2018 Publications

Selected publications of CREID investigators

Arnott A, Wang Q, Bachmann N, Sadsad R, Biswas C, Sotomayor C, Howard P, Rockett R, Wiklendt A, Iredell JRSintchenko V. 2018. Multidrug-resistant Salmonella enterica 4,[5],12: I:- sequence type 34, New South Wales, Australia, 2016-2017. Emerging Infectious Diseases 24:751-753

Barr IG, Cheng AC. 2018. Difficulties of predicting the timing, size and severity of influenza seasons. Respirology 23:562-563.

Basile K, Kok J, Dwyer DE. 2018. Point-of-care diagnostics for respiratory viral infections. Expert Review of Molecular Diagnostics 18:75-83

Beardsley J, Halliday CL, Chen SC, Sorrell TC. 2018. Responding to the emergence of antifungal drug resistance: perspectives from the bench and the bedside. Future Microbiol 13:1175-1191

Bhuiyan MU, Snelling TL, West R, Lang J, Rahman T, Granland C, De Gier C, Borland ML, Thornton RB, Kirkham LAS, Sikazwe C, Martin AC, Richmond PC, Smith DW, Jaffe A, Blyth CC.2018. The contribution of viruses and bacteria to community-acquired pneumonia in vaccinated children: A case - Control study. Thorax doi:10.1136/thoraxjnl-2018-212096

Britton PN, Jones CA, Macartney K, Cheng AC. 2018. Parechovirus: An important emerging infection in young infants. Medical Journal of Australia 208:365-369

Britton PN, Khandaker G, Khatami A, Teutsch S, Francis S, McMullan BJ, Jones CA. 2018. High prevalence of developmental concern amongst infants at 12 months following hospitalised parechovirus infection. Journal of Paediatrics and Child Health 54:289-295.


Byrne AL, Fox GJ, Marais BJ. 2018. Better than a pound of cure: Preventing the development of multidrug-resistant tuberculosis. Future Microbiology 13:577-588

Carter GP, Ussher JE, Da Silva AG, Baines SL, Heffernan H, Riley TV, Broadbent R, Van Der Linden A, Lee J, Monk IR, Stinear TP, Howden BP, Williamson DA. 2018. Genomic analysis of multiresistant staphylococcus capitis associated with neonatal sepsis. Antimicrobial Agents and Chemotherapy 62

Chawla K, Martinez E, Kumar A, Shenoy VP, Sintchenko V. 2018. Whole-genome sequencing reveals genetic signature of bedaquiline resistance in a clinical isolate of Mycobacterium tuberculosis. Journal of Global Antimicrobial Resistance 15:103-104

Cheng AC, Subbarao K. 2018. Epidemiological data on the effectiveness of influenza vaccine - Another piece of the puzzle. Journal of Infectious Diseases 218:176-178

Coiera E. 2018. The fate of medicine in the time of AI. The Lancet 392:2331-2332

Degeling C, Brookes V, Lea T, Ward M. 2018. Rabies response, One Health and more-than-human considerations in indigenous communities in northern Australia. Social Science and Medicine 212:60-67

Degeling CGilbert GL, Annand E, Taylor M, Walsh MG, Ward MP, Wilson A, Johnson J. 2018. Managing the risk of Hendra virus spillover in Australia using ecological approaches: A report on three community juries. PLoS ONE 13

Degeling CJohnson JIredell J, Nguyen KA, Norris JM, Turnidge JD, Dawson A, Carter SM, Gilbert GL. 2018. Assessing the public acceptability of proposed policy interventions to reduce the misuse of antibiotics in Australia: A report on two community juries. Health Expectations 21:90-99

Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DEHolmes ECEden JS. 2018. Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses 10:E476, doi: 10.3390/v10090476

Ford L, Carter GP, Wang Q, Seemann T, Sintchenko V, Glass K, Williamson DA, Howard P, Valcanis M, Castillo CFS, Sait M, Howden BP, Kirk MD. 2018. Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia. Foodborne Pathogens and Disease 15:161-167

Ford L, Wang Q, Stafford R, Ressler KA, Norton S, Shadbolt C, Hope K, Franklin N, Krsteski R, Carswell A, Carter GP, Seemann T, Howard P, Valcanis M, Castillo CFS, Bates J, Glass K, Williamson DA, Sintchenko VHowden BPKirk MD. 2018. Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing. Foodborne Pathogens and Disease 15:285-292.


Geoghegan JL, Holmes EC. 2018. The phylogenomics of evolving virus virulence. Nature Reviews Genetics 19:756-769.

Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC. 2018. Continental synchronicity of human influenza virus epidemics despite climactic variation. PLoS Pathogens 14:e1006780

Giles ML, Krishnaswamy S, Macartney K, Cheng A. 2018. The safety of inactivated influenza vaccines in pregnancy for birth outcomes: a systematic review. Human Vaccines and Immunotherapeutics doi:10.1080/21645515.2018.1540807

Giulieri SG, Baines SL, Guerillot R, Seemann T, Gonçalves da Silva A, Schultz M, Massey RC, Holmes NE, Stinear TP, Howden BP. 2018. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Medicine 10

Guérillot R, da Silva AG, Monk I, Giulieri S, Tomita T, Alison E, Porter J, Pidot S, Gao W, Peleg AY, Seemann T, Stinear TP, Howden BP. 2018. Convergent evolution driven by rifampin exacerbates the global burden of drug-resistant Staphylococcus aureus. mSphere 3:e00550-00517

Harapan H, Rajamoorthy Y, Anwar S, Bustamam A, Radiansyah A, Angraini P, Fasli R, Salwiyadi S, Bastian RA, Oktiviyari A, Akmal I, Iqbalamin M, Adil J, Henrizal F, Darmayanti D, Pratama R, Setiawan AM, Mudatsir M, Hadisoemarto PF, Dhimal ML, Kuch U, Groneberg DA, Imrie A, Dhimal M, Müller R. 2018. Knowledge, attitude, and practice regarding dengue virus infection among inhabitants of Aceh, Indonesia: A cross-sectional study. BMC Infectious Diseases 18

Harapan H, Mudatsir M, Yufika A, Nawawi Y, Wahyuniati N, Anwar S, Yusri F, Haryanti N, Wijayanti NP, Rizal R, Fitriani D, Maulida NF, Syahriza M, Ikram I, Fandoko TP, Syahadah M, Asrizal FW, Jamil KF, Rajamoorthy Y, Wagner AL, Groneberg DA, Kuch U, Müller R, Sasmono RT, Imrie A. 2018. Willingness to Participate and Associated Factors in a Zika Vaccine Trial in Indonesia: A Cross-Sectional Study. Viruses 10

Holmes EC, Rambaut A, Andersen KG. 2018. Pandemics: Spend on surveillance, not prediction comment. Nature 558:180-182

Imrie A. 2018. Dengue introduced by Travellers, Australia. Microbiology Australia 39:67-71

Jenkins A, Capon A, Negin J, Marais B, Sorrell T, Parkes M, Horwitz P. 2018. Watersheds in planetary health research and action. The Lancet Planetary Health 2:e510-e511

Kiely P, Wood EM, Cheng AC. 2018. Emerging infectious disease agents and blood safety in Australia: Spotlight on zika virus. Medical Journal of Australia 208:96

Kwong JC, Chow EPF, Stevens K, Stinear TP, Seemann T, Fairley CK, Chen MY, Howden BP. 2018. Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: An observational study. Sexually Transmitted Infections 94:151-157

Kwong JC, Lane CR, Romanes F, da Silva AG, Easton M, Cronin K, Waters MJ, Tomita T, Stevens K, Schultz MB, Baines SL, Sherry NL, Carter GP, Mu A, Sait M, Ballard SA, Seemann T, Stinear TP, Howden BP. 2018. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: Evidence from a complex multi-institutional KPC outbreak. PeerJ 2018:e4210

Lee JYH, Monk IR, Gonçalves da Silva A, Seemann T, Chua KYL, Kearns A, Hill R, Woodford N, Bartels MD, Strommenger B, Laurent F, Dodémont M, Deplano A, Patel R, Larsen AR, Korman TM, Stinear TP, Howden BP. 2018. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nature Microbiology 3:1175-1185

Lee RS, Gonçalves Da Silva A, Baines SL, Strachan J, Ballard S, Carter GP, Kwong JC, Schultz MB, Bulach DM, Seemann T, Stinear TP, Howden BP. 2018. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: A population-level genomic study. Journal of Antimicrobial Chemotherapy 73:3268-3278

Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P. 2018. Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses. Infection, Genetics and Evolution 58:279-289

Lilly DG, Dang K, Webb CE, Doggett SL. 2018. Are Australian field-collected strains of Cimex lectularius and Cimex hemipterus (Hemiptera: Cimicidae) resistant to deltamethrin and imidacloprid as revealed by topical assay? Austral Entomology 57:77-84

