Items where the Publication is Microbial genomics

Year Authors/Creators Item Type Full Text

2023

A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction. (2023) Hawkins, Paulina A; Chochua, Sopio; Lo, Stephanie W; Belman, Sophie; Antonio, Martin; Kwambana-Adams, Brenda; von Gottberg, Anne; du Plessis, Mignon; Cornick, Jen; Beall, Bernard; Breiman, Robert F; Bentley, Stephen D; McGee, Lesley; The Global Pneumococcal Sequencing Consortium

2022

Making microbial genomics work for clinical and public health microbiology. (2022) Azarian, Taj; Sherry, Norelle L; Baker, Kate; Holt, Kathryn E; Okeke, Iruka N

Linear plasmids in Klebsiella and other Enterobacteriaceae. (2022) Hawkey, Jane; Cottingham, Hugh; Tokolyi, Alex; Wick, Ryan R; Judd, Louise M; Cerdeira, Louise; de Oliveira Garcia, Doroti; Wyres, Kelly L; Holt, Kathryn E

Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. (2022) Lam, Margaret MC; Wick, Ryan R; Judd, Louise M; Holt, Kathryn E; Wyres, Kelly L

Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan. (2022) Le, Mi Nguyen-Tra; Kayama, Shizuo; Wyres, Kelly L; Yu, Liansheng; Hisatsune, Junzo; Suzuki, Masato; Yahara, Koji; Terachi, Tsuneko; Sawa, Kana; Takahashi, Shin; Okuhara, Toshihiko; Kohama, Kunihiko; Holt, Kathryn E; Mizutani, Tetsu; Ohge, Hiroki; Sugai, Motoyuki

Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals. (2022) Mellor, Kate C; Blackwell, Grace A; Cawthraw, Shaun A; Mensah, Nana E; Reid, Stuart WJ; Thomson, Nicholas R; Petrovska, Liljana; Mather, Alison E

A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. (2022) Ndlangisa, Kedibone M; du Plessis, Mignon; Lo, Stephanie; de Gouveia, Linda; Chaguza, Chrispin; Antonio, Martin; Kwambana-Adams, Brenda; Cornick, Jennifer; Everett, Dean B; Dagan, Ron; Hawkins, Paulina A; Beall, Bernard; Corso, Alejandra; Grassi Almeida, Samanta Cristine; Ochoa, Theresa J; Obaro, Stephen; Shakoor, Sadia; Donkor, Eric S; Gladstone, Rebecca A; Ho, Pak Leung; Paragi, Metka; Doiphode, Sanjay; Srifuengfung, Somporn; Ford, Rebecca; Moïsi, Jennifer; Saha, Samir K; Bigogo, Godfrey; Sigauque, Betuel; Eser, Özgen Köseoglu; Elmdaghri, Naima; Titov, Leonid; Turner, Paul; Kumar, KL Ravi; Kandasamy, Rama; Egorova, Ekaterina; Ip, Margaret; Breiman, Robert F; Klugman, Keith P; McGee, Lesley; Bentley, Stephen D; von Gottberg, Anne; The Global Pneumococcal Sequencing Consortium

Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements. (2022) Quek, Shannon; Cerdeira, Louise; Jeffries, Claire L; Tomlinson, Sean; Walker, Thomas; Hughes, Grant L; Heinz, Eva

In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors. (2022) Robinson, Luca; Liaw, Janie; Omole, Zahra; Corcionivoschi, Nicolae; Hachani, Abderrahman; Gundogdu, Ozan

Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. (2022) Senghore, Madikay; Chaguza, Chrispin; Bojang, Ebrima; Tientcheu, Peggy-Estelle; Bancroft, Rowan E; Lo, Stephanie W; Gladstone, Rebecca A; McGee, Lesley; Worwui, Archibald; Foster-Nyarko, Ebenezer; Ceesay, Fatima; Okoi, Catherine Bi; Klugman, Keith P; Breiman, Robert F; Bentley, Stephen D; Adegbola, Richard; Antonio, Martin; Hanage, William P; Kwambana-Adams, Brenda A

