-
Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Cerith Jones, Gordon Webster, Alex J. Mullins, Matthew Jenner, Matthew J. Bull, Yousef Dashti, Theodore Spilker, Julian Parkhill, Thomas R. Connor, John J. LiPuma, Gregory L. Challis and Eshwar Mahenthiralingam
Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective
-
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Kara K. Tsang, Finlay Maguire, Haley L. Zubyk, Sommer Chou, Arman Edalatmand, Gerard D. Wright, Robert G. Beiko and Andrew G. McArthur
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia
-
ActDES – a curated Actinobacterial Database for Evolutionary Studies Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Jana K. Schniete, Nelly Selem-Mojica, Anna S. Birke, Pablo Cruz-Morales, Iain S. Hunter, Francisco Barona-Gomez and Paul A. Hoskisson
Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large
-
Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Jo Hendrix, L. Elaine Epperson, David Durbin, Jennifer R. Honda and Michael Strong
Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium , many of the less common
-
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 James R. Knight, Eileen M. Dunne, E. Kim Mulholland, Sudipta Saha, Catherine Satzke, Adrienn Tothpal and Daniel M. Weinberger
Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and in the development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software
-
Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Swapnil Tichkule, Aaron R. Jex, Cock van Oosterhout, Anna Rosa Sannella, Ralf Krumkamp, Cassandra Aldrich, Oumou Maiga-Ascofare, Denise Dekker, Maike Lamshöft, Joyce Mbwana, Njari Rakotozandrindrainy, Steffen Borrmann, Thorsten Thye, Kathrin Schuldt, Doris Winter, Peter G. Kremsner, Kwabena Oppong, Prince Manouana, Mirabeau Mbong, Samwel Gesase, Daniel T. R. Minja, Ivo Mueller, Melanie Bahlo, Johanna
Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive
-
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly K.W. Yuen, Nadia Warner, Brigid Betz-Stablein, Fabio Luciani, Peter A. Revill and Chris M. Brown
Hepatitis B virus (HBV) is a major human pathogen that causes liver diseases. The main HBV RNAs are unspliced transcripts that encode the key viral proteins. Recent studies have shown that some of the HBV spliced transcript isoforms are predictive of liver cancer, yet the roles of these spliced transcripts remain elusive. Furthermore, there are nine major HBV genotypes common in different regions of
-
Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Stefanie Lüth, Carlus Deneke, Sylvia Kleta and Sascha Al Dahouk
Where classical epidemiology has proven to be inadequate for surveillance and control of foodborne pathogens, molecular epidemiology, using genomic typing methods, can add value. However, the analysis of whole genome sequencing (WGS) data varies widely and is not yet fully harmonised. We used genomic data on 494 Listeria monocytogenes isolates from ready-to-eat food products and food processing environments
-
Genomic epidemiology of Escherichia coli isolates from a tertiary referral center in Lilongwe, Malawi Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Gerald Tegha, Emily J. Ciccone, Robert Krysiak, James Kaphatika, Tarsizio Chikaonda, Isaac Ndhlovu, David van Duin, Irving Hoffman, Jonathan J. Juliano and Jeremy Wang
Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. The highly drug resistant Escherichia coli sequence type (ST) 131, which is associated with the extended spectrum
-
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ravi, Nicholas M. Thomson, Sheikh Jarju, Brenda A. Kwambana-Adams, Arss Secka, Justin O’Grady, Martin Antonio and Mark John Pallen
Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These
-
Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage Microb. Genom. (IF 4.632) Pub Date : 2021-01-01 Alex Remmington, Samuel Haywood, Julia Edgar, Luke R. Green, Thushan de Silva and Claire E. Turner
The major human pathogen Streptococcus pyogenes shares an intimate evolutionary history with mobile genetic elements, which in many cases carry genes encoding bacterial virulence factors. During recent whole-genome sequencing of a longitudinal sample of S. pyogenes isolates in England, we identified a lineage within emm4 that clustered with the reference genome MEW427. Like MEW427, this lineage was
