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Whole-genome assembly of a novel invertebrate herpesvirus from the gastropod Babylonia areolata Microb. Genom. (IF 3.9) Pub Date : 2024-04-24 Konstantin Divilov
Molluscan herpesviruses cause disease in species of major importance to aquaculture and are the only known herpesviruses to infect invertebrates, which lack an adaptive immune system. Understanding the evolution of malacoherpesviruses in relation to their hosts will likely require comparative genomic studies on multiple phylogenetic scales. Currently, only two malacoherpesvirus species have genomes
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Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus) Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Jack Pilgrim
Erwinia (Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe Candidatus Erwinia impunctatus (Erwimp) associated with the Highland midge Culicoides impunctatus (Diptera:
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Genome sequences of the first Autographiviridae phages infecting marine Roseobacter Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Sen Du, Ying Wu, Hanqi Ying, Zuqing Wu, Mingyu Yang, Feng Chen, Jiabing Shao, He Liu, Zefeng Zhang and Yanlin Zhao
The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that
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Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Beth Blane, Kathy E. Raven, Nicholas M. Brown, Ewan M. Harrison, Francesc Coll, Rachel Thaxter, David A. Enoch, Theodore Gouliouris, Danielle Leek, Sophia T. Girgis, Asha Akram, Marta Matuszewska, Paul Rhodes, Julian Parkhill and Sharon J. Peacock
Genomic epidemiology enhances the ability to detect and refute methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resource utilization. We performed a 12 month prospective study at Cambridge University Hospitals NHS Foundation Trust in the UK to capture its impact on hospital infection
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Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Kyle Schutz, Tina Melie, Stacey D. Smith and C. Alisha Quandt
Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, Candida auris, is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it
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Deep learning methods in metagenomics: a review Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Gaspar Roy, Edi Prifti, Eugeni Belda and Jean-Daniel Zucker
The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing
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Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Manuela Montoya-Giraldo, Kathryn R. Piper, Odion O. Ikhimiukor, Cooper J. Park, Nicole A. Caimi, Debbie C. Buecher, Ernest W. Valdez, Diana E. Northup and Cheryl P. Andam
Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of
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Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis Microb. Genom. (IF 3.9) Pub Date : 2024-04-17 Patrick A. da Roza, Héloïse Muller, Geraldine J. Sullivan, Roy S. K. Walker, Hugh D. Goold, Robert D. Willows, Brian Palenik and Ian T. Paulsen
Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins,
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A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco Microb. Genom. (IF 3.9) Pub Date : 2024-04-05 Hasnaa Talimi, Othmane Daoui, Giovanni Bussotti, Idris Mhaidi, Anne Boland, Jean-François Deleuze, Rachida Fissoune, Meryem Lemrani and Gerald F. Späth
In Morocco, cutaneous leishmaniasis (CL) caused by Leishmania (L.) tropica is an important health problem. Despite the high incidence of CL in the country, the genomic heterogeneity of these parasites is still incompletely understood. In this study, we sequenced the genomes of 14 Moroccan isolates of L. tropica collected from confirmed cases of CL to investigate their genomic heterogeneity. Comparative
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Identifying the best PCR enzyme for library amplification in NGS Microb. Genom. (IF 3.9) Pub Date : 2024-04-05 Michael A. Quail, Craig Corton, James Uphill, Jacqueline Keane and Yong Gu
Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [ 1, 2 ]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification
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Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria Microb. Genom. (IF 3.9) Pub Date : 2024-04-03 Alexia Suellen Fernandes, Kiara França Campos, Jéssica Catarine Silva de Assis, Osiel Silva Gonçalves, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli and Mateus Ferreira Santana
Genetic variability in phytopathogens is one of the main problems encountered for effective plant disease control. This fact may be related to the presence of transposable elements (TEs), but little is known about their role in host genomes. Here, we performed the most comprehensive analysis of insertion sequences (ISs) and transposons (Tns) in the genomes of the most important bacterial plant pathogens
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Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates Microb. Genom. (IF 3.9) Pub Date : 2024-03-28 Sara M. Klose, Alistair R. Legione, Rhys N. Bushell, Glenn F. Browning and Paola K. Vaz
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed
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Identifying the suite of genes central to swimming in the biocontrol bacterium Pseudomonas protegens Pf-5 Microb. Genom. (IF 3.9) Pub Date : 2024-03-28 B.K. Fabian, C. Foster, A. Asher, K.A. Hassan, I.T. Paulsen and S.G. Tetu
Swimming motility is a key bacterial trait, important to success in many niches. Biocontrol bacteria, such as Pseudomonas protegens Pf-5, are increasingly used in agriculture to control crop diseases, where motility is important for colonization of the plant rhizosphere. Swimming motility typically involves a suite of flagella and chemotaxis genes, but the specific gene set employed for both regulation
