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2. NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource

Author

Dicks, Jo, primary, Fazal, Mohammed-Abbas, additional, Oliver, Karen, additional, Grayson, Nicholas E., additional, Turnbull, Jake D., additional, Bane, Evangeline, additional, Burnett, Edward, additional, Deheer-Graham, Ana, additional, Holroyd, Nancy, additional, Kaushal, Dorota, additional, Keane, Jacqueline, additional, Langridge, Gemma, additional, Lomax, Jane, additional, McGregor, Hannah, additional, Picton, Steve, additional, Quail, Michael, additional, Singh, Deepak, additional, Tracey, Alan, additional, Korlach, Jonas, additional, Russell, Julie E., additional, Alexander, Sarah, additional, and Parkhill, Julian, additional

Published
2023
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5. Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A., Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E., Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison E., Mason, Carl J., Page, Andrew J., Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carle, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Le Hello, Simon, Blaser, Martin J., Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja P., Ezernitchi, Analia V., Guigon, Ghislaine, Harris, Simon R., Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A.M., Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A., Ye, Changyun, Žemličková, Helena, Herpay, Mária, Grimont, Patrick A. D., Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn E., Brisse, Sylvain, Thomson, Nicholas R., and Weill, François-Xavier

Published
2016
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6. First complete genome sequences of Streptococcus pyogenes NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies

Author

Salvà-Serra, Francisco, Jaén-Luchoro, Daniel, Jakobsson, Hedvig E., Gonzales-Siles, Lucia, Karlsson, Roger, Busquets, Antonio, Gomila, Margarita, Bennasar-Figueras, Antonio, Russell, Julie E., Fazal, Mohammed Abbas, Alexander, Sarah, and Moore, Edward R. B.

Abstract

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198 T and CCUG 4207 T , the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198 T and CCUG 4207 T are derived from deposit of the same strain at two different culture collections. NCTC 8198 T was sequenced, using a PacBio platform; the genome sequence was assembled de novo , using HGAP. CCUG 4207 T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies, yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus .

Published
2020
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7. First complete genome sequences ofStreptococcus pyogenesNCTC 8198Tand CCUG 4207T, the type strain of the type species of the genusStreptococcus: 100% match in length and sequence identity between PacBio solo and Illumina plus Oxford Nanopore hybrid assemblies

Author

Salvà-Serra, Francisco, primary, Jaén-Luchoro, Daniel, additional, Jakobsson, Hedvig E., additional, Gonzales-Siles, Lucia, additional, Karlsson, Roger, additional, Busquets, Antonio, additional, Gomila, Margarita, additional, Bennasar-Figueras, Antonio, additional, Russell, Julie E., additional, Fazal, Mohammed Abbas, additional, Alexander, Sarah, additional, and Moore, Edward R. B., additional

Published
2020
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8. Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839

Author

Fazal, Mohammed-Abbas, Alexander, Sarah, Grayson, Nicholas E, Deheer-Graham, Ana, Oliver, Karen, Holroyd, Nancy, Parkhill, Julian, Russell, Julie E, Parkhill, Julian [0000-0002-7069-5958], and Apollo - University of Cambridge Repository

Subjects
Pediatric, 3107 Microbiology, 3102 Bioinformatics and Computational Biology, fluids and secretions, FOS: Biological sciences, Human Genome, Genetics, bacteria, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, equipment and supplies, 3105 Genetics, 31 Biological Sciences
Abstract

Haemophilus haemolyticus is a Gram-negative bacterium that is a commensal of the respiratory tract in humans. Here, we report the complete genome sequence available for Haemophilus haemolyticus strain NCTC 10839, which was originally isolated from the nasopharynx of a child.

