tuberculosis strain diversity in TB/HIV co-infected patients in Ho Chi Minh City, Vietnam. Journal of Global Antimicrobial Resistance. 2017 Jul 22.


Choong MK, Tsafnat G, Hibbert P, Runciman WB, Coiera E. Linking clinical quality indicators to research evidence - a case study in asthma management for children. BMC Health Services Research. 2017 Jul 21;17(1):502.


Johansen CA, Williams SH, Melville LF, Nicholson J, Hall RA, Bielefeldt-Ohmann H, Prow NA, Chidlow GR, Wong S, Sinha R, Williams DT, Lipkin WI, Smith DW. Characterization of Fitzroy River Virus and serologic evidence of human and animal infection. Emerging Infectious Diseases. 2017 Aug;23(8):1289-1299.


Laranjo L, Lau AYS, Martin P, Tong HL, Coiera E. Use of a mobile social networking intervention for weight management: a mixed-methods study protocol. BMJ Open. 2017 Jul 12;7(7):e016665.


Cheng AC, Jenney AWJ. Macrolide resistance in pneumococci-is it relevant? Pneumonia. 2016 Jul 7;8:10.


Peel TN, Sedarski JA, Dylla BL, Shannon SK, Amirahmadi F, Hughes JG, Cheng AC, Patel R. Laboratory workflow analysis of culture of periprosthetic tissues in blood culture bottles. Journal of Clinical Microbiology. 2017 Jul 12. pii: JCM.00652-17.

Eden JS, Rose K, Ng J, Shi M, Wang Q, Sintchenko V, Holmes EC. Francisella tularensis ssp. holarctica in Ringtail Possums, Australia. Emerging Infectious Diseaases. 2017 Jul;23(7):1198-1201.


Vanderven HA, Liu L, Ana-Sosa-Batiz F, Nguyen TH, Wan Y, Wines B, Hogarth PM, Tilmanis D, Reynaldi A, Parsons MS, Hurt AC, Davenport MP, Kotsimbos T, Cheng AC, Kedzierska K, Zhang X, Xu J, Kent SJ. Fc functional antibodies in humans with severe H7N9 and seasonal influenza. JCI Insight. 2017 Jul 6;2(13).


Degeling C, Johnson J, Iredell J, Nguyen KA, Norris JM, Turnidge JD, Dawson A, Carter SM, Gilbert GL. Assessing the public acceptability of proposed policy interventions to reduce the misuse of antibiotics in Australia: A report on two community juries. Health Expectations. 2017 Jun 30.


Chow EPF, Walker S, Hocking JS, Bradshaw CS, Chen MY, Tabrizi SN, Howden BP, Law MG, Maddaford K, Read TRH, Lewis DA, Whiley DM, Zhang L, Grulich AE, Kaldor JM, Cornelisse VJ, Phillips S, Donovan B, McNulty AM, Templeton DJ, Roth N, Moore R, Fairley CK. A multicentre double-blind randomised controlled trial evaluating the efficacy of daily use of antibacterial mouthwash against oropharyngeal gonorrhoea among men who have sex with men: the OMEGA (Oral Mouthwash use to Eradicate GonorrhoeA) study protocol. BMC Infectious Diseases. 2017 Jun 28;17(1):456.


Britton PN, Dale RC, Blyth CC, Macartney K, Crawford N, Marshall H, Clark J, Elliott E, Webster RI, Cheng AC, Booy R, Jones CA; ACE study investigators and PAEDS network. Influenza-associated encephalitis/encephalopathy identified by the Australian Childhood Encephalitis Study 2013-2015. Pediatric Infectious Diseases Journal. 2017 Jun 24.


Coiera E, Choong MK, Tsafnat G, Hibbert P, Runciman WB. Linking quality indicators to clinical trials: an automated approach. International Journal for Quality in Health Care. 2017 Jun 23:1-8.