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Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France Microb. Genom. (IF 3.9) Pub Date : 2024-03-27 Manon Dechêne-Tempier, Claire de Boisséson, Pierrick Lucas, Stéphanie Bougeard, Virginie Libante, Corinne Marois-Créhan and Sophie Payot
Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal
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Integrative methylome and transcriptome analysis reveals epigenetic regulation of Fusobacterium nucleatum in laryngeal cancer Microb. Genom. (IF 3.9) Pub Date : 2024-03-27 Xiaohui Yuan, Hui-Ching Lau, Huiying Huang, Chi-Yao Hsueh, Hongli Gong and Liang Zhou
The aetiological mechanisms of Fusobacterium nucleatum in laryngeal cancer remain unclear. This study aimed to reveal the epigenetic signature induced by F. nucleatum in laryngeal squamous cell carcinoma (LSCC). Combined analysis of methylome and transcriptome data was performed to address the functional role of F. nucleatum in laryngeal cancer. Twenty-nine differentially expressed methylation-driven
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Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus) Microb. Genom. (IF 3.9) Pub Date : 2024-03-27 Melanie B. Prentice, Marie L. J. Gilbertson, Daniel J. Storm, Wendy C. Turner, Daniel P. Walsh, Marie E. Pinkerton and Pauline L. Kamath
With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating
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Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae Microb. Genom. (IF 3.9) Pub Date : 2024-03-26 Gherard Batisti Biffignandi, Leonid Chindelevitch, Marta Corbella, Edward J. Feil, Davide Sassera and John A. Lees
Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative
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Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly Microb. Genom. (IF 3.9) Pub Date : 2024-03-26 Rodolfo Enrique Ángeles-Argáiz, Luis Fernando Lozano Aguirre-Beltrán, Diana Hernández-Oaxaca, Christian Quintero-Corrales, Mauricio A. Trujillo-Roldán, Santiago Castillo-Ramírez and Roberto Garibay-Orijel
Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality
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Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism Microb. Genom. (IF 3.9) Pub Date : 2024-03-26 Claire Crowley, Ajith Selvaraj, Arvind Hariharan, Claire M. Healy and Gary P. Moran
Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant
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The influence of flocculation upon global gene transcription in a yeast CYC8 mutant Microb. Genom. (IF 3.9) Pub Date : 2024-03-26 Brenda Lee, Karsten Hokamp, Mohamed M. Alhussain, Atif A. Bamagoos and Alastair B. Fleming
The transcriptome from a Saccharomyces cerevisiae tup1 deletion mutant was one of the first comprehensive yeast transcriptomes published. Subsequent transcriptomes from tup1 and cyc8 mutants firmly established the Tup1-Cyc8 complex as predominantly acting as a repressor of gene transcription. However, transcriptomes from tup1/cyc8 gene deletion or conditional mutants would all have been influenced
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Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing Microb. Genom. (IF 3.9) Pub Date : 2024-03-26 Teresa L. Street, Nicholas D. Sanderson, Leanne Barker, James Kavanagh, Kevin Cole, The GonFast Investigators Group, Martin Llewelyn and David W. Eyre
Multi-drug-resistant Neisseria gonorrhoeae infection is a significant public health risk. Rapidly detecting N. gonorrhoeae and antimicrobial-resistant (AMR) determinants by metagenomic sequencing of urine is possible, although high levels of host DNA and overgrowth of contaminating species hamper sequencing and limit N. gonorrhoeae genome coverage. We performed Nanopore sequencing of nucleic acid amplification
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A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen Microb. Genom. (IF 3.9) Pub Date : 2024-03-21 Daniel Whiley, Keith Jolley, Adam Blanchard, Tracey Coffey and James Leigh
Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme
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Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover Microb. Genom. (IF 3.9) Pub Date : 2024-03-21 Rodrigo García-López, Blanca Taboada, Selene Zárate, José Esteban Muñoz-Medina, Angel Gustavo Salas-Lais, Alfredo Herrera-Estrella, Celia Boukadida, Joel Armando Vazquez-Perez, Bruno Gómez-Gil, Alejandro Sanchez-Flores and Carlos F. Arias
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic
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Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae Microb. Genom. (IF 3.9) Pub Date : 2024-03-19 Luke A. F. Barretto, Patryc-Khang T. Van and Casey C. Fowler
Two-component regulatory systems (TCSs) are a major mechanism used by bacteria to sense and respond to their environments. Many of the same TCSs are used by biologically diverse organisms with different regulatory needs, suggesting that the functions of TCS must evolve. To explore this topic, we analysed the amino acid sequence divergence patterns of a large set of broadly conserved TCS across different
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Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018 Microb. Genom. (IF 3.9) Pub Date : 2024-03-18 Eleonora Cella, Catherine G. Sutcliffe, Lindsay R. Grant, Carol Tso, Robert C. Weatherholtz, Shea Littlepage, Ladonna Becenti, Mohammad Jubair, Brenna C. Simons, Marcella Harker-Jones, Raymond Reid, Del Yazzie, Mathuram Santosham, Katherine L. O'Brien, Laura L. Hammitt and Taj Azarian
Background. Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In
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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