Published
2019
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14. Mycobacterial biomaterials and resources for researchers

Author

Hazbón, Manzour Hernando, primary, Rigouts, Leen, additional, Schito, Marco, additional, Ezewudo, Matthew, additional, Kudo, Takuji, additional, Itoh, Takashi, additional, Ohkuma, Moriya, additional, Kiss, Katalin, additional, Wu, Linhuan, additional, Ma, Juncai, additional, Hamada, Moriyuki, additional, Strong, Michael, additional, Salfinger, Max, additional, Daley, Charles L, additional, Nick, Jerry A, additional, Lee, Jung-Sook, additional, Rastogi, Nalin, additional, Couvin, David, additional, Hurtado-Ortiz, Raquel, additional, Bizet, Chantal, additional, Suresh, Anita, additional, Rodwell, Timothy, additional, Albertini, Audrey, additional, Lacourciere, Karen A, additional, Deheer-Graham, Ana, additional, Alexander, Sarah, additional, Russell, Julie E, additional, Bradford, Rebecca, additional, and Riojas, Marco A, additional

Published
2018
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15. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Author

Raven, Kathy E, Reuter, Sandra, Reynolds, Rosy, Brodrick, Hayley J, Russell, Julie E, Török, M Estée, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository

Subjects
Infection Control, Enterococcus faecium, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, United Kingdom, Anti-Bacterial Agents, Evolution, Molecular, Vancomycin, Drug Resistance, Bacterial, bacteria, Humans, Genome, Bacterial, Gram-Positive Bacterial Infections, Phylogeny
Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.

Published
2016

17. Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A, Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E, Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison AE, Mason, Carl J, Page, Andrew J, Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carles, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Hello, Simon Le, Blaser, Martin J, Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja GP, Ezernitchi, Analia V, Guigon, Ghislaine, Harris, Simon R, Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A M LA, Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A, Ye, Changyun, Zemlickova, Helena, Herpay, Mária, Grimont, Patrick A D PA, Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn KE, Brisse, Sylvain, Thomson, Nicholas R, Weill, François-Xavier, Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A, Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E, Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison AE, Mason, Carl J, Page, Andrew J, Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carles, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Hello, Simon Le, Blaser, Martin J, Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja GP, Ezernitchi, Analia V, Guigon, Ghislaine, Harris, Simon R, Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A M LA, Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A, Ye, Changyun, Zemlickova, Helena, Herpay, Mária, Grimont, Patrick A D PA, Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn KE, Brisse, Sylvain, Thomson, Nicholas R, and Weill, François-Xavier

Abstract

info:eu-repo/semantics/published

Published
2016

19. Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, primary, Fawal, Nizar, additional, Tran-Dien, Alicia, additional, Hawkey, Jane, additional, Strockbine, Nancy, additional, Jenkins, Claire, additional, Talukder, Kaisar A., additional, Bercion, Raymond, additional, Kuleshov, Konstantin, additional, Kolínská, Renáta, additional, Russell, Julie E., additional, Kaftyreva, Lidia, additional, Accou-Demartin, Marie, additional, Karas, Andreas, additional, Vandenberg, Olivier, additional, Mather, Alison E., additional, Mason, Carl J., additional, Page, Andrew J., additional, Ramamurthy, Thandavarayan, additional, Bizet, Chantal, additional, Gamian, Andrzej, additional, Carle, Isabelle, additional, Sow, Amy Gassama, additional, Bouchier, Christiane, additional, Wester, Astrid Louise, additional, Lejay-Collin, Monique, additional, Fonkoua, Marie-Christine, additional, Le Hello, Simon, additional, Blaser, Martin J., additional, Jernberg, Cecilia, additional, Ruckly, Corinne, additional, Mérens, Audrey, additional, Page, Anne-Laure, additional, Aslett, Martin, additional, Roggentin, Peter, additional, Fruth, Angelika, additional, Denamur, Erick, additional, Venkatesan, Malabi, additional, Bercovier, Hervé, additional, Bodhidatta, Ladaporn, additional, Chiou, Chien-Shun, additional, Clermont, Dominique, additional, Colonna, Bianca, additional, Egorova, Svetlana, additional, Pazhani, Gururaja P., additional, Ezernitchi, Analia V., additional, Guigon, Ghislaine, additional, Harris, Simon R., additional, Izumiya, Hidemasa, additional, Korzeniowska-Kowal, Agnieszka, additional, Lutyńska, Anna, additional, Gouali, Malika, additional, Grimont, Francine, additional, Langendorf, Céline, additional, Marejková, Monika, additional, Peterson, Lorea A.M., additional, Perez-Perez, Guillermo, additional, Ngandjio, Antoinette, additional, Podkolzin, Alexander, additional, Souche, Erika, additional, Makarova, Mariia, additional, Shipulin, German A., additional, Ye, Changyun, additional, Žemličková, Helena, additional, Herpay, Mária, additional, Grimont, Patrick A. D., additional, Parkhill, Julian, additional, Sansonetti, Philippe, additional, Holt, Kathryn E., additional, Brisse, Sylvain, additional, Thomson, Nicholas R., additional, and Weill, François-Xavier, additional

