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Genomic analysis of clinical Aeromonas isolates reveals genetic diversity but little evidence of genetic determinants for diarrhoeal disease Microb. Genom. (IF 3.9) Pub Date : 2024-03-07 Elizabeth J. Klemm, Muhammad Imran Nisar, Matt Bawn, Dilruba Nasrin, Farah Naz Qamar, Andrew Page, Farheen Qadri, Sadia Shakoor, Anita KM Zaidi, Myron M. Levine, Gordon Dougan and Robert A. Kingsley
Aeromonas spp. are associated with a number of infectious syndromes in humans including gastroenteritis and dysentery. Our understanding of the genetic diversity, population structure, virulence determinants and antimicrobial resistance of the genus has been limited by a lack of sequenced genomes linked to metadata. We performed a comprehensive analysis of the whole genome sequences of 447 Aeromonas
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Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals Microb. Genom. (IF 3.9) Pub Date : 2024-03-07 Edder D. Bustos-Diaz, Arely Cruz-Perez, Diego Garfias-Gallegos, Paul M. D'Agostino, Michelle M. Gehringer, Angelica Cibrian-Jaramillo and Francisco Barona-Gomez
Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots
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A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions Microb. Genom. (IF 3.9) Pub Date : 2024-03-06 Bianca Rodrigues Jardim, Cherie Gambley, Lucy T. T. Tran-Nguyen, Craig Webster, Monica Kehoe, Wycliff M. Kinoti, Samantha Bond, Richard Davis, Lynne Jones, Nandita Pathania, Murray Sharman, Toni Chapman, Brendan C. Rodoni and Fiona E. Constable
In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed
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Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages Microb. Genom. (IF 3.9) Pub Date : 2024-03-06 Ehsan Ghasemian, Nkoyo Faal, Harry Pickering, Ansumana Sillah, Judith Breuer, Robin L. Bailey, David Mabey and Martin J. Holland
Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovars A–C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors
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Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa Microb. Genom. (IF 3.9) Pub Date : 2024-02-29 Jamie Deery, Muireann Carmody, Rhiannon Flavin, Malwina Tomanek, Maria O'Keeffe, Gerard P. McGlacken and F. Jerry Reen
Pseudomonas aeruginosa, a harmful nosocomial pathogen associated with cystic fibrosis and burn wounds, encodes for a large number of LysR-type transcriptional regulator proteins. To understand how and why LTTR proteins evolved with such frequency and to establish whether any relationships exist within the distribution we set out to identify the patterns underpinning LTTR distribution in P. aeruginosa
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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling Microb. Genom. (IF 3.9) Pub Date : 2024-02-29 Monica Steffi Matchado, Malte Rühlemann, Sandra Reitmeier, Tim Kacprowski, Fabian Frost, Dirk Haller, Jan Baumbach and Markus List
Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM
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Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA Microb. Genom. (IF 3.9) Pub Date : 2024-02-26 Selvalakshmi Selvaraj Anand, Chin-Ting Wu, Jordan Bremer, Micah Bhatti, Todd J. Treangen, Awdhesh Kalia, Samuel A. Shelburne and William C. Shropshire
Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms
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Exploring the genetic basis of natural resistance to microcins Microb. Genom. (IF 3.9) Pub Date : 2024-02-26 Soufiane Telhig, Nguyen Phuong Pham, Laila Ben Said, Sylvie Rebuffat, Marc Ouellette, Séverine Zirah and Ismaïl Fliss
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the
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Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Anastasia Unitt, Martin Maiden and Odile Harrison
Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with
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ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Xiaokai Wang, Zhimin Ding, Ying Yang, Lifeng Liang, Yingshuai Sun, Chaojian Hou, Yuning Zheng, Yan Xia and Lixin Dong
Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers
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A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Helena B. Cooper, Ben Vezina, Jane Hawkey, Virginie Passet, Sebastián López-Fernández, Jonathan M. Monk, Sylvain Brisse, Kathryn E. Holt and Kelly L. Wyres
