2016 Publications

Selected publications of CREID investigators

Fu S, Octavia S, Wang Q, Tanaka MM, Tay CY, Sintchenko V, Lan R. Evolution of variable number tandem repeats and Its relationship with genomic diversity in Salmonella typhimurium. Frontiers in Microbiology. 2016 Dec 26;7:2002.


Cheng AC, Holmes M, Dwyer DE, Irving LB, Korman TM, Senenayake S, Macartney KK, Blyth CC, Brown S, Waterer G, Hewer R, Friedman ND, Wark PA, Simpson G, Upham J, Bowler SD, Lessing A, Kotsimbos T, Kelly PM. Influenza epidemiology in patients admitted to sentinel Australian hospitals in 2015: the Influenza Complications Alert Network. Communicable Diseases Intelligence Quarterly Report. 2016 Dec 24;40(4):E521-E526.


Dalton CB, Carlson SJ, Durrheim DN, Butler MT, Cheng AC, Kelly HA. Flutracking weekly online community survey of influenza-like illness annual report, 2015. Communicable Diseases Intelligence Quarterly Report. 2016 Dec 24;40(4):E512-E520.


Martin NV, Ong KS, Howden BP, Lahra MM, Lambert SB, Beard FH, Dowse GK, Saul N; Communicable Diseases Network Australia MenW Working Group. Rise in invasive serogroup W meningococcal disease in Australia 2013-2015. Communicable Diseases Intelligence Quarterly Report. 2016 Dec 24;40(4):E454-E459.


Coiera E, Magrabi F, Talmon J. Engineering technology resilience through informatics safety science. Journal of the American Medical Informatics Association. 2016 Dec 31. pii: ocw162.


Kim MO, Coiera E, Magrabi F. Problems with health information technology and their effects on care delivery and patient outcomes: a systematic review. Journal of the American Medical Informatics Association. 2016 Dec 23.


Kwong JC, Schultz MB, Williamson DA, Stinear TP, Seemann T, Howden BP. Comment on: Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. Journal of Antimicrobial Chemotherapy. 2016 Dec 20.


Chow EP, Howden BP, Walker S, Lee D, Bradshaw CS, Chen MY, Snow A, Cook S, Fehler G, Fairley CK. Antiseptic mouthwash against pharyngeal Neisseria gonorrhoeae: a randomised controlled trial and an in vitro study. Sexually Transmitted Infections. 2016 Dec 20.


Gilbert GL. Australia's response to Ebola Virus disease in West Africa, 2014-15. Public Health Research and Practice. 2016 Dec 14;26(5).


Hill-Cawthorne GA, Sorrell TC. Future directions for public health research in emerging infectious diseases. Public Health Research and Practice. 2016 Dec 14;26(5).


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).


Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H. Large-scale phylogenomic analysis reveals the complex evolutionary history of rabies virus in multiple carnivore hosts. PLoS Pathogens. 2016 Dec 15;12(12):e1006041.


Duggan AT, Perdomo MF, Piombino-Mascali D, Marciniak S, Poinar D, Emery MV, Buchmann JP, Duchêne S, Jankauskas R, Humphreys M, Golding GB, Southon J, Devault A, Rouillard JM, Sahl JW, Dutour O, Hedman K, Sajantila A, Smith GL, Holmes EC, Poinar HN. 17th century variola virus reveals the recent history of smallpox. Current Biology. 2016 Dec 5. pii: S0960-9822(16)31324-0.


Guo WP, Tian JH, Lin XD, Ni XB, Chen XP, Liao Y, Yang SY, Dumler JS, Holmes EC, Zhang YZ. Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species. Scientific Reports. 2016 Dec 9;6:38770.


Alsahafi AJ, Cheng AC. Knowledge, attitudes and behaviours of healthcare workers in the Kingdom of Saudi Arabia to MERS coronavirus and other emerging infectious diseases. International Journal of Environmental Research and Public Health. 2016 Dec 6;13(12).


Kanhutu K, Jones P, Cheng AC, Grannell L, Best E, Spelman D.Spleen Australia guidelines for the prevention of sepsis in patients with asplenia and hyposplenism in Australia and New Zealand. Internal Medicine Journal. 2016 Dec 7. doi: 10.1111/imj.13348. Review.


Marais BJ, Sintchenko V. Epidemic spread of multidrug-resistant tuberculosis in China. Lancet Infectious Diseases. 2016 Dec 2. pii: S1473-3099(16)30526-6.


Hor SY, Hooker C, Iedema R, Wyer M, Gilbert GL, Jorm C, O'Sullivan MV. Beyond hand hygiene: a qualitative study of the everyday work of preventing cross-contamination on hospital wards. BMJ Quality & Safety. 2016 Nov 30.


Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden M, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing (WGS) in antimicrobial susceptibility testing of bacteria: report from the EUCAST subcommittee. Clinical Microbiology and Infection. 2016 Nov 23. pii: S1198-743X(16)30568-7. Review.


Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ. Redefining the invertebrate RNA virosphere. Nature. 2016 Nov 23.


Liu W, Pickering P, Duchêne S, Holmes EC, Aaskov JG. Highly divergent dengue virus type 2 in traveler returning from Borneo to Australia. Emerging Infectious Diseases. 2016 Dec;22(12):2146-2148.


Goff DA, Kullar R, Goldstein EJ, Gilchrist M, Nathwani D, Cheng AC, Cairns KA, Escandón-Vargas K, Villegas MV, Brink A, van den Bergh D, Mendelson M. A global call from five countries to collaborate in antibiotic stewardship: united we succeed, divided we might fail. Lancet Infectious Diseases. 2016 Nov 17. pii: S1473-3099(16)30386-3. Review.


Gurjav U, Erkhembayar B, Burneebaatar B, Narmandakh E, Tumenbayar O, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Transmission of multi-drug resistant tuberculosis in Mongolia is driven by Beijing strains of Mycobacterium tuberculosis resistant to all first-line drugs. Tuberculosis. 2016 Dec;101:49-53.


Coiera E, Ash J, Berg M. The unintended consequences of health information technology revisited. Yearbook of Medical Informatics. 2016 Nov 10;(1):163-169.


Smithers-Sheedy H, Raynes-Greenow C, Badawi N, Fernandez MA, Kesson A, McIntyre S, Leung KC, Jones CA. Congenital cytomegalovirus among children with cerebral palsy. Journal of Pediatrics. 2016 Nov 3. pii: S0022-3476(16)31092-7.

Urbanowicz RA, McClure CP, Sakuntabhai A, Sall AA, Kobinger G, Müller MA, Holmes EC, Rey FA, Simon-Loriere E, Ball JK. Human Adaptation of Ebola Virus during the West African Outbreak. Cell. 2016 Nov 3;167(4):1079-1087.e5.


Gibney KB, Cheng AC, Hall R, Leder K. Sociodemographic and geographical inequalities in notifiable infectious diseases in Australia: a retrospective analysis of 21 years of national disease surveillance data. The Lancet Infectious Diseases. 2016 Oct 24. pii: S1473-3099(16)30309-7.


Tai AY, Easton M, Encena J, Rotty J, Valcanis M, Howden BP, Slota-Kan S, Gregory J. A review of the public health management of shigellosis in Australia in the era of culture-independent diagnostic testing. The Australian and New Zealand Journal of Public Health. 2016 Oct 23.


Aminnejad M, Cogliati M, Duan S, Arabatzis M, Tintelnot K, Castañeda E, Lazéra M, Velegraki A, Ellis D, Sorrell TC, Meyer W. 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. PLoS One. 2016 Oct 20;11(10):e0163955.


Subedi S, Kong F, Jelfs P, Gray TJ, Xiao M, Sintchenko V, Chen SC. 16S-23S internal transcribed spacer region PCR and sequencer-based capillary gel electrophoresis has potential as an alternative to high performance liquid chromatography for identification of slowly growing nontuberculous Mycobacteria. PLoS One. 2016 Oct 17;11(10):e0164138.


Gurjav U, Outhred AC, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Whole genome sequencing demonstrates limited transmission within identified Mycobacterium tuberculosis clusters in New South Wales, Australia. PLoS One. 2016 Oct 13;11(10): e0163612.


Holmes EC, Dudas G, Rambaut A, Andersen KG. The evolution of Ebola virus: Insights from the 2013-2016 epidemic. Nature. 2016 Oct 12;538(7624):193-200.


Moss R, McCaw JM, Cheng AC, Hurt AC, McVernon J. Reducing disease burden in an influenza pandemic by targeted delivery of neuraminidase inhibitors: mathematical models in the Australian context. BMC Infectious Diseases. 2016 Oct 10;16(1):552.


Holmes EC. The Expanding Virosphere. Cell Host & Microbe. 2016 Sep 14;20(3):279-80.


Phillips A, Sotomayor C, Wang Q, Holmes N, Furlong C, Ward K, Howard P, Octavia S, Lan R, Sintchenko V. Whole genome sequencing of Salmonella typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014. BMC Microbiology. 2016 Sep 15;16:211.


Giulieri SG, Holmes NE, Stinear TP, Howden BP. Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections. Expert Review of Anti-infective Therapy. 2016 Sep 14.


Abbadi M, Fusaro A, Ceolin C, Casarotto C, Quartesan R, Dalla Pozza M, Cattoli G, Toffan A, Holmes EC, Panzarin V. Molecular evolution and phylogeography of o-circulating IHNV and VHSV in Italy. Frontiers in Microbiology. 2016 Aug 23;7:1306.