Published
2016
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26. Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511

Author

Turnbull, Jake D, Russell, Julie E, Fazal, Mohammed-Abbas, Grayson, Nicholas E, Deheer-Graham, Ana, Oliver, Karen, Holroyd, Nancy, Parkhill, Julian, and Alexander, Sarah

Subjects
2 Aetiology, 3107 Microbiology, FOS: Biological sciences, Human Genome, Genetics, 2.2 Factors relating to the physical environment, Infection, 3105 Genetics, 3. Good health, 31 Biological Sciences, Skin
Abstract

Kocuria rosea is a Gram-positive coccus found in the environment and within normal human skin microbiota, and more recently, it has been potentially implicated as an opportunistic pathogen. Here, we describe the genome sequences of five strains of K. rosea (NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511).

27. Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases

Author

Fazal, Mohammed-Abbas, Alexander, Sarah, Grayson, Nicholas E, Deheer-Graham, Ana, Oliver, Karen, Holroyd, Nancy, Parkhill, Julian, and Russell, Julie E

Subjects
3107 Microbiology, FOS: Biological sciences, Human Genome, Genetics, bacteria, equipment and supplies, 3105 Genetics, 3. Good health, 31 Biological Sciences
Abstract

Raoultella terrigena is a bacterial species associated with soil and aquatic environments; however, sporadic cases of opportunistic disease in humans have been reported. Here, we report the first two complete genome sequences from clinical strains isolated from human sources that have been deposited in the National Collection of Type Cultures (NCTC).

28. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Author

Raven, Kathy E, Reuter, Sandra, Reynolds, Rosy, Brodrick, Hayley J, Russell, Julie E, Török, M Estée, Parkhill, Julian, and Peacock, Sharon J

Subjects
Infection Control, Enterococcus faecium, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, United Kingdom, 3. Good health, Anti-Bacterial Agents, Evolution, Molecular, Vancomycin, Drug Resistance, Bacterial, bacteria, Humans, Genome, Bacterial, Gram-Positive Bacterial Infections, Phylogeny
Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.

29. Control your controls.

Author

Russell, Julie E.

Subjects
*LABORATORY safety, *HAZARDOUS substances, *PUBLIC health, *IDENTIFICATION of pathogenic microorganisms, *FOODBORNE diseases, *DISEASE risk factors
Abstract

The article discusses the results of the research study conducted by the Public Health England (PHE) related to importance of sourcing and controlling control strains and biological test materials in science laboratories in Great Britain. It mentions that science laboratories used routinely in its scientific test for four common food-borne pathogenic microorganism. It also concludes that laboratories has long-established bioresource strains in the National Collection of Type Cultures (NCTC).

Published
2013

30. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland.

Author

Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE, Török ME, Parkhill J, and Peacock SJ

Subjects
Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial genetics, Enterococcus faecium classification, Enterococcus faecium isolation & purification, Enterococcus faecium pathogenicity, Gram-Positive Bacterial Infections microbiology, Gram-Positive Bacterial Infections prevention & control, Humans, Infection Control methods, Phylogeny, Sequence Analysis, DNA methods, United Kingdom, Vancomycin pharmacology, Enterococcus faecium genetics, Evolution, Molecular, Genome, Bacterial, Gram-Positive Bacterial Infections epidemiology
Abstract

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control., (© 2016 Raven et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2016
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