-
Fundamental differences in physiology of Bordetella pertussis dependent on the two-component system Bvg revealed by gene essentiality studies Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Thomas Belcher, Iain MacArthur, Jerry D. King, Gemma C. Langridge, Matthew Mayho, Julian Parkhill and Andrew Preston
The identification of genes essential for a bacterium’s growth reveals much about its basic physiology under different conditions. Bordetella pertussis , the causative agent of whooping cough, adopts both virulent and avirulent states through the activity of the two-component system, Bvg. The genes essential for B. pertussis growth in vitro were defined using transposon sequencing, for different Bvg-determined
-
Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Siew Woh Choo, Shusruto Rishik and Wei Yee Wee
Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum . Phylogenetic
-
Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Janetta Top, Sergio Arredondo-Alonso, Anita C. Schürch, Santeri Puranen, Maiju Pesonen, Johan Pensar, Rob J. L. Willems and Jukka Corander
Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here we further explored
-
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Emilie Lefoulon, Travis Clark, Ricardo Guerrero, Israel Cañizales, Jorge Manuel Cardenas-Callirgos, Kerstin Junker, Nathaly Vallarino-Lhermitte, Benjamin L. Makepeace, Alistair C. Darby, Jeremy M. Foster, Coralie Martin and Barton E. Slatko
Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia ‘species’
-
Molecular insights into meningococcal carriage isolates from Burkina Faso 7 years after introduction of a serogroup A meningococcal conjugate vaccine Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Nadav Topaz, Paul Arne Kristiansen, Susanna Schmink, Malika Congo-Ouédraogo, Dinanibè Kambiré, Sarah Mbaeyi, Marietou Paye, Mahamoudou Sanou, Lassana Sangaré, Rasmata Ouédraogo and Xin Wang
In 2010, Burkina Faso completed the first nationwide mass-vaccination campaign of a meningococcal A conjugate vaccine, drastically reducing the incidence of disease caused by serogroup A meningococci. Since then, other strains, such as those belonging to serogroups W, X and C, have continued to cause outbreaks within the region. A carriage study was conducted in 2016 and 2017 in the country to characterize
-
Chronic cigarette smoke exposure and pneumococcal infection induce oropharyngeal microbiota dysbiosis and contribute to long-lasting lung damage in mice Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Markus Hilty, Tsering M. Wüthrich, Aurélie Godel, Roberto Adelfio, Susanne Aebi, Sabrina S. Burgener, Brunhilde Illgen-Wilcke and Charaf Benarafa
Environmental factors, such as cigarette smoking or lung infections, may influence chronic obstructive pulmonary disease (COPD) progression by modifying the respiratory tract microbiome. However, whether the disease itself induces or maintains dysbiosis remains undefined. In this longitudinal study, we investigated the oropharyngeal microbiota composition and disease progression of mice (in cages of
-
NonClasGP-Pred: robust and efficient prediction of non-classically secreted proteins by integrating subset-specific optimal models of imbalanced data Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Chao Wang, Jin Wu, Lei Xu and Quan Zou
Non-classically secreted proteins (NCSPs) are proteins that are located in the extracellular environment, although there is a lack of known signal peptides or secretion motifs. They usually perform different biological functions in intracellular and extracellular environments, and several of their biological functions are linked to bacterial virulence and cell defence. Accurate protein localization
-
Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Magnus N. Osnes, Xavier Didelot, Jolinda de Korne-Elenbaas, Kristian Alfsnes, Ola B. Brynildsrud, Gaute Syversen, Øivind Jul Nilsen, Birgitte Freiesleben De Blasio, Dominique A. Caugant and Vegard Eldholm
Neisseria gonorrhoeae multilocus sequence type (ST)-7827 emerged in a dramatic fashion in Norway in the period 2016–2018. Here, we aim to shed light on the provenance and expansion of this ST. ST-7827 was found to be polyphyletic, but the majority of members belonged to a monophyletic clade we termed PopPUNK cluster 7827 (PC-7827). In Norway, both PC-7827 and ST-7827 isolates were almost exclusively