Loveday M, Sunkari B, Master I, Daftary A, Mehlomakulu V, Hlangu S, Marais BJ. 2018. Household context and psychosocial impact of childhood multidrug-resistant tuberculosis in KwaZulu-Natal, South Africa. International Journal of Tuberculosis and Lung Disease 22:40-46

Luang-Suarkia D, Mitja O, Ernst T, Bennett S, Tay A, Hays R, Smith DW, Imrie A. 2018. Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010. PLoS Neglected Tropical Diseases 12

Mai TQ, Martinez E, Menon R, Van Anh NT, Hien NT, Marais BJSintchenko V. 2018. Mycobacterium tuberculosis drug resistance and transmission among human immunodeficiency virus–infected patients in Ho Chi Minh City, Vietnam. American Journal of Tropical Medicine and Hygiene 99:1397-1406

Mak DB, Regan AK, Vo DT, Effler PV. 2018. Antenatal influenza and pertussis vaccination in Western Australia: A cross-sectional survey of vaccine uptake and influencing factors. BMC Pregnancy and Childbirth 18

Marais BJ. 2018. Preventing tuberculosis in household contacts crucial to protect children and contain epidemic spread. The Lancet Global Health 6:e1260-e1261

Marais BJ, Buddle BM, de Klerk-Lorist LM, Nguipdop-Djomo P, Quinn F, Greenblatt C. 2018. BCG vaccination for bovine tuberculosis; conclusions from the Jerusalem One Health workshop. Transboundary and Emerging Diseases doi:10.1111/tbed.13089

Martinez E, Hennessy D, Jelfs P, Crighton T, Chen SCA, Sintchenko V. 2018. Mutations associated with in vitro resistance to bedaquiline in Mycobacterium tuberculosis isolates in Australia. Tuberculosis 111:31-34

Moore HC, Fathima P, Gidding HF, de Klerk N, Liu B, Sheppeard V, Effler PV, Snelling TL, McIntyre P, Blyth CC, on behalf of the ALIG. 2018. Assessment of on-time vaccination coverage in population subgroups: A record linkage cohort study. Vaccine 36:4062-4069

Mor SM, Norris JM, Bosward KL, Toribio JALML, Ward MP, Gongora J, Vost M, Higgins PC, McGreevy PD, White PJ, Zaki S. 2018. One health in our backyard: Design and evaluation of an experiential learning experience for veterinary medical students. One Health 5:57-64

Parisi A, Crump JA, Glass K, Howden BP, Furuya-Kanamori L, Vilkins S, Gray DJ, Kirk MD. 2018. Health Outcomes from Multidrug-Resistant Salmonella Infections in High-Income Countries: A Systematic Review and Meta-Analysis. Foodborne Pathogens and Disease 15:428-436

Parvaresh L, Bag SK, Cho JG, Heron N, Assareh H, Norton S, Corbett S, Marais BJ. 2018. Monitoring tuberculosis contact tracing outcomes in Western Sydney, Australia. BMJ Open Respiratory Research 5

Parvaresh L, Crighton T, Martinez E, Bustamante A, Chen S, Sintchenko V. 2018. Recurrence of tuberculosis in a low-incidence setting: A retrospective cross-sectional study augmented by whole genome sequencing. BMC Infectious Diseases 18

Pinto AN, Hawke K, Castley A, Chibo D, Giallonardo FD, Cooper C, Sawleshwarkar S, Kelleher A, Dwyer DE. 2018. HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia. Future Virology 13:575-584

Rockett RJ, Oftadeh S, Bachmann NL, Timms VJ, Kong F, Gilbert GLSintchenko V. 2018. Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia. Scientific Reports 8

Rowe SL, Stephens N, Cowie BC, Nolan T, Leder K, Cheng AC. 2018. Use of data linkage to improve communicable disease surveillance and control in Australia: existing practices, barriers and enablers. Australian and New Zealand Journal of Public Health doi:10.1111/1753-6405.12846

Sellens E, Norris JM, Dhand NK, Heller J, Hayes L, Gidding HF, Willaby H, Wood N, Bosward KL. 2018. Willingness of veterinarians in Australia to recommend Q fever vaccination in veterinary personnel: Implications for workplace health and safety compliance. PLoS ONE 13

Shetty A, Macdonald SPJ, Keijzers G, Williams JM, Tang B, de Groot B, Thompson K, Fraser JF, Finfer S, Bellomo R, Iredell J. 2018. Review article: Sepsis in the emergency department – Part 2: Investigations and monitoring. EMA - Emergency Medicine Australasia 30:4-12.

Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ. 2018. The evolutionary history of vertebrate RNA viruses. Nature 556:197-202

Shi M, Zhang YZ, Holmes EC. 2018. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Research 243:83-90.

