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Microbial Genomics

Christine J Boinett, Amy K Cain, Jane Hawkey, Nhu Tran Do Hoang, Nhu Nguyen Thi Khanh, Duy Pham Thanh, Janina Dordel, James I Campbell, Nguyen Phu Huong Lan, Matthew Mayho, Gemma C Langridge, James Hadfield, Nguyen Van Vinh Chau, Guy E Thwaites, Julian Parkhill, Nicholas R Thomson, Kathryn E Holt, Stephen Baker
The increasing incidence and emergence of multi-drug resistant (MDR) Acinetobacter baumannii has become a major global health concern. Colistin is a historic antimicrobial that has become commonly used as a treatment for MDR A. baumannii infections. The increase in colistin usage has been mirrored by an increase in colistin resistance. We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A...
February 5, 2019: Microbial Genomics
Susannah J Salter, Paul Scott, Andrew J Page, Alan Tracey, Marcus C de Goffau, Claire Cormie, Bernardo Ochoa-Montaño, Clare L Ling, Jiraporn Tangmanakit, Paul Turner, Julian Parkhill
'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization...
February 5, 2019: Microbial Genomics
Charley G P McCarthy, David A Fitzpatrick
The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var...
February 4, 2019: Microbial Genomics
Leonor Sánchez-Busó, Simon R Harris
Gonorrhoea infections are on the increase and strains that are resistant to all antimicrobials used to treat the disease have been found worldwide. These observations encouraged the World Health Organization to include Neisseria gonorrhoeae on their list of high-priority organisms in need of new treatments. Fortunately, concurrent resistance to both antimicrobials used in dual therapy is still rare. The fight against antimicrobial resistance (AMR) must begin from an understanding of how it evolves and spreads in sexual networks...
January 30, 2019: Microbial Genomics
Max L Cummins, Cameron J Reid, Piklu Roy Chowdhury, Rhys N Bushell, Nicolas Esbert, Kelly A Tivendale, Amir H Noormohammadi, Shaiful Islam, Marc S Marenda, Glenn F Browning, Philip F Markham, Steven P Djordjevic
Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently...
January 23, 2019: Microbial Genomics
Joseph Crispell, Daniel Balaz, Stephen Vincent Gordon
A homoplasy is a nucleotide identity resulting from a process other than inheritance from a common ancestor. Importantly, by distorting the ancestral relationships between nucleotide sequences, homoplasies can change the structure of the phylogeny. Homoplasies can emerge naturally, especially under high selection pressures and/or high mutation rates, or be created during the generation and processing of sequencing data. Identification of homoplasies is critical, both to understand their influence on the analyses of phylogenetic data and to allow an investigation into how they arose...
January 21, 2019: Microbial Genomics
Aleisha Reimer, Kelly Weedmark, Aaron Petkau, Christy-Lynn Peterson, Matthew Walker, Natalie Knox, Heather Kent, Philip Mabon, Chrystal Berry, Shaun Tyler, Lorelee Tschetter, Morganne Jerome, Vanessa Allen, Linda Hoang, Sadjia Bekal, Clifford Clark, Celine Nadon, Gary Van Domselaar, Franco Pagotto, Morag Graham, Jeff Farber, Matthew Gilmour
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008...
January 16, 2019: Microbial Genomics
Mohammad Hamidian, Jane Hawkey, Ryan Wick, Kathryn E Holt, Ruth M Hall
Resistance to carbapenem and aminoglycoside antibiotics is a critical problem in Acinetobacter baumannii, particularly when genes conferring resistance are acquired by multiply or extensively resistant members of successful globally distributed clonal complexes, such as global clone 1 (GC1) . Here, we investigate the evolution of an expanding clade of lineage 1 of the GC1 complex via repeated acquisition of carbapenem- and aminoglycoside-resistance genes. Lineage 1 arose in the late 1970s and the Tn6168/OCL3 clade arose in the late 1990s from an ancestor that had already acquired resistance to third-generation cephalosporins and fluoroquinolones...