-
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Marina Muñoz, Enzo Guerrero-Araya, Catalina Cortés-Tapia, Angela Plaza-Garrido, Trevor D. Lawley and Daniel Paredes-Sabja
Sellimonas intestinalis is a Gram-positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who have recovered from intestinal homeostasis after dysbiosis events. In this context, the aim of the present study was to take advantage of a massive in vitro culture
-
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Dmitriy Li, Cameron J. Reid, Timothy Kudinha, Veronica M. Jarocki and Steven P. Djordjevic
Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here
-
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Katlego Kopotsa, Nontombi M. Mbelle and John Osei Sekyere
Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic
-
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 M. Hong Nguyen, Drishti Kaul, Carlene Muto, Shaoji J. Cheng, R. Alex Richter, Vincent M. Bruno, Guojun Liu, Sinem Beyhan, Alexander J. Sundermann, Stephanie Mounaud, A. William Pasculle, William C. Nierman, Eileen Driscoll, Richard Cumbie, Cornelius J. Clancy and Christopher L. Dupont
Mucormycoses are invasive infections by Rhizopus species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to Rhizopus microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at a median 31.5 days (range: 13–34) post-admission. We performed whole genome sequencing (WGS) on 72 Mucorales isolates (45 R. arrhizus,
-
Complete microbial genomes for public health in Australia and the Southwest Pacific Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Sarah L. Baines, Anders Gonçalves da Silva, Glen P. Carter, Amy Jennison, Irani Rathnayake, Rikki M. Graham, Vitali Sintchenko, Qinning Wang, Rebecca J. Rockett, Verlaine J. Timms, Elena Martinez, Susan Ballard, Takehiro Tomita, Nicole Isles, Kristy A. Horan, William Pitchers, Timothy P. Stinear, Deborah A. Williamson, Benjamin P. Howden, Torsten Seemann and Communicable Diseases Genomics Network (CDGN)
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete
-
Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Anish Pandey, Maria Victoria Humbert, Alexandra Jackson, Jade L. Passey, David J. Hampson, David W. Cleary, Roberto M. La Ragione and Myron Christodoulides
The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively
-
Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7 Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Alexander Bolotin, Benoit Quinquis, Hugo Roume, Michel Gohar, Didier Lereclus and Alexei Sorokin
Bacillus thuringiensis serovar israelensis is the most widely used natural biopesticide against mosquito larvae worldwide. Its lineage has been actively studied and a plasmid-free strain, B . thuringiensis serovar israelensis BGSC 4Q7 (4Q7), has been produced. Previous sequencing of the genome of this strain has revealed the persistent presence of a 235 kb extrachromosomal element, pBtic235, which
-
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019 Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Lingzi Xiaoli, Eileen Benoliel, Yanhui Peng, Janessa Aneke, Pamela K. Cassiday, Meagan Kay, Shelly McKeirnan, Jeffery S. Duchin, Vance Kawakami, Scott Lindquist, Anna M. Acosta, Chas DeBolt, Maria Lucia Tondella and Michael R. Weigand
Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated
-
Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Chulwoo Park, Bora Shin, Wonjae Kim, Hoon Cheong, Soyoon Park and Woojun Park
Deinococcus metallilatus MA1002 was exposed to ultraviolet radiation to generate mutants with enhanced biofilm production. Two strains (nos 5 and 6) were then selected based on their high biofilm formation, as well as their possession of higher concentrations of extracellular matrix components (eDNA, protein and saccharides) than the wild-type (WT). Genomic sequencing revealed the presence of large
-
Read trimming has minimal effect on bacterial SNP-calling accuracy Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Stephen J. Bush