The Klebsiella pneumoniae species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism
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The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Ryan Cook, Nathan Brown, Branko Rihtman, Slawomir Michniewski, Tamsin Redgwell, Martha Clokie, Dov J. Stekel, Yin Chen, David J. Scanlan, Jon L. Hobman, Andrew Nelson, Michael A. Jones, Darren Smith and Andrew Millard
Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio
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Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Anwar Hiralal, Jeanine S. Geelhoed, Silvia Hidalgo-Martinez, Bent Smets, Jesper R. van Dijk and Filip J. R. Meysman
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance
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PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Julian A. Paganini, Jesse J. Kerkvliet, Lisa Vader, Nienke L. Plantinga, Rodrigo Meneses, Jukka Corander, Rob J. L. Willems, Sergio Arredondo-Alonso and Anita C. Schürch
Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different
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Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing Microb. Genom. (IF 3.9) Pub Date : 2024-02-21 Norikazu Kitamura, Toshiki Kajihara, Camila Gazolla Volpiano, Myo Naung, Guillaume Méric, Aki Hirabayashi, Hirokazu Yano, Masaya Yamamoto, Fumiaki Yoshida, Tsunesaburo Kobayashi, Sari Yamanashi, Tadao Kawamura, Nobuaki Matsunaga, Jiro Okochi, Motoyuki Sugai and Koji Yahara
Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome–resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national
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HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data Microb. Genom. (IF 3.9) Pub Date : 2024-02-15 Budi Permana, Patrick N. A. Harris, Leah W. Roberts, Thom Cuddihy, David L. Paterson, Scott A. Beatson and Brian M. Forde
Existing tools for phylogeographic and epidemiological visualisation primarily provide a macro-geographic view of epidemic and pandemic transmission events but offer little support for detailed investigation of outbreaks in healthcare settings. Here, we present HAIviz, an interactive web-based application designed for integrating and visualising genomic epidemiological information to improve the tracking
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A novel synthetic nucleic acid mixture for quantification of microbes by mNGS Microb. Genom. (IF 3.9) Pub Date : 2024-02-15 Hailing Wanghu, Yingzhen Li, Jin Huang, Kangze Pu, Fengming Guo, Peiwen Zhong, Ting Wang, Jianying Yuan, Yan Yu, Jiachang Chen, Jun Liu, Jason J. Chen and Chaohui Hu
Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in
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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses Microb. Genom. (IF 3.9) Pub Date : 2024-02-15 Nadim Rahman, Colman O'Cathail, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Björn Grüning, Carla Cummins, Clara Amid, David F. Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae K. Prasad, Gábor Máté Gulyás, Gabriele Rinck, Jasmine McKinnon, Jeena Rajan, Jeff Knaggs, Jeffrey Edward Skiby, József Stéger, Judit Szarvas, Khadim Gueye, Krisztián Papp, Maarten Hoek, Manish Kumar, Marianna
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies
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Whole-Genome sequencing in routine Mycobacterium bovis epidemiology – scoping the potential Microb. Genom. (IF 3.9) Pub Date : 2024-02-14 Adrian Allen, Ryan Magee, Ryan Devaney, Tara Ardis, Caitlín McNally, Carl McCormick, Eleanor Presho, Michael Doyle, Purnika Ranasinghe, Philip Johnston, Raymond Kirke, Roland Harwood, Damien Farrell, Kevin Kenny, Jordy Smith, Stephen Gordon, Tom Ford, Suzan Thompson, Lorraine Wright, Kerri Jones, Paulo Prodohl and Robin Skuce
Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemiological links between outbreaks. However, they have limited utility owing to low
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Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population Microb. Genom. (IF 3.9) Pub Date : 2024-02-09 Ilinca I. Ciubotariu, Rebecca P. Wilkes, Jobin J. Kattoor, Erin N. Christian, Giovanna Carpi and Andrew Kitchen
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome
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Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families Microb. Genom. (IF 3.9) Pub Date : 2024-02-07 Colbie J. Reed, Rémi Denise, Jacob Hourihan, Jill Babor, Marshall Jaroch, Maria Martinelli, Geoffrey Hutinet and Valérie de Crécy-Lagard
