Publications

Publications

Complete list can be found on google scholar

Recent publications:

2021

Rapid discovery of novel prophages using biological feature engineering and  machine learning.  Kimmo Sirén, Andrew Millard, Bent Petersen, M Thomas P Gilbert, Martha R J Clokie, Thomas Sicheritz-Pontén
NAR Genomics and Bioinformatics, Volume 3, Issue 1, March 2021, lqaa109, https://doi.org/10.1093/nargab/lqaa109

 

2020

Complete genome sequence of a novel lytic phage infecting Aeromonas hydrophila, an infectious agent in striped catfish (Pangasianodon hypophthalmus)
VQ Tu, TT Nguyen, XTT Tran, AD Millard, HT Phan, NP Le, OTH Dang, …
Archives of Virology 165 (12), 2973-2977 2020

Use of bacteriophage vB_Pd_PDCC‐1 as biological control agent of Photobacterium damselae subsp. damselae during hatching of longfin yellowtail (Seriola rivoliana) eggs
B Veyrand‐Quirós, B Gómez‐Gil, CO Lomeli‐Ortega, …
Journal of Applied Microbiology 129 (6), 1497-1510 2020

Isolation and characterization of vibriophage vB_Vc_SrVc9: an effective agent in preventing Vibrio campbellii infections in brine shrimp nauplii (Artemia franciscana)
CO Lomelí‐Ortega, A de Jesús Martínez‐Sández, DR Barajas‐Sandoval, …
Journal of Applied Microbiology 2020

From Orphan Phage to a Proposed New Family–the Diversity of N4-Like Viruses
J Wittmann, D Turner, AD Millard, P Mahadevan, AM Kropinski, …
Antibiotics 9 (10), 663 1 2020

Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii
U Leungtongkam, R Thummeepak, T Kitti, K Tasanapak, J Wongwigkarn, …
Scientific Reports 10 (1), 1-11 2020

Insight into Molecular Epidemiology, Antimicrobial Resistance, and Virulence Genes of Extensively Drug-Resistant Acinetobacter baumannii in Thailand
P Kongthai, R Thummeepak, U Leungtongkam, R Pooarlai, T Kitti, …
Microbial Drug Resistance 2020

A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer
S Arya, H Todman, M Baker, S Hooton, A Millard, JU Kreft, JL Hobman, …
FEMS Microbiology Ecology 2 2020

Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages
R Zamudio, RD Haigh, JD Ralph, M De Ste Croix, T Tasara, K Zurfluh, …
Environmental Microbiology 1 2020
Investigating Bacteriophages Targeting the Opportunistic Pathogen Acinetobacter baumannii
KM Styles, R Thummeepak, U Leungtongkam, SE Smith, GS Christie, …
Antibiotics 9 (4), 200 3 2020

Genome Sequence and Characterization of Coliphage vB_Eco_SLUR29
I Besler, P Sazinas, C Harrison, L Gannon, T Redgwell, S Michniewski, …
PHAGE 1 (1), 38-44 2 2020
Bacteriophage Introductions
A Millard
PHAGE 1 (1), 37-37 2020
C

omparison of CRISPR and Marker-Based Methods for the Engineering of Phage T7
AM Grigonyte, C Harrison, PR MacDonald, A Montero-Blay, M Tridgett, …
Viruses 12 (2), 193 1 2020

Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii
L Udomluk, T Rapee, K Thawatchai, T Kannipa, W Jintana, KM Styles, …
Scientific Reports (Nature Publisher Group) 10 (1) 2020

Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria
MEK Haines, FE Hodges, JY Nale, J Mahony, D van Sinderen, …
bioRxiv 2020

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
R Cook, S Hooton, U Trivedi, L King, C Dodd, J Hobman, DJ Stekel, …
bioRxiv 2020

Rapid discovery of novel prophages using biological feature engineering and machine learning
K Sirén, A Millard, B Petersen, MTP Gilbert, MRJ Clokie, …
bioRxiv 2020

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses
VV Babenko, A Millard, EE Kulikov, NN Spasskaya, MA Letarova, …
Computational and structural biotechnology journal 18, 3457-3467 2020

Isolation and chacterisation of Klebsiella phages for phage therapy
E Townsend, L Kelly, L Gannon, G Muscatt, R Dunstan, S Michniewski, …
bioRxiv 1 2020

Essential Gene Clusters Involved in Copper Tolerance Identified in Acinetobacter baumannii Clinical and Environmental Isolates
R Thummeepak, R Pooalai, C Harrison, L Gannon, A Thanwisai, …
Pathogens 9 (1), 60