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. Problematic dichotomisation of risk for ICU-acquired invasive candidiasis: results using a risk predictive model to categorise three levels of risk from a multicentre prospective cohort of Australian ICU patients. Clinical Infectious Diseases. 2016 Sep 6. pii: ciw610.


Gibney KB, Cheng AC, Hall R, Leder K. An overview of the epidemiology of notifiable infectious diseases in Australia, 1991-2011. Epidemiology and Infection. 2016 Jun 22:1-15.


Geoghegan JL, Senior AM, Holmes EC. Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proceedings of the Royal Society B: Biological Sciences. 2016 Aug 31;283(1837).


Gude WT, van der Veer SN, de Keizer NF, Coiera E, Peek N. Optimizing digital health informatics interventions through unobtrusive quantitative process evaluations. Studies in Health Technology and Informatics. 2016;228:594-8.


Kothur K, Wienholt L, Mohammad SS, Tantsis EM, Pillai S, Britton PN, Jones CA, Angiti RR, Barnes EH, Schlub T, Bandodkar S, Brilot F, Dale RC. Utility of CSF cytokine/chemokines as markers of active intrathecal inflammation: comparison of demyelinating, anti-NMDAR and enteroviral encephalitis. PLoS One. 2016 Aug 30;11(8):e0161656.


Surian D, Nguyen DQ, Kennedy G, Johnson M, Coiera E, Dunn AG. Characterizing Twitter discussions about HPV vaccines using topic modeling and community detection. Journal of Medical Internet Research. 2016 Aug 29;18(8):e232.


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. Antifungal susceptibilities of non-Aspergillus filamentous fungi causing invasive infection in Australia: support for current antifungal guideline recommendations. International Journal of Antimicrobial Agents. 2016 Aug 12. pii: S0924-8579(16)30199-6.


Carter GP, Buultjens AH, Ballard SA, Baines SL, Tomita T, Strachan J, Johnson PD, Ferguson JK, Seemann T, Stinear TP, Howden BP. Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium. Journal of Antimicrobial Chemotherapy. 2016 Aug 15. pii: dkw314.


Coombs GW, Daley DA, Thin Lee Y, Pearson JC, Robinson JO, Nimmo GR, Collignon P, Howden BP, Bell JM, Turnidge JD; Australian Group on Antimicrobial Resistance. Australian group on antimicrobial resistance Australian Staphylococcus aureus sepsis outcome programme annual report, 2014. Communicable Diseases Intelligence Q Rep. 2016 Jun 30;40(2):E244-54.


Coghlan B, Kelly HA, Carlson SJ, Grant KA, Leder K, Dalton CB, Cheng AC. Estimates of influenza vaccine coverage from Victorian surveillance systems based in the community, primary care and hospitals. Communicable Diseases Intelligence Q Rep. 2016 Jun 30;40(2):E204-6.


Rambaut A, Dudas G, de Carvalho LM, Park DJ, Yozwiak NL, Holmes EC, Andersen KG. Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences". Science. 2016 Aug 12;353(6300):658.


Dunn AG, Zhou X, Hudgins J, Arachi D, Mandl KD, Coiera E, Bourgeois FT. Financial competing interests were associated with favourable conclusions and greater author productivity in non-systematic reviews of neuraminidase inhibitors. Journal of Clinical Epidemiology. 2016 Jul 23.


Lim FJ, Wake ZV, Levy A, Tempone S, Moore HC, Richmond PC, de Klerk N, Conway NT, Keil AD, Effler PV, Smith DW, Blyth CC; WAIVE group. Viral etiology and the impact of codetection in young children presenting with influenza-like illness. The Journal of the Pediatric Infectious Diseases Society. 2016 Jul 20. pii: piw042.


Khandaker G, Jung J, Britton PN, King C, Yin JK, Jones CA. Long-term outcomes of infective encephalitis in children: a systematic review and meta-analysis. Developmental Medicine & Child Neurology. 2016 Jul 16. doi: 10.1111/dmcn.13197. Review.


Inglis TJ, Bradbury RS, McInnes RL, Frances SP, Merritt AJ, Levy A, Nicholson J, Neville PJ, Lindsay M, Smith DW. Deployable molecular detection of arboviruses in the Australian outback. The American Journal of Tropical Medicine and Hygiene. 2016 Jul 11. pii: 15-0878.


Kwong JC, Stafford R, Strain E, Stinear TP, Seemann T, Howden BP. Sharing is caring: international sharing of data enhances genomic surveillance of Listeria monocytogenes. Clinical Infectious Diseases. 2016 Jun 9. pii: ciw359.