Capturing the published corpus of information on all members of a given protein family should be an essential step in any study focusing on specific members of that family. Using a previously gathered dataset of more than 280 references mentioning a member of the DUF34 (NIF3/Ngg1-interacting Factor 3) family, we evaluated the efficiency of different databases and search tools, and devised a workflow
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Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India Microb. Genom. (IF 3.9) Pub Date : 2024-02-05 Iftekhar M. Rafiqullah, Rosemol Varghese, K. Taylor Hellmann, Aravind Velmurugan, Ayyanraj Neeravi, Jones Lionel Kumar Daniel, Jorge E. Vidal, Rajeev Z. Kompithra, Valsan P. Verghese, Balaji Veeraraghavan and D. Ashley Robinson
Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected
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Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis Microb. Genom. (IF 3.9) Pub Date : 2024-02-05 Viktoria M. Brunner and Philip W. Fowler
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations
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Prevalence, antibiotic resistance, and genomic characterisation of Campylobacter spp. in retail chicken in Hanoi, Vietnam Microb. Genom. (IF 3.9) Pub Date : 2024-01-31 Luu Quynh Huong, Thomas Chisnall, John D. Rodgers, Shaun A. Cawthraw and Roderick M. Card
Campylobacter spp. are a leading cause of bacterial foodborne zoonosis worldwide, with poultry meat and products recognised as a significant source of human infection. In Vietnam there are few data regarding the occurrence, antimicrobial resistance, and genomic diversity of Campylobacter in poultry and poultry meat. The aim of this study was to estimate the prevalence of Campylobacter in chicken meat
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pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections Microb. Genom. (IF 3.9) Pub Date : 2024-01-30 Leonor Sánchez-Busó, Andrea Sánchez-Serrano, Daniel Golparian and Magnus Unemo
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability
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Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype Microb. Genom. (IF 3.9) Pub Date : 2024-01-25 Yuening Wang, Chenglin Chi, Jiajia Zhang, Kaili Zhang, Dafu Deng, Wanglong Zheng, Nanhua Chen, François Meurens and Jianzhong Zhu
African swine fever (ASF) is a severe haemorrhagic disease caused by the African swine fever virus (ASFV), transmitted by ticks, resulting in high mortality among domestic pigs and wild boars. The global spread of ASFV poses significant economic threats to the swine industry. This study employs diverse analytical methods to explore ASFV’s evolution and host adaptation, focusing on codon usage patterns
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Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan Microb. Genom. (IF 3.9) Pub Date : 2024-01-25 Nida Javaid, Stephanie W. Lo, Muhammad Imran Nisar, Asma Basharat, Hadiqa Jaleel, Karam Rasool, Qamar Sultana, Furqan Kabir, Aneeta Hotwani, Robert F. Breiman, Stephen D. Bentley, Sadia Shakoor and Shaper Mirza
Pakistan is amongst the four countries with the highest number of pneumococcal deaths. While the PCV10 vaccine was introduced in Pakistan in October 2012, data regarding the impact of the vaccine on the population dynamics of Streptococcus pneumoniae in Pakistan remain obscure. Using whole genome sequencing of 190 isolates (nasopharyngeal carriage=75, disease=113, unknown sites=2) collected between
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Phenotypic and genotypic characterization of Marinobacterium weihaiense sp. nov. and Marinobacterium marinum sp. nov., isolated from marine sediment, and genomic properties of the genus Marinobacterium Microb. Genom. (IF 3.9) Pub Date : 2024-01-24 Xin-Jiang Liu, Ke-Lei Zhu, Yu-Qi Ye, Ze-Tian Han, Xin-Yun Tan, Zong-Jun Du and Meng-Qi Ye
In this study, two novel bacterial strains were isolated from coastal sediment of Weihai, China. The two strains were Gram-stain-negative and facultatively aerobic, designated 3-1745T and A346T. Based on phenotypic, genetic and phylogenetic properties, strains 3-1745T and A346T represent two novel species of the genus Marinobacterium . The results of genome analysis revealed many central carbohydrate
