Whole genome sequencing based differentiation between re-infection and relapse in Indian patients with tuberculosis recurrence, with and without HIV co-infection von Shanmugam, Sivakumar, Bachmann, Nathan L., Martinez, Elena, Menon, Ranjeeta, Narendran, G., Narayanan, Sujatha, Tripathy, Srikanth P., Ranganathan, Uma Devi, Sawleshwarkar, Shailendra, Marais, Ben J., Sintchenko, Vitali

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Key Transitions in the Evolution of Rapid and Slow Growing Mycobacteria Identified by Comparative Genomics von Bachmann, Nathan L., Salamzade, Rauf, Manson, Abigail L., Whittington, Richard, Sintchenko, Vitali, Earl, Ashlee M., Marais, Ben J.

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Genomic Comparison of Translocating and Non-Translocating Escherichia coli von Bachmann, Nathan L, Katouli, Mohammad, Polkinghorne, Adam

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Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum von Bachmann, Nathan L, Sullivan, Mitchell J, Jelocnik, Martina, Myers, Garry S A, Timms, Peter, Polkinghorne, Adam

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Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics von Bachmann, Nathan L, Rockett, Rebecca J, Timms, Verlaine Joy, Sintchenko, Vitali

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Chlamydia genomics: providing novel insights into chlamydial biology von Bachmann, Nathan L, Polkinghorne, Adam, Timms, Peter

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A Novel Marine Mammal Coxiella burnetii -Genome Sequencing Identifies a New Genotype with Potential Virulence von Gardner, Brett R, Bachmann, Nathan L, Polkinghorne, Adam, Hufschmid, Jasmin, Tadepalli, Mythili, Marenda, Marc, Graves, Stephen, Arnould, John P Y, Stenos, John

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Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling von Rockett, Rebecca J., Arnott, Alicia, Lam, Connie, Sadsad, Rosemarie, Timms, Verlaine, Gray, Karen-Ann, Eden, John-Sebastian, Chang, Sheryl, Gall, Mailie, Draper, Jenny, Sim, Eby M., Bachmann, Nathan L., Carter, Ian, Basile, Kerri, Byun, Roy, O’Sullivan, Matthew V., Chen, Sharon C-A, Maddocks, Susan, Sorrell, Tania C., Dwyer, Dominic E., Holmes, Edward C., Kok, Jen, Prokopenko, Mikhail, Sintchenko, Vitali

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Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes von Taylor-Brown, Alyce, Bachmann, Nathan L, Borel, Nicole, Polkinghorne, Adam

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Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution von Jelocnik, Martina, Bachmann, Nathan L, Seth-Smith, Helena, Thomson, Nicholas R, Timms, Peter, Polkinghorne, Adam M

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Australian human and parrot Chlamydia psittaci strains cluster within the highly virulent 6BC clade of this important zoonotic pathogen von Branley, James, Bachmann, Nathan L., Jelocnik, Martina, Myers, Garry S. A., Polkinghorne, Adam

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Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia von Rockett, Rebecca J., Oftadeh, Shahin, Bachmann, Nathan L., Timms, Verlaine J., Kong, Fanrong, Gilbert, Gwendolyn L., Sintchenko, Vitali

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HapFlow: visualizing haplotypes in sequencing data von Sullivan, Mitchell J, Bachmann, Nathan L, Timms, Peter, Polkinghorne, Adam

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Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas von Jelocnik, Martina, Bachmann, Nathan L, Kaltenboeck, Bernhard, Waugh, Courtney, Woolford, Lucy, Speight, K Natasha, Gillett, Amber, Higgins, Damien P, Flanagan, Cheyne, Myers, Garry S A, Timms, Peter, Polkinghorne, Adam

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Genome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211 von Timms, Verlaine J, Rockett, Rebecca, Bachmann, Nathan L, Martinez, Elena, Wang, Qinning, Chen, Sharon C-A, Jeoffreys, Neisha, Howard, Peter J, Smith, Anna, Adamson, Sheena, Gilmour, Robin, Sheppeard, Vicky, Sintchenko, Vitali

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Comparative genomic analysis of human Chlamydia pneumoniae isolates from respiratory, brain and cardiac tissues von Roulis, Eileen, Bachmann, Nathan L., Myers, Garry S.A., Huston, Wilhelmina, Summersgill, James, Hudson, Alan, Dreses-Werringloer, Ute, Polkinghorne, Adam, Timms, Peter

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Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum von Bachmann, Nathan L, Fraser, Tamieka A, Bertelli, Claire, Jelocnik, Martina, Gillett, Amber, Funnell, Oliver, Flanagan, Cheyne, Myers, Garry S A, Timms, Peter, Polkinghorne, Adam

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Culture‐independent genomics of a novel chlamydial pathogen of fish provides new insight into host‐specific adaptations utilized by these intracellular bacteria von Taylor‐Brown, Alyce, Pillonel, Trestan, Bridle, Andrew, Qi, Weihong, Bachmann, Nathan L., Miller, Terrence L., Greub, Gilbert, Nowak, Barbara, Seth‐Smith, Helena M.B., Vaughan, Lloyd, Polkinghorne, Adam

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Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow von Bachmann, Nathan L, Petty, Nicola K, Ben Zakour, Nouri L, Szubert, Jan M, Savill, John, Beatson, Scott A

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Genome Sequence of the Emerging Pathogen Aeromonas caviae von BEATSON, Scott A, DAS GRACAS DE LUNA, Maria, SQUIRE, Derrick J. P, CUNNINGHAM, Adam F, FITZGERALD, J. Ross, HENDERSON, Ian R, BACHMANN, Nathan L, ALIKHAN, Nabil-Fareed, HANKS, Kirstin R, SULLIVAN, Mitchell J, WEE, Bryan A, FREITAS-ALMEIDA, Angela C, DOS SANTOS, Paula A, DE MELO, Janyne T. B

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