Wang W, Lin XD, Liao Y, Guan XQ, Guo WP, Xing JG, Holmes EC, Zhang YZ. Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses. Journal of Virology. 2017 Jun 21.


Shi M, Neville P, Nicholson J, Eden JS, Imrie A, Holmes EC. High resolution meta-transcriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia. Journal of Virology. 2017 Jun 21.


Williamson DA, Carter GP, Howden BP. Current and emerging topical antibacterials and antiseptics: agents, action, and resistance patterns. Clinical Microbiology Reviews. 2017 Jul;30(3):827-860.


Kiely P, Wood EM, Gambhir M, Cheng AC, McQuilten ZK, Seed CR. Emerging infectious disease agents and blood safety in Australia: spotlight on Zika virus. Medical Journal of Australia. 2017 Jun 5;206(10):455-460.


Dotel R, O'Sullivan M, Gilbert G. Staphylococcus aureus in critical care. Lancet Infectious Diseases. 2017 Jun;17(6):579-580.


Kiely P, Gambhir M, Cheng AC, McQuilten ZK, Seed CR, Wood EM. Emerging infectious diseases and blood safety: modeling the transfusion-transmission risk. Transfusion Medicine Reviews 2017 Jul;31(3):154-164


Fourment M, Darling AE, Holmes EC. The impact of migratory flyways on the spread of avian influenza virus in North America. BMC Evolutionary Biology. 2017 May 25;17(1):118.


Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. 2017 May 24. doi: 10.1038/nature22401. 


Raichand S, Dunn AG, Ong MS, Bourgeois FT, Coiera E, Mandl KD. Conclusions in systematic reviews of mammography for breast cancer screening and associations with review design and author characteristics. Systematic Reviews. 2017 May 22;6(1):105.


Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A diverse range of novel RNA viruses in geographically distinct honey bee populations. Journal of VIrology. 2017 Jul 27;91(16).


Luang-Suarkia D, Ernst T, Alpers MP, Garruto R, Smith D, Imrie A. Serological evidence for transmission of multiple dengue virus serotypes in Papua New Guinea and West Papua prior to 1963. PLoS Neglected Tropical Diseases 2017;11(4): e0005488. 


Chen SC, Patel S, Meyer W, Chapman B, Yu H, Byth K, Middleton PG, Nevalainen H, Sorrell TC. Pseudomonas aeruginosa inhibits the growth of scedosporium and lomentospora in vitro. Mycopathologia. 2017 May 16. 


Kearns TM, Currie BJ, Cheng AC, McCarthy J, Carapetis JR, Holt DC, Page W, Shield J, Gundjirryirr R, Mulholland E, Ward L, Andrews RM. Strongyloides seroprevalence before and after an ivermectin mass drug administration in a remote Australian Aboriginal community. PLoS Neglected Tropical Diseases. 2017 May 15;11(5):e0005607.


Sparham SJ, Kwong JC, Valcanis M, Easton M, Trott DJ, Seemann T, Stinear TP, Howden BP. Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9. International Journal of Antimicrobial Agents. 2017 May 2.

Thompson CK, Wang Q, Bag SK, Franklin N, Shadbolt CT, Howard P, Fearnley EJ, Quinn HE, Sintchenko V, Hope KG. Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015. Epidemiology and Infection. 2017 May 2:1-10.


Dunn AG, Surian D, Leask J, Dey A, Mandl KD, Coiera E. Mapping information exposure on social media to explain differences in HPV vaccine coverage in the United States. Vaccine. 2017 Apr 28. pii: S0264-410X(17)30552-2.


Britton PN, Blyth CC, Macartney K, Dale RC, Li-Kim-Moy J, Khandaker G, Crawford N, Marshall H, Clark J, Elliott E, Booy R, Cheng AC, Jones CA; ACE study investigators, FluCAN investigators and PAEDS network. The Spectrum and Burden of Influenza-Associated Neurological Disease in Children: Combined Encephalitis and Influenza Sentinel Site Surveillance from Australia 2013-2015. Clinical Infectious Diseases. 2017 Apr 29. doi: 10.1093/clinid/cix412.