2021

Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation. (2021) Bossé, Janine T; Li, Yanwen; Cohen, Liza Miriam; Stegger, Marc; Angen, Øystein; Lacouture, Sonia; Gottschalk, Marcelo; Lei, Liancheng; Koene, Miriam; Kuhnert, Peter; Bandara, Aloka B; Inzana, Thomas J; Holden, Matthew TG; Harris, David; Oshota, Olusegun; Maskell, Duncan J; Tucker, Alexander W; Wren, Brendan W; Rycroft, Andrew N; Langford, Paul R; On Behalf Of The BRaDP T Consortium

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. (2021) Coscolla, Mireia; Gagneux, Sebastien; Menardo, Fabrizio; Loiseau, Chloé; Ruiz-Rodriguez, Paula; Borrell, Sonia; Otchere, Isaac Darko; Asante-Poku, Adwoa; Asare, Prince; Sánchez-Busó, Leonor; Gehre, Florian; Sanoussi, C N'Dira; Antonio, Martin; Affolabi, Dissou; Fyfe, Janet; Beckert, Patrick; Niemann, Stefan; Alabi, Abraham S; Grobusch, Martin P; Kobbe, Robin; Parkhill, Julian; Beisel, Christian; Fenner, Lukas; Böttger, Erik C; Meehan, Conor J; Harris, Simon R; de Jong, Bouke C; Yeboah-Manu, Dorothy; Brites, Daniela

wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations. (2021) Dainty, Kimberley R; Hawkey, Jane; Judd, Louise M; Pacidônio, Etiene C; Duyvestyn, Johanna M; Gonçalves, Daniela S; Lin, Silk Yu; O'Donnell, Tanya B; O'Neill, Scott L; Simmons, Cameron P; Holt, Kathryn E; Flores, Heather A

Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. (2021) Dorman, Matthew J; Thomson, Nicholas R; Campos, Josefina

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. (2021) Edwards, David J; Duchene, Sebastián; Pope, Bernard; Holt, Kathryn E

gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. (2021) Fennell, Thea G; Blackwell, Grace A; Thomson, Nicholas R; Dorman, Matthew J

Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes. (2021) Gomes, Laura C; Campino, Susana; Marinho, Cláudio RF; Clark, Taane G; Phelan, Jody E

Detection of plasmid contigs in draft genome assemblies using customized Kraken databases. (2021) Gomi, Ryota; Wyres, Kelly L; Holt, Kathryn E

Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. (2021) Heinz, Eva; Holt, Kathryn E; Meehan, Conor J; Sheppard, Samuel K

A comprehensive and high-quality collection of Escherichia coli genomes and their genes. (2021) Horesh, Gal; Blackwell, Grace A; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R

Different evolutionary trends form the twilight zone of the bacterial pan-genome. (2021) Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R

Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. (2021) Kalizang'oma, Akuzike; Chaguza, Chrispin; Gori, Andrea; Davison, Charlotte; Beleza, Sandra; Antonio, Martin; Beall, Bernard; Goldblatt, David; Kwambana-Adams, Brenda; Bentley, Stephen D; Heyderman, Robert S

The evolutionary history of Shigella flexneri serotype 6 in Asia. (2021) Mai, Si-Nguyen T; Bodhidatta, Ladaporn; Turner, Paul; Wangchuk, Sonam; Ha Thanh, Tuyen; Voong Vinh, Phat; Pham, Duy Thanh; Rabaa, Maia A; Thwaites, Guy E; Thomson, Nicholas R; Baker, Stephen; Chung The, Hao

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. (2021) Sanoussi, C N'Dira; Coscolla, Mireia; Ofori-Anyinam, Boatema; Otchere, Isaac Darko; Antonio, Martin; Niemann, Stefan; Parkhill, Julian; Harris, Simon; Yeboah-Manu, Dorothy; Gagneux, Sebastien; Rigouts, Leen; Affolabi, Dissou; de Jong, Bouke C; Meehan, Conor J

