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Microbial Genomics

Christophe H Georgescu, Abigail L Manson, Alexander D Griggs, Christopher A Desjardins, Alejandro Pironti, Ilan Wapinski, Thomas Abeel, Brian J Haas, Ashlee M Earl
Accurate orthologue identification is a vital component of bacterial comparative genomic studies, but many popular sequence-similarity-based approaches do not scale well to the large numbers of genomes that are now generated routinely. Furthermore, most approaches do not take gene synteny into account, which is useful information for disentangling paralogues. Here, we present SynerClust, a user-friendly synteny-aware tool based on synergy that can process thousands of genomes. SynerClust was designed to analyse genomes with high levels of local synteny, particularly prokaryotes, which have operon structure...
November 12, 2018: Microbial Genomics
Sruti DebRoy, Xiqi Li, Awdhesh Kalia, Jessica Galloway-Pena, Brittany J Shah, Vance G Fowler, Anthony R Flores, Samuel A Shelburne
Group A Streptococcus (GAS) is classified on the basis of the sequence of the gene encoding the M protein (emm) and the patterns into which emm types are grouped. We discovered a novel emm pattern in emm4 GAS, historically considered pattern E, arising from a fusion event between emm and the adjacent enn gene. We identified the emm-enn fusion event in 51 out of 52 emm4 GAS strains isolated by national surveillance in 2015. GAS isolates with an emm-enn fusion event completely replaced pattern E emm4 strains over a 4-year span in Houston (2013-2017)...
November 9, 2018: Microbial Genomics
Laura M Nolan, Cynthia B Whitchurch, Lars Barquist, Marilyn Katrib, Christine J Boinett, Matthew Mayho, David Goulding, Ian G Charles, Alain Filloux, Julian Parkhill, Amy K Cain
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices...
November 1, 2018: Microbial Genomics
Sergio Arredondo-Alonso, Malbert R C Rogers, Johanna C Braat, Tess D Verschuuren, Janetta Top, Jukka Corander, Rob J L Willems, Anita C Schürch
Assembly of bacterial short-read whole-genome sequencing data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Complete genomes resolved by long-read sequencing can be used to generate and label short-read contigs. These were used to train several popular machine learning methods to classify the origin of contigs from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. We selected support-vector machine (SVM) models as the best classifier for all three bacterial species (F1-score E...
November 1, 2018: Microbial Genomics
Jack Aidley, Joesph J Wanford, Luke R Green, Samuel K Sheppard, Christopher D Bayliss
Hypermutable simple sequence repeats (SSRs) are drivers of phase variation (PV) whose stochastic, high-frequency, reversible switches in gene expression are a common feature of several pathogenic bacterial species, including the human pathogen Campylobacter jejuni. Here we examine the distribution and conservation of known and putative SSR-driven phase variable genes - the phasome - in the genus Campylobacter. PhasomeIt, a new program, was specifically designed for rapid identification of SSR-mediated PV. This program detects the location, type and repeat number of every SSR...
October 23, 2018: Microbial Genomics
Cameron J Reid, Matthew Z DeMaere, Steven P Djordjevic
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described...
October 10, 2018: Microbial Genomics
Kristian Alfsnes, Stephan A Frye, Jens Eriksson, Vegard Eldholm, Ola Brønstad Brynildsrud, Jon Bohlin, Odile B Harrison, Derek W Hood, Martin C J Maiden, Tone Tønjum, Ole Herman Ambur
The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR)...
September 25, 2018: Microbial Genomics
Amy Fleshman, Kristin Mullins, Jason Sahl, Crystal Hepp, Nathan Nieto, Kristin Wiggins, Heidie Hornstra, Daryl Kelly, Teik-Chye Chan, Rattanaphone Phetsouvanh, Sabine Dittrich, Phonepasith Panyanivong, Daniel Paris, Paul Newton, Allen Richards, Talima Pearson
No abstract text is available yet for this article.
October 2018: Microbial Genomics
Sophia David, Massimo Mentasti, Sandra Lai, Lalita Vaghji, Derren Ready, Victoria J Chalker, Julian Parkhill
The diversity of Legionella pneumophila populations within single water systems is not well understood, particularly in those unassociated with cases of Legionnaires' disease. Here, we performed genomic analysis of 235 L. pneumophila isolates obtained from 28 water samples in 13 locations within a large occupational building. Despite regular treatment, the water system of this building is thought to have been colonized by L. pneumophila for at least 30 years without evidence of association with Legionnaires' disease cases...
October 2018: Microbial Genomics
Steven J Dunn, Ben Pascoe, James Turton, Vicki Fleming, Mathew Diggle, Samuel K Sheppard, Alan McNally, Georgina Manning
Campylobacter is the leading cause of bacterial enteritis in the developed world, and infections with the organism are largely sporadic in nature. Links between sporadic cases have not been established, with the majority of infections thought to be caused by genetically distinct isolates. Using a read-mapping approach, 158 clinical isolates collected during 2014 from the greater Nottinghamshire area were analysed to assess the local population structure and investigate potential case linkages between sporadic cases of campylobacteriosis...