Read alignment is the central step of many analytic pipelines that perform variant calling. To reduce error, it is common practice to pre-process raw sequencing reads to remove low-quality bases and residual adapter contamination, a procedure collectively known as ‘trimming’. Trimming is widely assumed to increase the accuracy of variant calling, although there are relatively few systematic evaluations
-
Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12. Microb. Genom. (IF 4.632) Pub Date : 2020-12-01 Lin Zhao,Hongyou Chen,Xavier Didelot,Zhenpeng Li,Yinghui Li,Meiling Chen,Yu Du,Hongqun Zhao,Jie Li,Qinghua Hu,Biao Kan,Min Chen,Bo Pang
Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has
-
Hogwash: three methods for genome-wide association studies in bacteria Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Katie Saund and Evan S. Snitkin
Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence-based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three
-
A comprehensive human minimal gut metagenome extends the host’s metabolic potential Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Marcos Parras-Moltó and Daniel Aguirre de Cárcer
Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study
-
Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Benjamin Mubemba, Jan F. Gogarten, Verena J. Schuenemann, Ariane Düx, Alexander Lang, Kathrin Nowak, Kamilla Pléh, Ella Reiter, Markus Ulrich, Anthony Agbor, Gregory Brazzola, Tobias Deschner, Paula Dieguez, Anne-Céline Granjon, Sorrel Jones, Jessica Junker, Erin Wessling, Mimi Arandjelovic, Hjalmar Kuehl, Roman M. Wittig, Fabian H. Leendertz and Sébastien Calvignac-Spencer
Many non-human primate species in sub-Saharan Africa are infected with Treponema pallidum subsp. pertenue , the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while T. pallidum subsp. pallidum causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other
-
Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Danae M. Suchan, Jordyn Bergsveinson, Lori Manzon, Alexa Pierce, Yuriy Kryachko, Darren Korber, Yifang Tan, Dinah D. Tambalo, Nurul H. Khan, Michael Whiting and Christopher K. Yost
The plant growth-promoting rhizobacterium Delftia acidovorans RAY209 is capable of establishing strong root attachment during early plant development at 7 days post-inoculation. The transcriptional response of RAY209 was measured using RNA-seq during early (day 2) and sustained (day 7) root colonization of canola plants, capturing RAY209 differentiation from a medium-suspended cell state to a strongly
-
Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Maxim Prokchorchik, Ankita Pandey, Hayoung Moon, Wanhui Kim, Hyelim Jeon, Gayoung Jung, Jay Jayaraman, Stephen Poole, Cécile Segonzac, Kee Hoon Sohn and Honour C. McCann
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) threatens the cultivation of important crops worldwide. We sequenced 30 RSSC phylotype I ( R. pseudosolanacearum ) strains isolated from pepper (Capsicum annuum) and tomato (Solanum lycopersicum) across the Republic of Korea. These isolates span the diversity of phylotype I, have extensive effector repertoires and are subject
-
In silico analysis of the chemotactic system of Agrobacterium tumefaciens Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Nan Xu, Mingqi Wang, Xiaojing Yang, Yujuan Xu and Minliang Guo
Agrobacterium tumefaciens is an efficient tool for creating transgenic host plants. The first step in the genetic transformation process involves A. tumefaciens chemotaxis, which is crucial to the survival of A. tumefaciens in changeable, harsh and even contaminated soil environments. However, a systematic study of its chemotactic signalling pathway is still lacking. In this study, the distribution
-
Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Zhencheng Fang and Hongwei Zhou
Plasmids are the key element in horizontal gene transfer in the microbial community. Recently, a large number of experimental and computational methods have been developed to obtain the plasmidomes of microbial communities. Distinguishing transmissible plasmid sequences, which are derived from conjugative or at least mobilizable plasmids, from non-transmissible plasmid sequences in the plasmidome is
-
Functional genomics reveals the toxin–antitoxin repertoire and AbiE activity in Serratia Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Hannah G. Hampton, Leah M. Smith, Shaun Ferguson, Sean Meaden, Simon A. Jackson and Peter C. Fineran
Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin–antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to ‘shut down’,
-
Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Fang Liu, Siying Chen, Laurence Don Wai Luu, Seul A. Lee, Alfred Chin Yen Tay, Ruochen Wu, Stephen M. Riordan, Ruiting Lan, Lu Liu and Li Zhang
Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity
-
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Eleonora Tassinari, Matt Bawn, Gaetan Thilliez, Oliver Charity, Luke Acton, Mark Kirkwood, Liljana Petrovska, Timothy Dallman, Catherine M. Burgess, Neil Hall, Geraldine Duffy and Robert A. Kingsley
Epidemic and pandemic clones of bacterial pathogens with distinct characteristics continually emerge, replacing those previously dominant through mechanisms that remain poorly characterized. Here, whole-genome-sequencing-powered epidemiology linked horizontal transfer of a virulence gene, sopE, to the emergence and clonal expansion of a new epidemic Salmonella enterica serovar Typhimurium (S. Typhimurium)
-
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Fanny Berglund, Maria-Elisabeth Böhm, Anton Martinsson, Stefan Ebmeyer, Tobias Österlund, Anna Johnning, D. G. Joakim Larsson and Erik Kristiansson
Tetracyclines are broad-spectrum antibiotics used to prevent or treat a variety of bacterial infections. Resistance is often mediated through mobile resistance genes, which encode one of the three main mechanisms: active efflux, ribosomal target protection or enzymatic degradation. In the last few decades, a large number of new tetracycline-resistance genes have been discovered in clinical settings
-
Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Hélène Gingras, Kévin Patron, Philippe Leprohon and Marc Ouellette
We report on the combination of chemical mutagenesis, azithromycin selection and next-generation sequencing (Mut-Seq) for the identification of small nucleotide variants that decrease the susceptibility of Streptococcus pneumoniae to the macrolide antibiotic azithromycin. Mutations in the 23S ribosomal RNA or in ribosomal proteins can confer resistance to macrolides and these were detected by Mut-Seq
-
Optimized use of Oxford Nanopore flowcells for hybrid assemblies Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Samuel Lipworth, Hayleah Pickford, Nicholas Sanderson, Kevin K. Chau, James Kavanagh, Leanne Barker, Alison Vaughan, Jeremy Swann, Monique Andersson, Katie Jeffery, Marcus Morgan, Timothy E. A. Peto, Derrick W. Crook, Nicole Stoesser and A. Sarah Walker
Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The widespread application of this technique is currently primarily limited by cost. Recent data have suggested
-
The glycan alphabet is not universal: a hypothesis Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Jaya Srivastava, P. Sunthar and Petety V. Balaji
Several monosaccharides constitute naturally occurring glycans, but it is uncertain whether they constitute a universal set like the alphabets of proteins and DNA. Based on the available experimental observations, it is hypothesized herein that the glycan alphabet is not universal. Data on the presence/absence of pathways for the biosynthesis of 55 monosaccharides in 12 939 completely sequenced archaeal
-
Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Henry Secaira-Morocho, José A. Castillo and Adam Driks
Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly
-
Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Yuanwei Xu, Jessica E. Stockdale, Vijay Naidu, Hollie Hatherell, James Stimson, Helen R. Stagg, Ibrahim Abubakar and Caroline Colijn
Outbreaks of tuberculosis (TB) – such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 – provide excellent opportunities to model transmission of this devastating disease. Transmission chains for TB are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential to contribute to
-
Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Anna Janowicz, Fabrizio De Massis, Katiuscia Zilli, Massimo Ancora, Manuela Tittarelli, Flavio Sacchini, Elisabetta Di Giannatale, Jason W. Sahl, Jeffrey T. Foster and Giuliano Garofolo