January 16, 2019: Microbial Genomics
Marie Anne Chattaway, Nastassya Chandra, Anaïs Painset, Victoria Shah, Peter Lamb, Elsie Acheampong, Janice Lo, Bharat Patel, Lesley Larkin, Martin Sergeant, Martin Cormican, Eva Litrup, Paul Crook
In 2017, an outbreak of gastroenteritis in England attributed to Salmonella Adjame was detected and investigated. With the introduction of whole genome sequencing (WGS) for microbial typing, methods for comparing international outbreak data require evaluation. A case was defined as a person resident in England with a clinical sample from 1 June 2017 to 27 July 2017 from whom S. Adjame was isolated. Cases were interviewed and exposures analysed. Backward tracing of food provenance was undertaken. WGS was performed on isolates from cases and historical isolates and compared using Public Health England's SnapperDB high-quality SNP pipeline and Enterobase's Salmonella core genome multi-locus sequence typing (cgMLST) scheme...
January 16, 2019: Microbial Genomics
Lauren Elisabeth Brooks, Mo Kaze, Mark Sistrom
Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database...
January 9, 2019: Microbial Genomics
James Doonan, Sandra Denman, Justin A Pachebat, James E McDonald
The UK's native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom of AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria goodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additional bacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their role in tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissue necrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in the aetiology of AOD...
January 8, 2019: Microbial Genomics
Robert Söderlund, Mikhayil Hakhverdyan, Anna Aspán, Eva Jansson
The pathogen Flavobacterium psychrophilum is a major problem for the expanding salmonid fish farming industry in Sweden as well as worldwide. A better understanding of the phylogeography and infection routes of F. psychrophilum outbreaks could help to improve aquaculture profitability and the welfare of farmed fish while reducing the need for antibiotics. In the present study, high-throughput genome sequencing was applied to a collection of F. psychrophilum isolates (n=38) from outbreaks on fish farms in different regions of Sweden between 1988 and 2016...
December 13, 2018: Microbial Genomics
Tanya Parish, Mark Harris, Norman Fry, Kalai Mathee, Martha E Trujillo, Stephen Bentley, Nicholas Thomson
No abstract text is available yet for this article.
December 5, 2018: Microbial Genomics
Anna E Sheppard, Nicole Stoesser, Ian German-Mesner, Kasi Vegesana, A Sarah Walker, Derrick W Crook, Amy J Mathers
Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic-resistance genes...
November 22, 2018: Microbial Genomics
Khalil Abudahab, Joaquín M Prada, Zhirong Yang, Stephen D Bentley, Nicholas J Croucher, Jukka Corander, David M Aanensen
The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm...
November 22, 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
No abstract text is available yet for this article.
January 2019: Microbial Genomics
Yasuhiro Gotoh, Takako Taniguchi, Dai Yoshimura, Keisuke Katsura, Yuji Saeki, Yasutoshi Hirabara, Mayumi Fukuda, Ichiro Takajo, Junko Tomida, Yoshiaki Kawamura, Yoshitoshi Ogura, Takehiko Itoh, Naoaki Misawa, Akihiko Okayama, Tetsuya Hayashi
Helicobacter cinaedi is an emerging pathogen causing bacteraemia and cellulitis. Nosocomial transmission of this microbe has been described, but detailed molecular-epidemiological analyses have not been performed. Here, we describe the results of a multi-step genome-wide phylogenetic analysis of a suspected intra-hospital outbreak of H. cinaedi that occurred in a hospital in Japan. The outbreak was recognized by the infectious control team (ICT) of the hospital as a sudden increase in H. cinaedi bacteraemia...
December 2018: Microbial Genomics
Natalie Ring, Jonathan S Abrahams, Miten Jain, Hugh Olsen, Andrew Preston, Stefan Bagby
The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run...
November 2018: Microbial Genomics
Anna Johnning, Nahid Karami, Erika Tång Hallbäck, Vilhelm Müller, Lena Nyberg, Mariana Buongermino Pereira, Callum Stewart, Tobias Ambjörnsson, Fredrik Westerlund, Ingegerd Adlerberth, Erik Kristiansson
Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing...
November 2018: 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 2018: Microbial Genomics
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