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Prophages: an integral but understudied component of the human microbiome Microb. Genom. (IF 3.9) Pub Date : 2024-01-24 Laura K. Inglis, Michael J. Roach and Robert A. Edwards
Phages integrated into a bacterial genome – called prophages – continuously monitor the vigour of the host bacteria to determine when to escape the genome and to protect their host from other phage infections, and they may provide genes that promote bacterial growth. Prophages are essential to almost all microbiomes, including the human microbiome. However, most human microbiome studies have focused
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Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes Microb. Genom. (IF 3.9) Pub Date : 2024-01-19 Jeremy D. Mirza, Lilian de Oliveira Guimarães, Sam Wilkinson, Esmenia C. Rocha, Mayara Bertanhe, Vanessa Christe Helfstein, Juliana Telles de-Deus, Ingra M. Claro, Nicola Cumley, Joshua Quick, Nuno R. Faria, Ester C. Sabino, Karin Kirchgatter and Nicholas J. Loman
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol
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Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent Microb. Genom. (IF 3.9) Pub Date : 2024-01-19 Emanuel Martínez-Ugalde, Víctor Ávila-Akerberg, Tanya M. González Martínez and Eria A. Rebollar
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a
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Complete genome sequence of a winter season Vibrio facilitates discovery of a novel subclade of cold-adapted species in the albus clade Microb. Genom. (IF 3.9) Pub Date : 2024-01-17 Paul D. Kastner, Stephen E. Noell and David A. Essig
In temperate marine climate zones, seasonal changes in water temperature contribute to distinct populations of warm- and cold-water vibrios. We report here the complete genome sequence (BUSCO score=94.8) of the novel strain Vibrio sp. VB16 isolated in late winter from the intertidal zone near Virginia Beach, Virginia, USA with the ability to form colonies at 4 °C. The 5.2 Mbp genome is composed of
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Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections Microb. Genom. (IF 3.9) Pub Date : 2024-01-16 Yue Wang, Jianping Xu, Fatma Ben Abid, Husam Salah, Sathyavathi Sundararaju, Khalil Al Ismail, Kun Wang, Lisa Sara Matthew, Saad Taj-Aldeen, Emad B. Ibrahim, Patrick Tang, Andres Perez-Lopez and Clement K. M. Tsui
Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely
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Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections Microb. Genom. (IF 3.9) Pub Date : 2024-01-16 Daniel Peñas-Utrilla, Patricia Muñóz, Laura Pérez-Lago and Darío García de Viedma
Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality
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Genomic and clinical characteristics of campylobacteriosis in Australia Microb. Genom. (IF 3.9) Pub Date : 2024-01-12 Danielle M. Cribb, Cameron R. M. Moffatt, Rhiannon L. Wallace, Angus T. McLure, Dieter Bulach, Amy V. Jennison, Nigel French, Mary Valcanis, Kathryn Glass and Martyn D. Kirk
Campylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors. We recruited 571 campylobacteriosis cases from three Australian states and territories (2018–2019). We collected demographic
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The macronuclear genomic landscape within Tetrahymena thermophila Microb. Genom. (IF 3.9) Pub Date : 2024-01-11 Romain Derelle, Rik Verdonck, Staffan Jacob, Michèle Huet, Ildem Akerman, Hervé Philippe and Delphine Legrand
The extent of intraspecific genomic variation is key to understanding species evolutionary history, including recent adaptive shifts. Intraspecific genomic variation remains poorly explored in eukaryotic micro-organisms, especially in the nuclear dimorphic ciliates, despite their fundamental role as laboratory model systems and their ecological importance in many ecosystems. We sequenced the macronuclear
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A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies Microb. Genom. (IF 3.9) Pub Date : 2024-01-10 Lea Schäfer, Johannes A. Jehle, Regina G. Kleespies and Jörg T. Wennmann
Generating complete, high-quality genome assemblies is key for any downstream analysis, such as comparative genomics. For bacterial genome assembly, various algorithms and fully automated pipelines exist, which are free-of-charge and easily accessible. However, these assembly tools often cannot unambiguously resolve a bacterial genome, for example due to the presence of sequence repeat structures on