Warren AM, Cheng AC, Watson K, Lewin SR, Hoy JF. Outcomes following detection of low level plasma HIV RNA in HIV-infected patients previously virologically suppressed on antiretroviral therapy: a retrospective observational study. Sex Health. 2017 Apr 27. doi: 10.1071/SH16165.


Cheng AC, Macartney KK, Waterer GW, Kotsimbos T, Kelly PM, Blyth CC. Reply to Skowronski and Chambers. Clinical Infectious Diseases. 2017 Apr 19. doi: 10.1093/cid/cix376.


Yong MK, Cameron PU, Slavin M, Morrissey CO, Bergin K, Spencer A, Ritchie D, Cheng AC, Samri A, Carcelain G, Autran B, Lewin SR. Identifying cytomegalovirus (CMV) complications using the quantiferon-CMV assay after allogeneic hematopoietic stem cell transplantation. Journal of Infectious Diseases. 2017 Apr 18. doi: 10.1093/infdis/jix192.


Lu M, Tian JH, Yu B, Guo WP, Holmes EC, Zhang YZ. Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China. Ticks and Tick-borne Diseases. 2017 Mar 24. pii: S1877-959X(17)30141-3.


Sharma S, Sneath E, Cheng AC, Friedman ND. Community-acquired syndromes causing morbidity and mortality in Australia. Communicable Diseases Intelligence Quarterly Report. 2017 Mar 31;41(1): E49-E57.


Lewin SR, Andrews RM, McVernon J, Milland J, Smith MZ, Sorrell TC; investigators of the Australian Partnership for Preparedness Research on Infectious Disease Emergencies. Developing research priorities for Australia's response to infectious disease emergencies. Communicable Diseases Intelligence Quarterly Report. 2017 Mar 31;41(1):E1-E3.


Lin XD, Wang W, Hao ZY, Wang ZX, Guo WP, Guan XQ, Wang MR, Wang HW, Zhou RH, Li MH, Tang GP, Wu J, Holmes EC, Zhang YZ. Extensive diversity of coronaviruses in bats from China. Virology. 2017 Apr 3;507:1-10.


Zozaya-Valdés E, Porter JL, Coventry J, Fyfe JA, Carter GP, da Silva AG, Schultz MB, Seemann T, Johnson PD, Stewardson AJ, Bastian I, Roberts SA, Howden BP, Williamson DA, Stinear TP. A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA. Journal of Clinical Microbiology. 2017 Apr 5. pii: JCM.00197-17.


Hill-Cawthorne GA, Capon AG, Sorrell TC, Marais BJ. A planetary health approach to emerging infections in Australia. Lancet. 2017 Apr 1;389(10076):1293.


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. Changing epidemiology of candidaemia in Australia. Journal of Antimicrobial Chemotherapy. 2017 Apr 1;72(4):1103-1108.


Nicholson LJ, Mahar JE, Strive T, Zheng T, Holmes EC, Ward VK, Duckworth JA. Discovery and characterization of a benign rabbit calicivirus in New Zealand. Applied Environmental Microbiology. 2017 Mar 31. pii: AEM.00090-17.


Braithwaite J, Westbrook J, Coiera E, Runciman WB, Day R, Hillman K, Herkes J. A systems science perspective on the capacity for change in public hospitals. Israel Journal of Health Policy Research. 2017 Mar 24;6:16.


Gonçalves da Silva A, Baines SL, Carter GP, Heffernan H, French NP, Ren X, Seemann T, Bulach D, Kwong J, Stinear TP, Howden BP, Williamson DA. A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus. Microbial Genomics. 2017 Jan 31;3(1):e000105.


Biswas C, Chen SC, Halliday C, Kennedy K, Playford EG, Marriott DJ, Slavin MA, Sorrell TC, Sintchenko V. Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata by next generation sequencing: a feasibility study. Clinical Microbiology and Infection. 2017 Mar 23.