Sankalp Arya, Henry Todman, Michelle Baker, Steven Hooton, Andrew Millard, Jan-Ulrich Kreft, Jon L Hobman, Dov J Stekel 2020. A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. https://doi.org/10.1093/femsec/fiaa100

2019

Michniewski S, Redgwell T, Grigonyte A, et al. Riding the wave of genomics to investigate aquatic coliphage diversity and activity. Environ Microbiol. 2019;00:1462-2920.14590. doi:10.1111/1462-2920.14590

Cyanophage MazG is a pyrophosphohydrolase but unable to hydrolyse magic spot nucleotides  Branko Rihtman Sabine Bowman‐Grahl Andrew Millard Rebecca M. Corrigan Martha R. J. Clokie David J. Scanlan PDF

Metagenomics of the Viral Community in Three Cattle Slurry Samples
Pavelas Sazinas, Slawomir Michniewski, Branko Rihtman, Tamsin Redgwell, Aurelija Grigonyte, Amelia Brett, Bethany Guck, Rebecca Smith, Steven P. Hooton, Jon L. Hobman, Andrew D. Millard PDF 

2018

Relative stability of ploidy in a marine Synechococcus across various growth conditions. B Perez‐Sepulveda, F Pitt, AN N’Guyen, Laurence Garczarek, Andrew Millard & David J. Scanlan  – Environmental Microbiology Reports, 2018

Livingstone PG, Millard AD, Swain MT, Whitworth DE. 2018. Transcriptional changes when Myxococcus xanthus preys on Escherichia coli suggest myxobacterial predators are constitutively toxic but regulate their feeding Growth conditions. 1–13. doi: 10.1099/mgen.0.000152.

Pavelas Sazinas, Tamsin Redgwell, Branko Rihtman, Aurelija Grigonyte, Slawomir Michniewski, David J Scanlan, Jon Hobman, Andrew Millard; Comparative Genomics of Bacteriophage of the Genus SeuratvirusGenome Biology and Evolution, Volume 10, Issue 1, 1 January 2018, Pages 72–76, https://doi.org/10.1093/gbe/evx275

2017

Scherer Pia I., Millard Andrew D., Miller Andreas, Schoen Renate, Raeder Uta, Geist Juergen, Zwirglmaier Katrin . Temporal Dynamics of the Microbial Community Composition with a Focus on Toxic Cyanobacteria and Toxin Presence during Harmful Algal Blooms in Two South German Lakes   Frontiers in Microbiology ,8 , 2017

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
S Silas, KS Makarova, S Shmakov, D Páez-Espino, G Mohr, Y Liu, et al
mBio 8 (4), e00897-17 . PDF

Spatio-temporal distribution pattern of the picocyanobacterium Synechococcus in lakes of different trophic states: a comparison of flow cytometry and sequencing approaches
J Ruber, J Geist, M Hartmann, A Millard, U Raeder, M Zubkov, …
Hydrobiologia, 1-16

Draft genome sequence of bacteriophage vB_Eco_swan01. Genome Announc 5: e00501-17 S Michniewski, T Redgwell, DJ Scanlan, AD Millard

Identification of the anti‐mycobacterial functional properties of piperidinol derivatives
Collette S Guy, Esther Tichauer, Gemma L Kay, Daniel J Phillips, Trisha L Bailey, James Harrison, Christopher M Furze, Andrew D Millard, Matthew I Gibson, Mark J Pallen, Elizabeth Fullam. British Journal of Pharmacology

2016

Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. Srwa J. Rashid ,†, Jakub Barylski ,†, Katherine R. Hargreaves , Andrew A. Millard , Gurinder K. Vinner  and Martha R. J. Clokie. Viruses 2016, 8(11), 310; doi: 10.3390/v8110310. PDF

Joachim Ruber, Franziska Bauer, Andrew Millard, Uta Raeder, Jürgen Geist, Katrin Zwirglmaier. Synechococcus diversity along a trophic gradient in the Osterseen Lake District, Bavaria . Microbiology .2016   link

Pitt FD, Millard A, Ostrowski M, Dervish S, Mazard S, Paulsen IT, Zubkov MV, and Scanlan DJ. 2016. A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus. Frontiers in Microbiology 7. 10.3389/fmicb.2016.01592 PDF 

Higgins PG, Koehler D, Chan JZM, Cornely OA, Fätkenheuer G, Gillis M, Pallen MJ, Tien J, Seifert H, Vehreschild MJGT, Millard AD. 2016. Draft genome sequences of nine clinical isolates of vancomycin-resistant enterococci. Genome Announc 4(4):e00803-16. doi:10.1128/genomeA.00803-16. PDF

Blanca Perez Sepulveda, Tamsin Redgwell, Branko Rihtman, Frances Pitt, David J. Scanlan, Andrew Millard FEMS Microbiol Lett (2016) fnw158 DOI:http://dx.doi.org/10.1093/femsle/fnw158