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction. (2021) Senghore, Madikay; Tientcheu, Peggy-Estelle; Worwui, Archibald Kwame; Jarju, Sheikh; Okoi, Catherine; Suso, Sambou MS; Foster-Nyarko, Ebenezer; Ebruke, Chinelo; Sonko, Mohamadou; Kourna, Mamdou Hama; Agossou, Joseph; Tsolenyanu, Enyonam; Renner, Lorna Awo; Ansong, Daniel; Sanneh, Bakary; Cisse, Catherine Boni; Boula, Angeline; Miwanda, Berthe; Lo, Stephanie W; Gladstone, Rebecca A; Schwartz, Stephanie; Hawkins, Paulina; McGee, Lesley; Klugman, Keith P; Breiman, Robert F; Bentley, Stephen D; Mwenda, Jason M; Kwambana-Adams, Brenda Anna; Antonio, Martin

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. (2021) Viehweger, Adrian; Blumenscheit, Christian; Lippmann, Norman; Wyres, Kelly L; Brandt, Christian; Hans, Jörg B; Hölzer, Martin; Irber, Luiz; Gatermann, Sören; Lübbert, Christoph; Pletz, Mathias W; Holt, Kathryn E; König, Brigitte

Recovery of small plasmid sequences via Oxford Nanopore sequencing. (2021) Wick, Ryan R; Judd, Louise M; Wyres, Kelly L; Holt, Kathryn E

2020

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia. (2020) Foster-Nyarko, Ebenezer; Alikhan, Nabil-Fareed; Ravi, Anuradha; Thilliez, Gaëtan; Thomson, Nicholas M; Baker, David; Kay, Gemma; Cramer, Jennifer D; O'Grady, Justin; Antonio, Martin; Pallen, Mark J

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. (2020) Gladstone, Rebecca A; Lo, Stephanie W; Goater, Richard; Yeats, Corin; Taylor, Ben; Hadfield, James; Lees, John A; Croucher, Nicholas J; van Tonder, Andries J; Bentley, Leon J; Quah, Fu Xiang; Blaschke, Anne J; Pershing, Nicole L; Byington, Carrie L; Balaji, Veeraraghavan; Hryniewicz, Waleria; Sigauque, Betuel; Ravikumar, KL; Almeida, Samanta Cristine Grassi; Ochoa, Theresa J; Ho, Pak Leung; du Plessis, Mignon; Ndlangisa, Kedibone M; Cornick, Jennifer E; Kwambana-Adams, Brenda; Benisty, Rachel; Nzenze, Susan A; Madhi, Shabir A; Hawkins, Paulina A; Pollard, Andrew J; Everett, Dean B; Antonio, Martin; Dagan, Ron; Klugman, Keith P; von Gottberg, Anne; Metcalf, Benjamin J; Li, Yuan; Beall, Bernard W; McGee, Lesley; Breiman, Robert F; Aanensen, David M; Bentley, Stephen D; The Global Pneumococcal Sequencing Consortium

Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing. (2020) Knight, James R; Dunne, Eileen M; Mulholland, E Kim; Saha, Sudipta; Satzke, Catherine; Tothpal, Adrienn; Weinberger, Daniel M

Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. (2020) Perdigão, João; Modesto, Ana; Pereira, AL; Neto, O; Matos, V; Godinho, A; Phelan, Jody; Charleston, James; Spadar, Anton; de Sessions, Paola Florez; Hibberd, Martin; Campino, Susana; Costa, A; Fernandes, F; Ferreira, F; Correia, AB; Gonçalves, Luisa; Clark, Taane G; Duarte, Aida

Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data. (2020) Xu, Yuanwei; Stockdale, Jessica E; Naidu, Vijay; Hatherell, Hollie; Stimson, James; Stagg, Helen R; Abubakar, Ibrahim; Colijn, Caroline

2019

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. (2019) Boinett, Christine J; Cain, Amy K; Hawkey, Jane; Do Hoang, Nhu Tran; Khanh, Nhu Nguyen Thi; Thanh, Duy Pham; Dordel, Janina; Campbell, James I; Lan, Nguyen Phu Huong; Mayho, Matthew; Langridge, Gemma C; Hadfield, James; Chau, Nguyen Van Vinh; Thwaites, Guy E; Parkhill, Julian; Thomson, Nicholas R; Holt, Kathryn E; Baker, Stephen

Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. (2019) Hamidian, Mohammad; Wick, Ryan R; Hartstein, Rebecca M; Judd, Louise M; Holt, Kathryn E; Hall, Ruth M