Sikazwe CT, Chidlow GR, Imrie A, Smith DW. Reliable quantification of rhinovirus species C using real-time PCR. Journal of Virological Methods. 2016 May 20.


Lam TT, Zhu H, Guan Y, Holmes EC. Genomic analysis of the emergence, evolution, and spread of human respiratory RNA viruses. Annual Review of Genomics and Human Genetics. 2016 May 23.

Magrabi F, Ong MS, Coiera E. Health IT for patient safety and improving the safety of health IT. Studies in Health Technology and Informatics. 2016; 222: 25-36.


Read P, Tagg KA, Jeoffreys N, Guy RJ, Gilbert GL, Donovan B. Treponema pallidum strain-types and association with macrolide resistance in Sydney, Australia: New tp0548 types identified. Journal of Clinical Microbiology. 2016 May 18.


Kee PP, Chinnappan M, Nair A, Yeak D, Chen A, Starr M, Daley AJ, Cheng AC, Burgner D. Diagnostic yield of timing blood culture collection relative to fever. The Pediatric Infectious Disease Journal. 2016 May 9.

Li K, Lin XD, Huang KY, Zhang B, Shi M, Guo WP, Wang MR, Wang W, Xing JG, Li MH, Hong WS, Holmes EC, Zhang YZ. Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans. Virology. 2016 Apr 22; 494: 168-177.


Britton PN, Dale RC, Elliott E, Festa M, Macartney K, Booy R, Jones CA. Pilot surveillance for childhood encephalitis in Australia using the Paediatric Active Enhanced Disease Surveillance (PAEDS) network - CORRIGENDUM. Epidemiology and Infection. 2016 Apr 20:1.


Bond KA, Stevens K, Bulach D, Carville K, Ong KS, Howden BP. Rising incidence of invasive meningococcal disease caused by Neisseria meningitidis serogroup W in Victoria. Medical Journal of Australia. 2016 Apr 18; 204(7): 265-6.


Trauer JM, Cheng AC. Multidrug-resistant tuberculosis in Australia and our region. Medical Journal of Australia. 2016 Apr 18; 204(7): 251-3.


Jones CA, Davis JS, Looke DF. The ASID test. Medical Journal of Australia. 2016 Apr 18; 204(7): 250-1.


Shetty AL, Brown T, Booth T, Van KL, Dor-Shiffer DE, Vaghasiya MR, Eccleston CE, Iredell J. Systemic inflammatory response syndrome-based severe sepsis screening algorithms in emergency department patients with suspected sepsis. Emergency Medicine Australasia. 2016 Apr 12.


Trubiano JA, Cheng AC, Korman TM, Roder C, Campbell A, May ML, Blyth CC, Ferguson JK, Blackmore TK, Riley TV, Athan E. Australasian Society of Infectious  Diseases updated guidelines for the management of Clostridium difficile infection in adults and children in Australia and New Zealand. Internal Medicine Journal. 2016 Apr; 46(4): 479-93.


Trinh QM, Nguyen HL, Do TN, Nhung NV, Hoa NB, Nguyen TV, Sintchenko V, Marais BJ. Tuberculosis and HIV co-infection in Vietnam. International Journal of Infectious Diseases. 2016 Mar 29.


Li C, Lev S, Saiardi A, Desmarini D, Sorrell TC, Djordjevic JT. Identification of a major IP5 kinase in Cryptococcus neoformans confirms that PP-IP5/IP7, not IP6, is essential for virulence. Scientific Reports. 2016 Apr 1; 6: 23927.


Tong SY, Nelson J, Paterson DL, Fowler VG Jr, Howden BP, Cheng AC, Chatfield M, Lipman J, Van Hal S, O'Sullivan M, Robinson JO, Yahav D, Lye D, Davis JS; CAMERA2 study group and the Australasian Society for Infectious Diseases Clinical Research Network. CAMERA2 - combination antibiotic therapy for methicillin-resistant Staphylococcus aureus infection: study protocol for a randomised controlled trial. Trials. 2016 Mar 31; 17(1): 170.


Cheng AC, Collins DA, Elliott B, Ferguson JK, Paterson DL, Thean S, Riley TV. Laboratory-based surveillance of Clostridium difficile circulating in Australia, September - November 2010. Pathology. 2016 Apr; 48(3): 257-60.


Dickeson DJ, Chen SC, Sintchenko VG. Concordance of four commercial enzyme immunoassay and three immunoblot formats for the detection of Lyme borreliosis antibodies in human serum: the two-tier approach remains. Pathology. 2016 Apr; 48(3): 251-6.


Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC. Virological factors that increase the transmissibility of emerging human viruses. Proceedings of the National Academy of Sciences USA. 2016 Mar 21.