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Microbial Genomics

Aldert Zomer, Nao Otsuka, Yukihiro Hiramatsu, Kazunari Kamachi, Naoko Nishimura, Takao Ozaki, Jan Poolman, Jeroen Geurtsen
Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982-2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008-2013...
May 17, 2018: Microbial Genomics
Luisa Berná, Matias Rodriguez, María Laura Chiribao, Adriana Parodi-Talice, Sebastián Pita, Gastón Rijo, Fernando Alvarez-Valin, Carlos Robello
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T...
April 30, 2018: Microbial Genomics
Matthew Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J Sadowsky
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume-rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons...
April 19, 2018: Microbial Genomics
Leonardo T Rosa, Vicki Springthorpe, Matheus E Bianconi, Gavin H Thomas, David J Kelly
Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower...
April 18, 2018: Microbial Genomics
Apostolos Almpanis, Martin Swain, Derek Gatherer, Neil McEwan
Based on complete bacterial genome sequence data, we demonstrate a correlation between bacterial chromosome length and the G+C content of the genome, with longer genomes having higher G+C contents. The correlation value decreases at shorter genome sizes, where there is a wider spread of G+C values. However, although significant (P<0.001), the correlation value (Pearson R=0.58) suggests that other factors also have a significant influence. A similar pattern was seen for plasmids; longer plasmids had higher G+C values, although the large number of shorter plasmids had a wide spread of G+C values...
April 10, 2018: Microbial Genomics
Matthew A Croxen, Tracy D Lee, Robert Azana, Linda M Hoang
Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome...
April 9, 2018: Microbial Genomics
Shivakumara Siddaramappa, Vandana Viswanathan, Saravanamuthu Thiyagarajan, Anushree Narjala
The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C40 carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales...
April 5, 2018: Microbial Genomics
Kathy Raven, Beth Blane, Carol Churcher, Julian Parkhill, Sharon J Peacock
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality...
April 5, 2018: Microbial Genomics
Li Hao, Matthew T G Holden, Xin Wang, Lubomira Andrew, Sabine Wellnitz, Fang Hu, Melissa Whaley, Scott Sammons, Kristen Knipe, Mike Frace, Lucy A McNamara, Paul Liberator, Annaliesa S Anderson
Neisseria meningitidis serogroup B (MnB) was responsible for two independent meningococcal disease outbreaks at universities in the USA during 2013. The first at University A in New Jersey included nine confirmed cases reported between March 2013 and March 2014. The second outbreak occurred at University B in California, with four confirmed cases during November 2013. The public health response to these outbreaks included the approval and deployment of a serogroup B meningococcal vaccine that was not yet licensed in the USA...
April 4, 2018: Microbial Genomics
Hao Chung The, Stephen Baker
Shigella are ranked among the most prevalent aetiologies of diarrhoeal disease worldwide, disproportionately affecting young children in developing countries and high-risk communities in developed settings. Antimicrobial treatment, most commonly with fluoroquinolones, is currently recommended for Shigella infections to alleviate symptoms and control disease transmission. Resistance to fluoroquinolones has emerged in differing Shigella species (S. dysenteriae, flexneri and sonnei) since the turn of the 21st century, originating in endemic areas, and latterly spreading into non-endemic regions...
March 29, 2018: Microbial Genomics
Tomaž Accetto, Nika Janež
In Bacteria, a working consensus of species circumscription may have been reached and one of the most prominent criteria is high average nucleotide identity (ANI). ANI in effect groups strains that may recombine more or less frequently, depending on their biology, as opposed to rare interspecies gene transfer. For bacteriophages, which show various lifestyles, the nature of the fundamental natural unit, if it exists in a biological sense, is not well understood and defined. The approaches based on dot-plots are useful to group similar bacteriophages, yet are not quantitative and use arbitrarily set cut-offs...
March 27, 2018: Microbial Genomics
Vanessa Rew, Piers Mook, Suzan Trienekens, Kate S Baker, Timothy J Dallman, Claire Jenkins, Paul D Crook, Nicholas R Thomson
In December 2013, Public Health England (PHE) observed an increase in the number of cases of Shigella sonnei linked to the Orthodox Jewish Community (OJC). Ultimately, 52 cases of S. sonnei phage type (PT) P and PT7 were notified between November 2013 and July 2014. Whole-genome sequencing (WGS) was performed on a HiSeq 2500 platform (Illumina) on isolates of S. sonnei submitted to PHE during the investigation. Quality trimmed sequence reads were mapped to a reference genome using BWA-MEM, and single-nucleotide polymorphisms (SNPs) were identified using GATK2...
March 27, 2018: Microbial Genomics
Kerri M Malone, Kévin Rue-Albrecht, David A Magee, Kevin Conlon, Olga T Schubert, Nicolas C Nalpas, John A Browne, Alicia Smyth, Eamonn Gormley, Ruedi Aebersold, David E MacHugh, Stephen V Gordon
Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M...
March 20, 2018: Microbial Genomics
Stefanie Lutz, Jenine McCutcheon, James B McQuaid, Liane G Benning
The Arctic is being disproportionally affected by climate change compared with other geographic locations, and is currently experiencing unprecedented melt rates. The Greenland Ice Sheet (GrIS) can be regarded as the largest supraglacial ecosystem on Earth, and ice algae are the dominant primary producers on bare ice surfaces throughout the course of a melt season. Ice-algal-derived pigments cause a darkening of the ice surface, which in turn decreases albedo and increases melt rates. The important role of ice algae in changing melt rates has only recently been recognized, and we currently know little about their community compositions and functions...
March 16, 2018: Microbial Genomics
David Williams, Joanne L Fothergill, Benjamin Evans, Jessica Caples, Sam Haldenby, Martin J Walshaw, Michael A Brockhurst, Craig Winstanley, Steve Paterson
Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the most common strain infecting the UK CF population. Previously we have shown that highly divergent lineages of LES can be found within a single infection, consistent with super-infection among a cross-sectional cohort of patients...
March 16, 2018: Microbial Genomics
Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt
Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing...
March 16, 2018: Microbial Genomics
Mickael Silva, Miguel P Machado, Diogo N Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, João André Carriço
Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers...
March 15, 2018: Microbial Genomics
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J Klemm, Nicholas R Thomson, Jacqueline A Keane
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data...
March 12, 2018: Microbial Genomics
Bruno D'Alessandro, Victoria Pérez Escanda, Lucía Balestrazzi, Andrés Iriarte, Derek Pickard, Lucía Yim, José Alejandro Chabalgoity, Laura Betancor
Salmonella enterica serovar Enteritidis is a major agent of foodborne diseases worldwide. In Uruguay, this serovar was almost negligible until the mid 1990s but since then it has become the most prevalent. Previously, we characterized a collection of strains isolated from 1988 to 2005 and found that the two oldest strains were the most genetically divergent. In order to further characterize these strains, we sequenced and annotated eight genomes including those of the two oldest isolates. We report on the identification and characterization of a novel 44 kbp Salmonella prophage found exclusively in these two genomes...
March 6, 2018: Microbial Genomics
Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H Aliyu, Nazreen F Hadjirin, Mark A Holmes, Estée Török, Nicholas M Brown, Julian Parkhill, Sharon Peacock
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C...
March 2, 2018: Microbial Genomics
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