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Insights gained from sequencing Australian non-invasive and invasive Streptococcus pyogenes isolates Microb. Genom. (IF 3.9) Pub Date : 2024-01-10 Trent A.J. Butler, Chloe Story, Emily Green, Kirsten M. Williamson, Peter Newton, Frances Jenkins, Hemalatha Varadhan and Sebastiaan van Hal
Epidemiological data have indicated that invasive infections caused by the Gram-positive cocci Streptococcus pyogenes (group A streptococcus, GAS) have increased in many Australian states over the past two decades. In July 2022, invasive GAS (iGAS) infections became nationally notifiable in Australia via public-health agencies. Surveillance for S. pyogenes infections has been sporadic within the state
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A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates Microb. Genom. (IF 3.9) Pub Date : 2024-01-08 Diego E. Gutierrez-Castillo, Emma Barrett and Robyn Roberts
Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive
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Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli Microb. Genom. (IF 3.9) Pub Date : 2024-01-08 Christian J. Field, Kate L. Bowerman and Philip Hugenholtz
Many peptidoglycan-deficient bacteria such as the Mycoplasmatales are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating Bacilli through reductive evolution. Here we annotate 2650
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Complete genomes of Clostridium botulinum type B(F) isolates associated with a 1995 foodborne botulism outbreak from commercial pâté reveals a recombination event disrupting the ntnh gene Microb. Genom. (IF 3.9) Pub Date : 2024-01-04 Richard A. Harris, Annika Flint, Madeleine Blondin Brosseau, Kelly Weedmark and John W. Austin
Foodborne botulism is a neuroparalytic disease caused by ingestion of foods contaminated with botulinum neurotoxin (BoNT), produced by Clostridium botulinum . In 1995 a husband and wife from Québec, Canada, were hospitalized for several months with prolonged muscle paralysis after ingesting a commercial pâté de campagne. Examination of faecal samples from both patients and the pâté produced viable
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Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations Microb. Genom. (IF 3.9) Pub Date : 2024-01-04 Imraan Alas, Doug R. Braun, Spencer S. Ericksen, Rauf Salamzade, Lindsay Kalan, Scott R. Rajski and Tim S. Bugni
Investigations of the bacterial family Micromonosporaceae have enabled the development of secondary metabolites critical to human health. Historical investigation of bacterial families for natural product discovery has focused on terrestrial strains, where time-consuming isolation processes often lead to the rediscovery of known compounds. To investigate the secondary metabolite potential of marine-derived
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An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows Microb. Genom. (IF 3.9) Pub Date : 2024-01-04 Luke B. Harrison, Vivek Kapur and Marcel A. Behr
Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such
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Emergence and genomic characteristics of multi-drug-resistant Salmonella in pet turtles and children with diarrhoea Microb. Genom. (IF 3.9) Pub Date : 2024-01-03 Wei Wang, Feng Liu, Hui Li, Menghan Li, Yujie Hu, Fengqin Li, Jing Xiao and Yinping Dong
Pet turtles are a well-recognized source of human salmonellosis, posing a threat to human health, particularly children who commonly keep pet turtles. To date, the genomic characteristics of Salmonella among pet turtles and children has not been well described. We investigated the prevalence, antimicrobial resistance (AMR) and genomic characteristics of Salmonella from pet turtles in Beijing, China
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Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK Microb. Genom. (IF 3.9) Pub Date : 2024-01-02 Emily T. Fotopoulou, Claire Jenkins, Clare R. Barker, Anais Painset, Xavier Didelot, Ameze Simbo, Amy Douglas, Gauri Godbole, Frieda Jorgensen, Saheer Gharbia and Jim McLauchlin†
Listeria monocytogenes is a food-borne pathogen, typically affecting the elderly, immunocompromised patients and pregnant women. The aim of this study was to determine the population structure of L. monocytogenes clonal complex 1 (CC1) in the UK and describe the genomic epidemiology of this clinically significant CC. We interrogated a working dataset of 4073 sequences of L. monocytogenes isolated between