Cobbin JC, Alfelali M, Barasheed O, Taylor J, Dwyer DE, Kok J, Booy R, Holmes EC, Rashid H; Hajj Research Team. Multiple sources of genetic diversity of influenza A viruses during the Hajj. Journal of Virology. 2017 Mar 22. pii: JVI.00096-17.


Cheng AC, Macartney KK, Waterer GW, Kotsimbos T, Kelly PM, Blyth CC; FluCAN Investigators. Repeated vaccination does not appear to impact on influenza vaccine effectiveness against hospitalisation with confirmed influenza. Clinical Infectious Diseases. 2017 Mar 17. doi: 10.1093/cid/cix209.

Lyell D, Magrabi F, Raban MZ, Pont LG, Baysari MT, Day RO, Coiera E. Automation bias in electronic prescribing. BMC Medical Informatics and Decision Making. 2017 Mar 16;17(1):28

Flint A, Aubron C, Bailey M, Bellomo R, Pilcher D, Cheng AC, Hegarty C, Reade MC, McQuilten Z. Duration of platelet storage and outcomes of critically ill patients. Transfusion. 2017 Mar;57(3):599-60


Rawlinson WD, Boppana SB, Fowler KB, Kimberlin DW, Lazzarotto T, Alain S, Daly K, Doutré S, Gibson L, Giles ML, Greenlee J, Hamilton ST, Harrison GJ, Hui L, Jones CA, Palasanthiran P, Schleiss MR, Shand AW, van Zuylen WJ. Congenital cytomegalovirus infection in pregnancy and the neonate: consensus recommendations for prevention, diagnosis, and therapy. Lancet Infectious Diseases. 2017 Mar 10.

Kerr PJ, Cattadori IM, Rogers MB, Fitch A, Geber A, Liu J, Sim DG, Boag B, Eden JS, Ghedin E, Read AF, Holmes EC. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. PLoS Pathogens. 2017 Mar 2;13(3):e1006252.


Kamruzzaman M, Shoma S, Thomas CM, Partridge SR, Iredell JR. Plasmid interference for curing antibiotic resistance plasmids in vivo. PLoS One. 2017 Feb 28;12(2):e0172913.


Luu LD, Octavia S, Zhong L, Raftery M, Sintchenko V, Lan R. Characterisation of the Bordetella pertussis secretome under different media. Journal of Proteomics. 2017 Feb 24. pii: S1874-3919(17)30059-3.


Ginn AN, Hazelton B, Shoma S, Cullen M, Solano T, Iredell JR. Quantitative multiplexed-tandem PCR for direct detection of bacteraemia in critically ill patients. Pathology. 2017 Feb 23. pii: S0031-3025(16)40346-6.


Chen LJ, Lin XD, Tian JH, Liao Y, Ying XH, Shao JW, Yu B, Guo JJ, Wang MR, Peng Y, Shi M, Holmes EC, Yang ZQ, Zhang YZ. Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China. Virology. 2017 Feb 18;505:33-41.


Stewardson AJ, Stuart RL, Cheng AC, Johnson PD. Mycobacterium chimaera and cardiac surgery. Medical Journal of Australia. 2017 Feb 20;206(3):132-135.


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. Changing epidemiology of candidaemia in Australia. Journal of Antimicrobial Chemotherapy. 2017 Feb 13. doi: 10.1093/jac/dkx047.


Kong Q, Xiaoft M, Kong F, Yuen M, Brown M, Ng J, Ahuja V, Hicks L, Shen L, Xu H, Sintchenko V, Gilbert GL, James G. Assignment of recA reference sequence types for enhanced identification of the Burkholderia cepacia complex. Pathology. 2012 Jun;44(4):373-375.


Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathogens. 2017 Feb 8;13(2):e1006215.