Viruses Inhibit CO2 Fixation in the Most Abundant Phototrophs on Earth
Richard J. Puxty, Andrew D. Millard*, David J. Evans, David J. Scanlan* (2016).Current Biology .  *Co-senior authors

Nicholas A. Duggett, Gemma L. Kay, Martin J. Sergeant, Michael Bedford, Chrystala I. Constantinidou, Charles W. Penn, Andrew D. Millard, Mark J. Pallen (2016). Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca. Genome Announcements. pdf

B. Rihtman, S. Meaden, B. Koskell, M. Clokie, A Millard. Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes (2016) . PeerJ, pdf

P. Higgins, J M-Z Chan, H. Seifert, M.J.Pallen, A. D. Millard (2016).Draft genome sequence of 11 clinical isolates of Acinetobacter baumannii. Genome Annoucements. PMC

A.D. Millard D. A. Pearce . K. Zwirglmaier. Biogeography of bacteriophages at four hydrothermal vent sites in the Antarctic based on gp23 sequence diversity. FEMS Microbiology Letters pdf

S. Rashid, M.R.J Clokie A.D. Millard (2016) . Draft Genome Sequence of three novel Clostridrium isolates from Northern Iraq . Genome Announcements . 4:e00033-16; doi:10.1128/genomeA.00033-16 pdf

R.Smith, M. O’Hara, J. L. Hobman, A. D. Millard (2015). Draft Genome Sequences of 14 Escherichia coli phages isolated from cattle slurry. Genome Announcements. 3 (6), e01364-15pdf

A. D. Millard, L. F. Westblade, J. J. LiPuma, K. Vavikolanu, T. D. Read, M. J. Pallen, E. M. Burd C. I. Constantinidou. Draft Genome Sequence of thePandoraea apista LMG 16407 Type Strain. 2015. Genome Announcements. 3 (6), e01300-15 (pdf)

Puxty RJ, Perez-Sepulveda B, Rihtman B, Evans DJ, Millard AD, Scanlan DJ. Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage. PLoS One. 2015 Jul 15;10(7):e0132642. doi: 10.1371/journal.pone.0132642. eCollection 2015. PubMed PMID: 26177354; PubMed Central PMCID: PMC4503421.

Kay GL, Millard A, Sergeant MJ, Midzi N, Gwisai R, Mduluza T, Ivens A, Nausch N, Mutapi F, Pallen M. Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children. PLoS Negl Trop Dis. 2015 Jun 26;9(6):e0003861. doi:10.1371/journal.pntd.0003861. eCollection 2015 Jun. PubMed PMID: 26114287; PubMed Central PMCID: PMC4482744.

Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, Lawley TD, Clokie MR. As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile. Genome Biol Evol. 2015 May 27;7(7):1842-55. doi: 10.1093/gbe/evv094. PubMed PMID: 26019165.

Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun. 2015 Apr 7;6:6717. doi: 10.1038/ncomms7717. PubMed PMID:25848958; PubMed Central PMCID: PMC4396363.

Chan YW, Millard AD, Wheatley PJ, Holmes AB, Mohr R, Whitworth AL, Mann NH, Larkum AW, Hess WR, Scanlan DJ, Clokie MR. Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina. Environ Microbiol. 2014 Dec 4. doi:10.1111/1462-2920.12735. [Epub ahead of print] PubMed PMID: 25472545.

Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. Photosynth Res. 2014 Nov 9. [Epub ahead of print PubMed PMID:25381655.

Chan JZ, Millard AD, Mann NH, Schäfer H. Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Front Microbiol. 2014 Oct 10;5:506. doi:10.3389/fmicb.2014.00506. eCollection 2014. PubMed PMID: 25346726; PubMed Central PMCID: PMC4193335.

Millard AD, Hands-Portman I, Zwirglmaier K. Morphotypes of virus-like particles in two hydrothermal vent fields on the East Scotia Ridge, Antarctica. Bacteriophage. 2014 Apr 2;4:e28732. eCollection 2014. PubMed PMID: 25105058; PubMed Central PMCID: PMC4124060.

Shilova IN, Robidart JC, James Tripp H, Turk-Kubo K, Wawrik B, Post AF, Thompson AW, Ward B, Hollibaugh JT, Millard A, Ostrowski M, Scanlan DJ, Paerl RW, Stuart R, Zehr JP. A microarray for assessing transcription from pelagic marine microbial taxa. ISME J. 2014 Jul;8(7):1476-91. doi: 10.1038/ismej.2014.1. Epub 2014 Jan 30. PubMed PMID: 24477198; PubMed Central PMCID: PMC4069398.