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Genomic characterization of a unique Panton–Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting on Australian indigenous communities Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Joshua P. Ramsay, Nipuna Parahitiyawa, Shakeel Mowlaboccus, Christopher A. Mullally, Nicholas W.T. Yee, Princy Shoby, Elena Colombi, Hui-Leen Tan, Julie C. Pearson and Geoffrey W. Coombs
In 2010 a single isolate of a trimethoprim-resistant multilocus sequence type 5, Panton–Valentine leucocidin-positive, community-associated methicillin-resistant Staphylococcus aureus (PVL-positive ST5 CA-MRSA), colloquially named WA121, was identified in northern Western Australia (WA). WA121 now accounts for ~14 % of all WA MRSA infections. To gain an understanding of the genetic composition and
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SOCfinder: a genomic tool for identifying social genes in bacteria Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Laurence J. Belcher, Anna E. Dewar, Chunhui Hao, Zohar Katz, Melanie Ghoul and Stuart A. West
Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic
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Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020–2022: implications for future outbreak preparedness Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Pakorn Aiewsakun, Bharkbhoom Jamsai, Worakorn Phumiphanjarphak, Waritta Sawaengdee, Prasit Palittapongarnpim and Surakameth Mahasirimongkol
Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has previously been characterized in Thailand, but a detailed spatiotemporal analysis is still lacking
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Visualizing and quantifying structural diversity around mobile resistance genes Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Liam P. Shaw and Richard A. Neher
Understanding the evolution of mobile genes is important for understanding the spread of antimicrobial resistance (AMR). Many clinically important AMR genes have been mobilized by mobile genetic elements (MGEs) on the kilobase scale, such as integrons and transposons, which can integrate into both chromosomes and plasmids and lead to rapid spread of the gene through bacterial populations. Looking at
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Genomic characterization of Bordetella pertussis in South Africa, 2015–2019 Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Fahima Moosa, Mignon du Plessis, Michael R. Weigand, Yanhui Peng, Dineo Mogale, Linda de Gouveia, Marta C. Nunes, Shabir A. Madhi, Heather J. Zar, Gary Reubenson, Arshad Ismail, M. Lucia Tondella, Cheryl Cohen, Sibongile Walaza, Anne von Gottberg and Nicole Wolter
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB
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Characterization of the RofA regulon in the pandemic M1global and emergent M1UK lineages of Streptococcus pyogenes Microb. Genom. (IF 3.9) Pub Date : 2023-12-20 Xiangyun Zhi, Ana Vieira, Kristin K. Huse, Paulo J. Martel, Ludmila Lobkowicz, Ho Kwong Li, Nick Croucher, Ivan Andrew, Laurence Game and Shiranee Sriskandan
The standalone regulator RofA is a positive regulator of the pilus locus in Streptococcus pyogenes . Found in only certain emm genotypes, RofA has been reported to regulate other virulence factors, although its role in the globally dominant emm1 S. pyogenes is unclear. Given the recent emergence of a new emm1 (M1UK) toxigenic lineage that is distinguished by three non-synonymous SNPs in rofA, we characterized
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Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences Microb. Genom. (IF 3.9) Pub Date : 2023-12-19 Alison L. Gould and James B. Henderson
This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences
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The population structure of vancomycin-resistant and -susceptible Enterococcus faecium in a low-prevalence antimicrobial resistance setting is highly influenced by circulating global hospital-associated clones Microb. Genom. (IF 3.9) Pub Date : 2023-12-19 Mushtaq AL Rubaye, Jessin Janice, Jørgen Vildershøj Bjørnholt, Oliver Kacelnik, Bjørg C. Haldorsen, Randi M. Nygaard, Joachim Hegstad, Arnfinn Sundsfjord, Kristin Hegstad and the Norwegian VRE study group