Smith DW. 2018. Endemic Australian arboviruses of human health significance. Microbiology Australia 39:88-90

Smith-Vaughan HC, Binks MJ, Beissbarth J, Chang AB, McCallum GB, Mackay IM, Morris PS, Marsh RL, Torzillo PJ, Wurzel DF, Grimwood K, Nosworthy E, Gaydon JE, Leach AJ, MacHunter B, Chatfield MD, Sloots TP, Cheng AC. 2018. Bacteria and viruses in the nasopharynx immediately prior to onset of acute lower respiratory infections in Indigenous Australian children. European Journal of Clinical Microbiology and Infectious Diseases 37:1785-1794

Somerville LK, Basile K, Dwyer DE, Kok J. 2018. The impact of influenza virus infection in pregnancy. Future Microbiology 13:263-274.

Sotomayor C, Wang Q, Arnott A, Howard P, Hope K, Lan R, Sintchenko V. 2018. Novel salmonella enterica serovar typhimurium genotype levels as herald of seasonal salmonellosis epidemics. Emerging Infectious Diseases 24:1079-1082

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 SCA. 2018. Surveillance for azole resistance in clinical and environmental isolates of Aspergillus fumigatus in Australia and cyp51A homology modelling of azole-resistant isolates. Journal of Antimicrobial Chemotherapy 73:2347-2351

Thapa K, Ellem JA, Basile K, Carter I, Olma T, Chen SCA, Dwyer DE, Kok J. 2018. Simultaneous co-detection of wild-type and vaccine strain measles virus using the BD MAX system. Pathology 50:450-454

Timms VJ, Nguyen T, Crighton T, Yuen M, Sintchenko V. 2018. Genome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains 11 Medical and Health Sciences 1108 Medical Microbiology. BMC Genomics 19

Timms VJRockett R, Bachmann NL, Martinez E, Wang Q, Chen SCA, Jeoffreys N, Howard PJ, Smith A, Adamson S, Gilmour R, Sheppeard V, Sintchenko V. 2018. Genome sequencing links persistent outbreak of legionellosis in Sydney (New South Wales, Australia) to an emerging clone of Legionella pneumophila sequence type 211. Applied and Environmental Microbiology 84

van Hal SJ, Beukers AG, Timms VJ, Ellem JA, Taylor P, Maley MW, Newton PJ, Ferguson JK, Lee A, Chen SC, Sintchenko V. 2018. Relentless spread and adaptation of non-typeable vanA vancomycin resistant Enterococcus faecium: A genome-wide investigation. Journal of Antimicrobial Chemotherapy 73:1487-1491

Varrone L, Stafford RJ, Lilly K, Selvey L, Glass K, Ford L, Bulach D, Kirk MD. 2018. Investigating locally relevant risk factors for Campylobacter infection in Australia: Protocol for a case-control study and genomic analysis. BMJ Open 8

Walsh MG, Webb C. 2018. Hydrological features and the ecological niches of mammalian hosts delineate elevated risk for Ross River virus epidemics in anthropogenic landscapes in Australia. Parasites and Vectors 11

Williamson DA, Lane CR, Easton M, Valcanis M, Strachan J, Veitch MG, Kirk MDHowden BP. 2018. Increasing antimicrobial resistance in nontyphoidal salmonella isolates in Australia from 1979 to 2015. Antimicrobial Agents and Chemotherapy 62:e02012-02017

Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. 2018. Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds. Molecular Ecology doi:10.1111/mec.14918

Worthing KA, Abraham S, Coombs GW, Pang S, Saputra S, Jordan D, Trott DJ, Norris JM. 2018. Clonal diversity and geographic distribution of methicillin-resistant Staphylococcus pseudintermedius from Australian animals: Discovery of novel sequence types. Veterinary Microbiology 213:58-65

Worthing KA, Brown J, Gerber L, Trott DJ, Abraham S, Norris JM. 2018. Methicillin-resistant staphylococci amongst veterinary personnel, personnel-owned pets, patients and the hospital environment of two small animal veterinary hospitals. Veterinary Microbiology 223:79-85

Zhang YZ, Shi M, Holmes EC. 2018. Using Metagenomics to Characterize an Expanding Virosphere. Cell 172:1168-1172

Zhang YZ, Wu WC, Shi M, Holmes EC. 2018. The diversity, evolution and origins of vertebrate RNA viruses. Current Opinion in Virology 31:9-16

Zhuo A, Labbate M, Norris JMGilbert 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. 2018. 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. BMJ Open 8: e020439