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. (2019) Hawkey, Jane; Le Hello, Simon; Doublet, Benoît; Granier, Sophie A; Hendriksen, Rene S; Fricke, W Florian; Ceyssens, Pieter-Jan; Gomart, Camille; Billman-Jacobe, Helen; Holt, Kathryn E; Weill, François-Xavier

Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data. (2019) Mitchell, Holly D; Mikhail, Amy FW; Painset, Anaïs; Dallman, Timothy J; Jenkins, Claire; Thomson, Nicholas R; Field, Nigel; Hughes, Gwenda

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. (2019) Ravi, Anuradha; Halstead, Fenella D; Bamford, Amy; Casey, Anna; Thomson, Nicholas M; van Schaik, Willem; Snelson, Catherine; Goulden, Robert; Foster-Nyarko, Ebenezer; Savva, George M; Whitehouse, Tony; Pallen, Mark J; Oppenheim, Beryl A

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. (2019) Wailan, Alexander M; Coll, Francesc; Heinz, Eva; Tonkin-Hill, Gerry; Corander, Jukka; Feasey, Nicholas A; Thomson, Nicholas R

Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress. (2019) Willcocks, Samuel; Huse, Kristin K; Stabler, Richard; Oyston, Petra CF; Scott, Andrew; Atkins, Helen S; Wren, Brendan W

2018

The importance of cross-disciplinary research to combat antimicrobial resistance: introducing a new pop-up journal, X-AMR. (2018) Knight, Gwen; Lambert, Helen; Feil, Edward; Holmes, Mark; Lindsay, Jodi

2017

Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. (2017) Ludden, Catherine; Reuter, Sandra; Judge, Kim; Gouliouris, Theodore; Blane, Beth; Coll, Francesc; Naydenova, Plamena; Hunt, Martin; Tracey, Alan; Hopkins, Katie L; Brown, Nicholas M; Woodford, Neil; Parkhill, Julian; Peacock, Sharon J

2016

The diversity of Klebsiella pneumoniae surface polysaccharides. (2016) Follador, Rainer; Heinz, Eva; Wyres, Kelly L; Ellington, Matthew J; Kowarik, Michael; Holt, Kathryn E; Thomson, Nicholas R

Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic. (2016) Jamrozy, Dorota M; Harris, Simon R; Mohamed, Naglaa; Peacock, Sharon J; Tan, Charles Y; Parkhill, Julian; Anderson, Annaliesa S; Holden, Matthew TG

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology. (2016) Judge, Kim; Hunt, Martin; Reuter, Sandra; Tracey, Alan; Quail, Michael A; Parkhill, Julian; Peacock, Sharon J

Identification of Klebsiella capsule synthesis loci from whole genome data. (2016) Wyres, Kelly L; Wick, Ryan R; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R; Holt, Kathryn E

2015

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. (2015) Chung The, Hao; Rabaa, Maia A; Thanh, Duy Pham; Ruekit, Sirigade; Wangchuk, Sonam; Dorji, Tshering; Tshering, Kinzang Pem; Nguyen, To Nguyen Thi; Vinh, Phat Voong; Thanh, Tuyen Ha; Minh, Chau Nguyen Ngoc; Turner, Paul; Sar, Poda; Thwaites, Guy; Holt, Kathryn E; Thomson, Nicholas R; Bodhidatta, Ladaporn; Jeffries Mason, Carl; Baker, Stephen

Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. (2015) Cornick, Jennifer E; Chaguza, Chrispin; Harris, Simon R; Yalcin, Feyruz; Senghore, Madikay; Kiran, Anmol M; Govindpershad, Shanil; Ousmane, Sani; Plessis, Mignon Du; Pluschke, Gerd; Ebruke, Chinelo; McGee, Lesley; Sigaùque, Beutel; Collard, Jean-Marc; Antonio, Martin; von Gottberg, Anne; French, Neil; Klugman, Keith P; Heyderman, Robert S; Bentley, Stephen D; Everett, Dean B; For The PAGe Consortium

Directional gene flow and ecological separation in Yersinia enterocolitica. (2015) Reuter, Sandra; Corander, Jukka; de Been, Mark; Harris, Simon; Cheng, Lu; Hall, Miquette; Thomson, Nicholas R; McNally, Alan