Publications
109 results found
Croucher NJ, Harris SR, Barquist L, et al., 2012, A High-Resolution View of Genome-Wide Pneumococcal Transformation, PLOS PATHOGENS, Vol: 8, ISSN: 1553-7374
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- Citations: 74
Strouts FR, Power P, Croucher NJ, et al., 2012, Lineage-specific Virulence Determinants of Haemophilus influenzae Biogroup aegyptius, Emerging Infectious Diseases, Vol: 18, Pages: 449-457
An emergent clone of Haemophilus influenzae biogroup aegyptius (Hae) is responsible for outbreaks of Brazilian purpuric fever (BPF). First recorded in Brazil in 1984, the so-called BPF clone of Hae caused a fulminant disease that started with conjunctivitis but developed into septicemic shock; mortality rates were as high as 70%. To identify virulence determinants, we conducted a pan-genomic analysis. Sequencing of the genomes of the BPF clone strain F3031 and a noninvasive conjunctivitis strain, F3047, and comparison of these sequences with 5 other complete H. influenzae genomes showed that >77% of the F3031 genome is shared among all H. influenzae strains. Delineation of the Hae accessory genome enabled characterization of 163 predicted protein-coding genes; identified differences in established autotransporter adhesins; and revealed a suite of novel adhesins unique to Hae, including novel trimeric autotransporter adhesins and 4 new fimbrial operons. These novel adhesins might play a critical role in host-pathogen interactions.
Marttinen P, Hanage WP, Croucher NJ, et al., 2012, Detection of recombination events in bacterial genomes from large population samples, NUCLEIC ACIDS RESEARCH, Vol: 40, ISSN: 0305-1048
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- Citations: 148
Arnvig KB, Comas I, Thomson NR, et al., 2011, Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of <i>Mycobacterium tuberculosis</i>, PLOS PATHOGENS, Vol: 7, ISSN: 1553-7366
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- Citations: 161
Donati C, Hiller NL, Tettelin H, et al., 2011, Correction: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species., Genome Biol, Vol: 12
Mutreja A, Kim DW, Thomson NR, et al., 2011, Evidence for several waves of global transmission in the seventh cholera pandemic, NATURE, Vol: 477, Pages: 462-U111, ISSN: 0028-0836
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- Citations: 470
Croucher NJ, Vernikos GS, Parkhill J, et al., 2011, Identification, variation and transcription of pneumococcal repeat sequences, BMC GENOMICS, Vol: 12, ISSN: 1471-2164
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- Citations: 39
Croucher NJ, Harris SR, Fraser C, et al., 2011, Rapid Pneumococcal Evolution in Response to Clinical Interventions, SCIENCE, Vol: 331, Pages: 430-434, ISSN: 0036-8075
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- Citations: 663
Croucher NJ, Thomson NR, 2010, Studying bacterial transcriptomes using RNA-seq, CURRENT OPINION IN MICROBIOLOGY, Vol: 13, Pages: 619-624, ISSN: 1369-5274
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- Citations: 182
Donati C, Hiller NL, Tettelin H, et al., 2010, Structure and dynamics of the pan-genome of <i>Streptococcus pneumoniae</i> and closely related species, GENOME BIOLOGY, Vol: 11, ISSN: 1474-760X
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- Citations: 268
Croucher NJ, Fookes MC, Perkins TT, et al., 2009, A simple method for directional transcriptome sequencing using Illumina technology., Nucleic Acids Research, Vol: 37, Pages: e148-e148, ISSN: 1362-4962
High-throughput sequencing of cDNA has been used to study eukaryotic transcription on a genome-wide scale to single base pair resolution. In order to compensate for the high ribonuclease activity in bacterial cells, we have devised an equivalent technique optimized for studying complete prokaryotic transcriptomes that minimizes the manipulation of the RNA sample. This new approach uses Illumina technology to sequence single-stranded (ss) cDNA, generating information on both the direction and level of transcription throughout the genome. The protocol, and associated data analysis programs, are freely available from http://www.sanger.ac.uk/Projects/Pathogens/Transcriptome/. We have successfully applied this method to the bacterial pathogens Salmonella bongori and Streptococcus pneumoniae and the yeast Schizosaccharomyces pombe. This method enables experimental validation of genetic features predicted in silico and allows the easy identification of novel transcripts throughout the genome. We also show that there is a high correlation between the level of gene expression calculated from ss-cDNA and double-stranded-cDNA sequencing, indicting that ss-cDNA sequencing is both robust and appropriate for use in quantitative studies of transcription. Hence, this simple method should prove a useful tool in aiding genome annotation and gene expression studies in both prokaryotes and eukaryotes.
Lawley TD, Croucher NJ, Yu L, et al., 2009, Proteomic and Genomic Characterization of Highly Infectious <i>Clostridium difficile</i> 630 Spores, JOURNAL OF BACTERIOLOGY, Vol: 191, Pages: 5377-5386, ISSN: 0021-9193
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- Citations: 168
Croucher NJ, 2009, From small reads do mighty genomes grow, NATURE REVIEWS MICROBIOLOGY, Vol: 7, Pages: 621-621, ISSN: 1740-1526
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- Citations: 3
Lawley TD, Clare S, Walker AW, et al., 2009, Antibiotic Treatment of <i>Clostridium difficile</i> Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts, INFECTION AND IMMUNITY, Vol: 77, Pages: 3661-3669, ISSN: 0019-9567
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- Citations: 261
Romero P, Croucher NJ, Hiller NL, et al., 2009, Comparative Genomic Analysis of Ten <i>Streptococcus pneumoniae</i> Temperate Bacteriophages, JOURNAL OF BACTERIOLOGY, Vol: 191, Pages: 4854-4862, ISSN: 0021-9193
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- Citations: 54
Holden MTG, Hauser H, Sanders M, et al., 2009, Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis, PLOS One, Vol: 4, ISSN: 1932-6203
Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections inhumans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has beendescribed in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorlyunderstood.Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides opportunities toinvestigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the samelineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis wasused to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species forwhich genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is unique in comparison toother Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation;virtually all of the genome is common to the S. suis strains. The only exceptions are three ,90 kb regions, present in the twoisolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are codingsequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes inputative virulence and colonization factors.Conclusions/Significance: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts anddiseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer hascontributed to the evolution of drug resistance.
Perkins TT, Kingsley RA, Fookes MC, et al., 2009, A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus <i>Salmonella</i> Typhi, PLOS GENETICS, Vol: 5, ISSN: 1553-7404
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- Citations: 182
Seth-Smith H, Croucher NJ, 2009, Breaking the Ice, NATURE REVIEWS MICROBIOLOGY, Vol: 7, Pages: 328-329, ISSN: 1740-1526
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- Citations: 22
Croucher NJ, Walker D, Romero P, et al., 2009, Role of Conjugative Elements in the Evolution of the Multidrug-Resistant Pandemic Clone <i>Streptococcus pneumoniae</i><SUP>Spain23F</SUP> ST81, JOURNAL OF BACTERIOLOGY, Vol: 191, Pages: 1480-1489, ISSN: 0021-9193
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- Citations: 125
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