A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen
Microbial Genomics | Microbiology Society Journals
by Daniel Whiley, Keith Jolley, Adam Blanchard, Tracey Coffey and James Leigh
5d ago
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. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97  %) isola ..read more
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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
Microbial Genomics | Microbiology Society Journals
by 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
5d ago
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 consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of con ..read more
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Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018
Microbial Genomics | Microbiology Society Journals
by 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
1w ago
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 the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001–2009 and 6.2/100 000 in 2011–2019); in children the disease persisted although the rates dropped from 5.8/10 ..read more
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Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages
Microbial Genomics | Microbiology Society Journals
by Ehsan Ghasemian, Nkoyo Faal, Harry Pickering, Ansumana Sillah, Judith Breuer, Robin L. Bailey, David Mabey and Martin J. Holland
2w ago
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 contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002–2003 collected ocular swabs across nine Gambian vi ..read more
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Genomic analysis of clinical Aeromonas isolates reveals genetic diversity but little evidence of genetic determinants for diarrhoeal disease
Microbial Genomics | Microbiology Society Journals
by 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
2w ago
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 isolates from children in Karachi, Pakistan, with moderate-to-severe diarrhoea (MSD) and from matched controls without diarrhoea that were collected as part of the Global Enteric Multicenter Study ..read more
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Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals
Microbial Genomics | Microbiology Society Journals
by Edder D. Bustos-Diaz, Arely Cruz-Perez, Diego Garfias-Gallegos, Paul M. D'Agostino, Michelle M. Gehringer, Angelica Cibrian-Jaramillo and Francisco Barona-Gomez
2w ago
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 sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach ..read more
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Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa
Microbial Genomics | Microbiology Society Journals
by Jamie Deery, Muireann Carmody, Rhiannon Flavin, Malwina Tomanek, Maria O'Keeffe, Gerard P. McGlacken and F. Jerry Reen
3w ago
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 and to uncover cluster-based relationships within the pangenome. Comparative genomic studies revealed that in the JGI IMG database alone ~86 000 LTTRs are present across the sequenced genomes (n ..read more
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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
Microbial Genomics | Microbiology Society Journals
by Monica Steffi Matchado, Malte Rühlemann, Sandra Reitmeier, Tim Kacprowski, Fabian Frost, Dirk Haller, Jan Baumbach and Markus List
3w ago
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 infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evalua ..read more
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Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers
Microbial Genomics | Microbiology Society Journals
by Daniel R. Leadbeater, Neil C. Bruce and Thierry Tonon
3w ago
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Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA
Microbial Genomics | Microbiology Society Journals
by Selvalakshmi Selvaraj Anand, Chin-Ting Wu, Jordan Bremer, Micah Bhatti, Todd J. Treangen, Awdhesh Kalia, Samuel A. Shelburne and William C. Shropshire
1M ago
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. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 ..read more
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