Williamson DA, Baines SL, Carter GP, da Silva AG, Ren X, Sherwood J, Dufour M, Schultz MB, French NP, Seemann T, Stinear TP, Howden BP. Genomic insights into a sustained national outbreak of Yersinia pseudotuberculosis. Genome Biology and Evolution. 2016 Dec 1;8(12):3806-3814.


Monk IR, Howden BP, Seemann T, Stinear TP. Correspondence: Spontaneous secondary mutations confound analysis of the essential two-component system WalKR in Staphylococcus aureus. Nature Communications. 2017 Feb 6;8:14403.


Li-Kim-Moy J, Yin JK, Blyth CC, Kesson A, Booy R, Cheng AC, Macartney K. Influenza hospitalizations in Australian children. Epidemiology and Infection. 2017 Feb 6:1-10.


Buultjens AH, Lam MM, Ballard S, Monk IR, Mahony AA, Grabsch EA, Grayson ML, Pang S, Coombs GW, Robinson JO, Seemann T, Johnson PD, Howden BP, Stinear TP. Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium. PeerJ. 2017 Jan 24;5:e2916.


Di Giallonardo F, Schlub TE, Shi M, Holmes EC. Dinucleotide composition in animal RNA viruses is shaped more by virus family than host species. Journal of Virology. 2017 Feb 1. pii: JVI.02381-16.


Lev S, Kaufman-Francis K, Desmarini D, Juillard PG, Li C, Stifter SA, Feng CG, Sorrell TC, Grau GE, Bahn YS, Djordjevic JT. Pho4 Is essential for dissemination of Cryptococcus neoformans to the host brain by promoting phosphate uptake and growth at alkaline pH. mSphere. 2017 Jan 25;2(1). pii: e00381-16.


Bjerregaard A, Laing IA, Poulsen N, Backer V, Sverrild A, Fally M, Khoo SK, Barrett L, Baltic S, Thompson PJ, Chidlow G, Sikazwe C, Smith DW, Bochkov YA, Le Souëf P, Porsbjerg C. Characteristics associated with clinical severity and inflammatory phenotype of naturally occurring virus-induced exacerbations of asthma in adults. Respiratory Medicine. 2017 Feb;123:34-41.

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. The case for adopting the "species complex" nomenclature for the etiologic agents of Cryptococcosis. mSphere. 2017 Jan 11;2(1). pii: e00357-16.


Beardmore RE, Pena-Miller R, Gori F, Iredell J. Antibiotic cycling and antibiotic mixing: which one best mitigates antibiotic resistance? Molecular Biology and Evolution. 2017 Jan 17. pii: msw292.

Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S. Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. Journal of Virology. 2017 Jan 11. pii: JVI.01953-16.


Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS. A molecular portrait of maternal sepsis from Byzantine Troy. Elife. 2017 Jan 10;6. pii: e20983.


Williamson DA, Baines SL, Carter G, Gonçalves da Silva A, Ren X, Sherwood J, Dufour M, Schultz MB, French NP, Seemann T, Stinear TP, Howden BP. Genomic insights into a sustained national outbreak of Yersinia pseudotuberculosis. Genome Biology Evolution. 2017 Jan 9. pii: evw285.


Gibney KB, Cheng AC, Hall R, Leder K. Australia's National Notifiable Diseases Surveillance System 1991-2011: expanding, adapting and improving. Epidemiology and Infection. 2017 Jan 9:1-12.


Aubron C, Flint AW, Bailey M, Pilcher D, Cheng AC, Hegarty C, Martinelli A, Reade MC, Bellomo R, McQuilten Z. Is platelet transfusion associated with hospital-acquired infections in critically ill patients? Critical Care. 2017 Jan 6;21(1):2.

Denning DW, Perlin DS, Muldoon EG, Colombo AL, Chakrabarti A, Richardson MD, Sorrell TC. Delivering on antimicrobial resistance agenda not possible without improving fungal diagnostic capabilities. Emerging Infectious Diseases. 2017 Feb 15;23(2).