Between 2010 and 2015 the incidence of vancomycin-resistant Enterococcus faecium (VREfm) in Norway increased dramatically. Hence, we selected (1) a random subset of vancomycin-resistant enterococci (VRE) from the Norwegian Surveillance System for Communicable Diseases (2010–15; n=239) and (2) Norwegian vancomycin-susceptible E. faecium (VSEfm) bacteraemia isolates from the national surveillance system
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SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico Microb. Genom. (IF 3.9) Pub Date : 2023-12-19 Blanca Itzelt Taboada, Selene Zárate, Rodrigo García-López, José Esteban Muñoz-Medina, Bruno Gómez-Gil, Alfredo Herrera-Estrella, Alejandro Sanchez-Flores, Angel Gustavo Salas-Lais, Benjamin Roche, Gabriela Martínez-Morales, Hermilo Domínguez Zárate, Célida Duque Molina, Ricardo Avilés Hernández, Susana López and Carlos F. Arias
In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants' abundance, distribution, and genetic diversity in Mexico from April to August 2022. Over 35 % of the sequenced genomes in this
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Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance Microb. Genom. (IF 3.9) Pub Date : 2023-12-15 Iman Yassine, Rayane Rafei, Maria Pardos de la Gandara, Marwan Osman, Laetitia Fabre, Fouad Dabboussi, Monzer Hamze and François-Xavier Weill
In this study, we characterized 54 clinical isolates of Shigella collected in North Lebanon between 2009 and 2017 through phenotypic and genomic analyses. The most prevalent serogroup was S. sonnei, accounting for 46.3 % (25/54) of the isolates, followed by S. flexneri (27.8 %, 15/54), S. boydii (18.5 %, 10/54) and S. dysenteriae (7.4 %, 4/54). Only three isolates were pan-susceptible, and 87 % (47/54)
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Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli Microb. Genom. (IF 3.9) Pub Date : 2023-12-15 Timothy J. Davies, Jeremy Swann, Anna E. Sheppard, Hayleigh Pickford, Samuel Lipworth, Manal AbuOun, Matthew J. Ellington, Philip W. Fowler, Susan Hopkins, Katie L. Hopkins, Derrick W. Crook, Timothy E. A. Peto, Muna F. Anjum, A. Sarah Walker and Nicole Stoesser
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli , is of major importance, because
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Genomic insights into Enterococcus faecium isolates from marine bivalves highlight One Health concerns and healthcare linkages Microb. Genom. (IF 3.9) Pub Date : 2023-12-12 Amalie von Barner Tvedegaard Heim, Jessin Janice, Jørgen Vildershøj Bjørnholt, Bjørn Tore Lunestad, Kristin Hegstad and Cecilie Smith Svanevik
Enterococci, especially Enterococcus faecium , are one of today’s leading causes of multidrug-resistant infections in hospital settings. The marine environment may harbour enterococci, but its role as an evolutionary niche and as a vector for the spread of enterococci is sparsely investigated. Hence, by applying enterococci in bivalves as a sentinel tool, this study aimed to describe the prevalence
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The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247 Microb. Genom. (IF 3.9) Pub Date : 2023-12-12 Lorenzo Colombini, Francesco Santoro, Mariana Tirziu, Elisa Lazzeri, Lorenzo Morelli, Gianni Pozzi and Francesco Iannelli
Lactobacillus crispatus is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which
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Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications Microb. Genom. (IF 3.9) Pub Date : 2023-12-12 Ruth E. Timme, Ilene Karsch-Mizrachi, Zahra Waheed, Masanori Arita, Duncan MacCannell, Finlay Maguire, Robert Petit III III, Andrew J. Page, Catarina Inês Mendes, Muhammad Ibtisam Nasar, Paul Oluniyi, Andrea D. Tyler, Amogelang R. Raphenya, Jennifer L. Guthrie, Idowu Olawoye, Gabriele Rinck, Colman O’Cathail, John Lees, Guy Cochrane, Carla Cummins, J. Rodney Brister, William Klimke, Michael Feldgarden
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather
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Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258 Microb. Genom. (IF 3.9) Pub Date : 2023-12-11 Alejandro Piña-Iturbe, Guillermo Hoppe-Elsholz, Isidora D. Suazo, Alexis M. Kalergis and Susan M. Bueno
The ICEKp258.2 genomic island (GI) has been proposed as an important factor for the emergence and success of the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type (ST) 258. However, a characterization of this horizontally acquired element is lacking. Using bioinformatic and experimental approaches, we found that ICEKp258.2 is not confined to ST258 and ST512, but also carried