Ovine and caprine brucellosis, caused by Brucella melitensis , is one of the world’s most widespread zoonoses and is a major cause of economic losses in domestic ruminant production. In Italy, the disease remains endemic in several southern provinces, despite an ongoing brucellosis eradication programme. In this study, we used whole-genome sequencing to detail the genetic diversity of circulating strains
-
Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim. Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Miquel Sánchez-Osuna,Pilar Cortés,Montserrat Llagostera,Jordi Barbé,Ivan Erill
Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydropteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants
-
Ancestral state reconstruction of metabolic pathways across pangenome ensembles. Microb. Genom. (IF 4.632) Pub Date : 2020-11-01 Fotis E Psomopoulos,Jacques van Helden,Claudine Médigue,Anastasia Chasapi,Christos A Ouzounis
As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny. Elaborate approaches for the reconstruction of ancestral states
-
Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Sandra Janezic, Kate Dingle, Joseph Alvin, Tomaž Accetto, Xavier Didelot, Derrick W. Crook, D. Borden Lacy and Maja Rupnik
Clostridioides difficile is a common cause of nosocomial diarrhoea. Toxins TcdA and TcdB are considered to be the main virulence factors and are encoded by the PaLoc region, while the binary toxin encoded in the CdtLoc region also contributes to pathogenicity. Variant toxinotypes reflect the genetic diversity of a key toxin-encoding 19 kb genetic element (the PaLoc). Here, we present analysis of a
-
Genomic instability in an interspecific hybrid of the genus Saccharomyces: a matter of adaptability Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Miguel Morard, Clara Ibáñez, Ana C. Adam, Amparo Querol, Eladio Barrio and Christina Toft
Ancient events of polyploidy have been linked to huge evolutionary leaps in the tree of life, while increasing evidence shows that newly established polyploids have adaptive advantages in certain stress conditions compared to their relatives with a lower ploidy. The genus Saccharomyces is a good model for studying such events, as it contains an ancient whole-genome duplication event and many sequenced
-
Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2 Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Kelle C. Freel, Stephanie Fouteau, David Roche, Julien Farasin, Aline Huber, Sandrine Koechler, Martina Peres, Olfa Chiboub, Hugo Varet, Caroline Proux, Julien Deschamps, Romain Briandet, Rachel Torchet, Stephane Cruveiller, Didier Lièvremont, Jean-Yves Coppée, Valérie Barbe and Florence Arsène-Ploetze
Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was
-
Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Domenico Giosa, Maria Rosa Felice, Letterio Giuffrè, Riccardo Aiese Cigliano, Andreu Paytuví-Gallart, Carla Lo Passo, Cinzia Barresi, Enrico D'Alessandro, Huaiqiu Huang, Giuseppe Criseo, Héctor M. Mora-Montes, Sybren de Hoog and Orazio Romeo
Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii
-
Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Giovanni Bussotti, Alia Benkahla, Fakhri Jeddi, Oussama Souiaï, Karim Aoun, Gerald F. Späth and Aïda Bouratbine
Although several studies have investigated genetic diversity of Leishmania infantum in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven L. infantum isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral
-
Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Takumi Anzai, Sousuke Imamura, Akira Ishihama and Tomohiro Shimada
The transcription factor PdhR has been recognized as the master regulator of the pyruvate catabolism pathway in Escherichia coli , including both NAD-linked oxidative decarboxylation of pyruvate to acetyl-CoA by PDHc (pyruvate dehydrogenase complex) and respiratory electron transport of NADH to oxygen by Ndh-CyoABCD enzymes. To identify the whole set of regulatory targets under the control of pyruvate-sensing
-
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens Microb. Genom. (IF 4.632) Pub Date : 2020-10-01 Yuqing Feng, Xuezheng Fan, Liangquan Zhu, Xinyue Yang, Yan Liu, Shiguang Gao, Xiaolu Jin, Dan Liu, Jiabo Ding, Yuming Guo and Yongfei Hu
Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C