October 2018: Microbial Genomics
Michael A Martin, Robyn S Lee, Lauren A Cowley, Jennifer L Gardy, William P Hanage
Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. tuberculosis outbreaks can be extremely limited - making it difficult to determine precisely who transmitted to whom. In addition to consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) has been proposed to improve resolution. However, few studies have examined the potential biases in detecting these hSNPs...
October 2018: Microbial Genomics
Laila Viana Almeida, Anderson Coqueiro-Dos-Santos, Gabriela F Rodriguez-Luiz, Richard McCulloch, Daniella Castanheira Bartholomeu, João Luís Reis-Cunha
Although aneuploidy usually results in severe abnormalities in multicellular eukaryotes, recent data suggest that it could be beneficial for unicellular eukaryotes, such as yeast and trypanosomatid parasites, providing increased survival under stressful conditions. Among characterized trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the genus Leishmania stand out due to their importance in public health, infecting around 20 million people worldwide. The presence of aneuploidies in T...
October 2018: Microbial Genomics
Charlotte J Houldcroft, Mathew A Beale, Md Abu Sayeed, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Novel adenovirus genotypes are associated with outbreaks of disease, such as acute gastroenteritis, renal disease, upper respiratory tract infection and keratoconjunctivitis. Here, we identify novel and variant adenovirus genotypes in children coinfected with enterotoxigenic Escherichia coli, in Bangladesh. Metagenomic sequencing of stool was performed and whole adenovirus genomes were extracted. A novel species D virus, designated genotype 90 (P33H27F67) was identified, and the partial genome of a putative recombinant species B virus was recovered...
October 2018: Microbial Genomics
David R Greig, Timothy J Dallman, Katie L Hopkins, Claire Jenkins
The aim of this study was to use single-molecule, nanopore sequencing to explore the genomic environment of the resistance determinants in a multidrug-resistant (MDR) strain of enteroaggregative Escherichia coli serotype O51 : H30, sequence type (ST) 38. Sequencing was performed on the MinION Flow cell MIN-106 R9.4. Nanopore raw FAST5 reads were base-called using Albacore v1.2.1, converted to FASTA and FASTQ formats using Poretools v0.6.0, and assembled using Unicycler v0.4.2, combining the long-read sequencing data with short-read data produced by Illumina sequencing...
October 2018: Microbial Genomics
Diepreye Ayabina, Janne O Ronning, Kristian Alfsnes, Nadia Debech, Ola B Brynildsrud, Trude Arnesen, Gunnstein Norheim, Anne-Torunn Mengshoel, Rikard Rykkvin, Ulf R Dahle, Caroline Colijn, Vegard Eldholm
In many countries the incidence of tuberculosis (TB) is low and is largely shaped by immigrant populations from high-burden countries. This is the case in Norway, where more than 80 % of TB cases are found among immigrants from high-incidence countries. A variable latent period, low rates of evolution and structured social networks make separating import from within-border transmission a major conundrum to TB control efforts in many low-incidence countries. Clinical Mycobacterium tuberculosis isolates belonging to an unusually large genotype cluster associated with people born in the Horn of Africa have been identified in Norway over the last two decades...
October 2018: Microbial Genomics
Javier Rodríguez Hernáez, Maria Esperanza Cerón Cucchi, Silvio Cravero, Maria Carolina Martinez, Sergio Gonzalez, Andrea Puebla, Joaquin Dopazo, Marisa Farber, Norma Paniego, Máximo Rivarola
Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology...
October 2018: Microbial Genomics
Hayley Wilson, M Estée Török
No abstract text is available yet for this article.
September 2018: Microbial Genomics
Koji Yahara, Shu-Ichi Nakayama, Ken Shimuta, Ken-Ichi Lee, Masatomo Morita, Takuya Kawahata, Toshiro Kuroki, Yuko Watanabe, Hitomi Ohya, Mitsuru Yasuda, Takashi Deguchi, Xavier Didelot, Makoto Ohnishi
No abstract text is available yet for this article.
September 2018: Microbial Genomics
G Royer, J W Decousser, C Branger, M Dubois, C Médigue, E Denamur, D Vallenet
Plasmid prediction may be of great interest when studying bacteria of medical importance such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing Enterobacteriaceae. Several tools are now available to explore the 'plasmidome' from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity...
September 2018: Microbial Genomics
Eva Heinz
Haemophilus influenzae, originally named Pfeiffer's bacillus after its discoverer Richard Pfeiffer in 1892, was a major risk for global health at the beginning of the 20th century, causing childhood pneumonia and invasive disease as well as otitis media and other upper respiratory tract infections. The implementation of the Hib vaccine, targeting the major capsule type of H. influenzae, almost eradicated the disease in countries that adapted the vaccination scheme. However, a rising number of infections are caused by non-typeable H...
September 2018: Microbial Genomics
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