Zhao, Huizhang Zhou, Ting Xie, Jiatao Cheng, Jiasen Chen, Tao Jiang, Daohong Fu, Yanping
Published in
Microbial Genomics
Coniothyrium minitans is a mycoparasite of the notorious plant pathogen Sclerotinia sclerotiorum . To further understand the parasitism of C. minitans , we assembled and analysed its genome and performed transcriptome analyses. The genome of C. minitans strain ZS-1 was assembled into 350 scaffolds and had a size of 39.8 Mb. A total of 11 437 predic...
Mendes, Catarina I. Lizarazo, Erley Machado, Miguel P. Silva, Diogo N. Tami, Adriana Ramirez, Mário Couto, Natacha Rossen, John W. A. Carriço, João A.
Published in
Microbial Genomics
Dengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (sh...
Lobb, Briallen Tremblay, Benjamin Jean-Marie Moreno-Hagelsieb, Gabriel Doxey, Andrew C.
Published in
Microbial Genomics
Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated...
Omaleki, Lida Blackall, Patrick J. Cuddihy, Thom Beatson, Scott A. Forde, Brian M. Turni, Conny
Published in
Microbial Genomics
Fowl cholera, caused by Pasteurella multocida, continues to be a challenge in meat-chicken-breeder operations and has emerged as a problem for free-range meat chickens. Here, using whole-genome sequencing (WGS) and phylogenomic analysis, we investigate isolate relatedness during outbreaks of fowl cholera on a free-range meat chicken farm over a 5-y...
Wyres, Kelly L. Cahill, Sarah M. Holt, Kathryn E. Hall, Ruth M. Kenyon, Johanna J.
Published in
Microbial Genomics
Multiply antibiotic-resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological mark...
Marques, Andreia T. Vítor, Jorge M. B. Santos, Andrea Oleastro, Mónica Vale, Filipa F.
Published in
Microbial Genomics
For a long time Helicobacter pylori infections have been treated using the macrolide antibiotic, clarithromycin. Clarithromycin resistance is increasing worldwide and is the most common cause of H. pylori treatment failure. Here we review the mechanisms of antibiotic resistance to clarithromycin, detailing the individual and combinations of point m...
Fong, Winkie Rockett, Rebecca Timms, Verlaine Sintchenko, Vitali
Published in
Microbial Genomics
Bordetella pertussis , the aetiological agent of whooping cough, is re-emerging globally despite widespread vaccination. B. pertussis is highly infectious and, prior to vaccination programmes, was the leading cause of infant mortality. The WHO estimated that over 600 000 deaths are prevented annually by pertussis vaccination, but B. pertussis infec...
Coipan, Claudia E. Dallman, Timothy J. Brown, Derek Hartman, Hassan van der Voort, Menno van den Berg, Redmar R. Palm, Daniel Kotila, Saara van Wijk, Tom Franz, Eelco
...
Published in
Microbial Genomics
A large European multi-country Salmonella enterica serovar Enteritidis outbreak associated with Polish eggs was characterized by whole-genome sequencing (WGS)-based analysis, with various European institutes using different analysis workflows to identify isolates potentially related to the outbreak. The objective of our study was to compare the out...
Saber, Morteza M. Shapiro, B. Jesse
Published in
Microbial Genomics
Genome-wide association studies (GWASs) have the potential to reveal the genetics of microbial phenotypes such as antibiotic resistance and virulence. Capitalizing on the growing wealth of bacterial sequence data, microbial GWAS methods aim to identify causal genetic variants while ignoring spurious associations. Bacteria reproduce clonally, leadin...
Yara, Daniel A. Greig, David R. Gally, David L. Dallman, Timothy J. Jenkins, Claire
Published in
Microbial Genomics
Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983–1995, Ia, I/IIa and I/IIb; 1996–2014, Ic; and 2015–2018, IIb). The acquisition of a stx2a -encoding bacteriophage by these five sub-lineages app...
