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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...
September 14, 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...
September 14, 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 12, 2018: Microbial Genomics
Keely A Dulmage, Cynthia L Darnell, Angie Vreugdenhil, Amy K Schmid
Genomic instability, although frequently deleterious, is also an important mechanism for microbial adaptation to environmental change. Although widely studied in bacteria, in archaea the effect of genomic instability on organism phenotypes and fitness remains unclear. Here we use DNA segmentation methods to detect and quantify genome-wide copy number variation (CNV) in large compendia of high-throughput datasets in a model archaeal species, Halobacterium salinarum. CNV hotspots were identified throughout the genome...
August 24, 2018: Microbial Genomics
Luc Cornet, Amandine R Bertrand, Marc Hanikenne, Emmanuelle J Javaux, Annick Wilmotte, Denis Baurain
Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures...
August 23, 2018: Microbial Genomics
David Cleary, Vanessa Devine, Denise Morris, Karen Osman, Rebecca Gladstone, Stephen Bentley, Saul Faust, Stuart Clarke
The implementation of pneumococcal conjugate vaccines (PCVs) has led to a decline in vaccine-type disease. However, there is evidence that the epidemiology of non-typeable Haemophilus influenzae (NTHi) carriage and disease can be altered as a consequence of PCV introduction. We explored the epidemiological shifts in NTHi carriage using whole genome sequencing over a 5-year period that included PCV13 replacement of PCV7 in the UK's National Immunization Programme in 2010. Between 2008/09 and 2012/13 (October to March), nasopharyngeal swabs were taken from children <5 years of age...
August 6, 2018: Microbial Genomics
Catherine Branger, Alice Ledda, Typhaine Billard-Pomares, Benoît Doublet, Stéphanie Fouteau, Valérie Barbe, David Roche, Stéphane Cruveiller, Claudine Médigue, Miguel Castellanos, Dominique Decré, Laurence Drieux-Rouze, Olivier Clermont, Jérémy Glodt, Olivier Tenaillon, Axel Cloeckaert, Guillaume Arlet, Erick Denamur
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs...
August 6, 2018: Microbial Genomics
Marianne Elizabeth Alexandra Clemence, Martin Christopher James Maiden, Odile Barbara Harrison
The genus Neisseria comprises a diverse group of commensal bacteria, which typically colonize the mucosal surfaces of humans and other animals. Neisseria meningitidis, the meningococcus, is notable for its potential to cause invasive meningococcal disease (IMD) in humans; however, IMD is comparatively rare, and meningococci normally colonize the nasopharynx asymptomatically. Possession of a polysaccharide capsule has been shown to be a prerequisite for disease in almost all IMD cases, and was previously considered unique to N...
August 3, 2018: Microbial Genomics
Sion C Bayliss, David W Verner-Jeffreys, David Ryder, Rudy Suarez, Roxana Ramirez, Jaime Romero, Ben Pascoe, Sam K Sheppard, Marcos Godoy, Edward J Feil
Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD), which is a commercially important disease of farmed salmonids. Typing by conventional methods provides limited information on the evolution and spread of this pathogen, as there is a low level of standing variation within the R. salmoninarum population. Here, we apply whole-genome sequencing to 42 R. salmoninarum isolates from Chile, primarily from salmon farms, in order to understand the epidemiology of BKD in this country...
July 24, 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
Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes...
July 23, 2018: Microbial Genomics
Margaret M C Lam, Ryan R Wick, Kelly L Wyres, Claire L Gorrie, Louise M Judd, Adam W J Jenney, Sylvain Brisse, Kathryn E Holt
Mobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria's ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in the opportunistic pathogen Klebsiella pneumoniae, which is a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants in K. pneumoniae include the polyketide synthesis loci ybt and clb (also known as pks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin, respectively...
July 9, 2018: Microbial Genomics
Lennard Epping, Andries J van Tonder, Rebecca A Gladstone, The Global Pneumococcal Sequencing Consortium, Stephen D Bentley, Andrew J Page, Jacqueline A Keane
No abstract text is available yet for this article.
August 2018: Microbial Genomics
Prashant P Patil, Sanjeet Kumar, Samriti Midha, Vikas Gautam, Prabhu B Patil
Stenotrophomonas maltophilia has evolved as one of the leading multidrug-resistant pathogens responsible for a variety of nosocomial infections especially in highly debilitated patients. As information on the genomic and intraspecies diversity of this clinically important pathogen is limited, we sequenced the whole genome of 27 clinical isolates from hospitalized patients. Phylogenomic analysis along with the genomes of type strains suggested that the clinical isolates are distributed over the Stenotrophomonas maltophilia complex (Smc) within the genus Stenotrophomonas...
August 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
The first extensively drug resistant (XDR) Neisseria gonorrhoeae strain with high resistance to the extended-spectrum cephalosporin ceftriaxone was identified in 2009 in Japan, but no other strain with this antimicrobial-resistance profile has been reported since. However, surveillance to date has been based on phenotypic methods and sequence typing, not genome sequencing. Therefore, little is known about the local population structure at the genomic level, and how resistance determinants and lineages are distributed and evolve...
August 2018: Microbial Genomics
Elizabeth A Malinich, Carl E Bauer
Several Gram-negative soil bacteria have the ability to differentiate into dormant cysts when faced with harsh environmental conditions. For example, when challenged with nutrient deprivation or desiccation, the plant-growth-promoting bacterium Azospirillum brasilense differentiates from a replicative and motile rod-shaped vegetative cell into a non-motile dormant spherical cyst. Currently, little is known about either the metabolic differences that exist between vegetative and cyst cell types, or about aspects of cyst physiology that allow dormant cells to survive harsh conditions...
August 2018: Microbial Genomics
Scott V Nguyen, Dayna M Harhay, James L Bono, Timothy P L Smith, Patricia I Fields, Blake A Dinsmore, Monica Santovenia, Rong Wang, Joseph M Bosilevac, Gregory P Harhay
Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources...
August 2018: Microbial Genomics
James Robertson, John H E Nash
Large-scale bacterial population genetics studies are now routine due to cost-effective Illumina short-read sequencing. However, analysing plasmid content remains difficult due to incomplete assembly of plasmids. Bacterial isolates can contain any number of plasmids and assembly remains complicated due to the presence of repetitive elements. Numerous tools have been developed to analyse plasmids but the performance and functionality of the tools are variable. The MOB-suite was developed as a set of modular tools for reconstruction and typing of plasmids from draft assembly data to facilitate characterization of plasmids...
August 2018: Microbial Genomics
Erin P Price, Linda T Viberg, Timothy J Kidd, Scott C Bell, Bart J Currie, Derek S Sarovich
The melioidosis bacterium, Burkholderia pseudomallei, is increasingly being recognised as a pathogen in patients with cystic fibrosis (CF). We have recently catalogued genome-wide variation of paired, isogenic B. pseudomallei isolates from seven Australasian CF cases, which were collected between 4 and 55 months apart. Here, we extend this investigation by documenting the transcriptomic changes in B. pseudomallei in five cases. Following growth in an artificial CF sputum medium, four of the five paired isolates exhibited significant differential gene expression (DE) that affected between 32 and 792 genes...
August 2018: Microbial Genomics
Alison C MacFadyen, Elizabeth A Fisher, Ben Costa, Cassie Cullen, Gavin K Paterson
Species of the genus Macrococcus are widespread commensals of animals but are becoming increasingly recognised as veterinary pathogens. They can encode methicillin resistance and are implicated in its spread to the closely-related, but more pathogenic, staphylococci. In this study we have identified 33 isolates of methicillin-resistant Macrococcus caseolyticus from bovine bulk tank milk from England and Wales. These isolates were characterised to provide insight into the molecular epidemiology of M. caseolyticus and to discern the genetic basis for their methicillin resistance...
August 2018: Microbial Genomics
Hayley Wilson, M Estée Török
Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactamase-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae. In this review, we highlight the mechanisms of resistance and the genomic epidemiology of these organisms, and the impact of AMR.
July 2018: Microbial Genomics
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