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Feodorova VA, Zaitsev SS, Khizhnyakova MA, Lavrukhin MS, Saltykov YV, Zaberezhny AD, Larionova OS. Complete genome of the Listeria monocytogenes strain AUF, used as a live listeriosis veterinary vaccine. Sci Data 2024; 11:643. [PMID: 38886393 PMCID: PMC11183264 DOI: 10.1038/s41597-024-03440-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 05/28/2024] [Indexed: 06/20/2024] Open
Abstract
Listeria monocytogenes (Lm) is a highly pathogenic bacterium that can cause listeriosis, a relatively rare food-borne infectious disease that affects farm, domestic, wild animals and humans as well. The infected livestock is the frequent sources of Lm. Vaccination is one of the methods of controlling listeriosis in target farm animals to prevent Lm-associated food contamination. Here we report the complete sequence of the Lm strain AUF attenuated from a fully-virulent Lm strain by ultraviolet irradiation, successfully used since the 1960s as a live whole-cell veterinary vaccine. The de novo assembled genome consists of a circular chromosome of 2,942,932 bp length, including more than 2,800 CDSs, 17 pseudogenes, 5 antibiotic resistance genes, and 56/92 virulence genes. Two wild Lm strains, the EGD and the 10403S that is also used in cancer Immunotherapy, were the closest homologs for the Lm strain AUF. Although all three strains belonged to different sequence types (ST), namely ST12, ST85, and ST1538, they were placed in the same genetic lineage II, CC7.
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Affiliation(s)
- Valentina A Feodorova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia.
- Department for Microbiology and Biotechnology, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia.
| | - Sergey S Zaitsev
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Mariya A Khizhnyakova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Maxim S Lavrukhin
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Yury V Saltykov
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
| | - Alexey D Zaberezhny
- All-Russian Scientific Research and Technological Institute of Biological Industry, Biocombinat, Moscow, Russia
| | - Olga S Larionova
- Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
- Department for Microbiology and Biotechnology, Saratov State University of Genetics, Biotechnology and Engineering named after N.I. Vavilov, Saratov, Russia
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2
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Geller AM, Shalom M, Zlotkin D, Blum N, Levy A. Identification of type VI secretion system effector-immunity pairs using structural bioinformatics. Mol Syst Biol 2024; 20:702-718. [PMID: 38658795 PMCID: PMC11148199 DOI: 10.1038/s44320-024-00035-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The type VI secretion system (T6SS) is an important mediator of microbe-microbe and microbe-host interactions. Gram-negative bacteria use the T6SS to inject T6SS effectors (T6Es), which are usually proteins with toxic activity, into neighboring cells. Antibacterial effectors have cognate immunity proteins that neutralize self-intoxication. Here, we applied novel structural bioinformatic tools to perform systematic discovery and functional annotation of T6Es and their cognate immunity proteins from a dataset of 17,920 T6SS-encoding bacterial genomes. Using structural clustering, we identified 517 putative T6E families, outperforming sequence-based clustering. We developed a logistic regression model to reliably quantify protein-protein interaction of new T6E-immunity pairs, yielding candidate immunity proteins for 231 out of the 517 T6E families. We used sensitive structure-based annotation which yielded functional annotations for 51% of the T6E families, again outperforming sequence-based annotation. Next, we validated four novel T6E-immunity pairs using basic experiments in E. coli. In particular, we showed that the Pfam domain DUF3289 is a homolog of Colicin M and that DUF943 acts as its cognate immunity protein. Furthermore, we discovered a novel T6E that is a structural homolog of SleB, a lytic transglycosylase, and identified a specific glutamate that acts as its putative catalytic residue. Overall, this study applies novel structural bioinformatic tools to T6E-immunity pair discovery, and provides an extensive database of annotated T6E-immunity pairs.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maor Shalom
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Blum
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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3
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Spatz S, Afonso CL. Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases. Vet Sci 2024; 11:239. [PMID: 38921986 PMCID: PMC11209166 DOI: 10.3390/vetsci11060239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology's operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the "core" of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through "implementation research" by a consortium of interested institutions working on common samples.
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Affiliation(s)
- Stephen Spatz
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA;
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4
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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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5
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Paniz-Mondolfi AE, Ramírez JD. FDA's proposed rule and its regulatory impact on emerging and reemerging neglected tropical diseases in the United States. PLoS Negl Trop Dis 2024; 18:e0012116. [PMID: 38722919 PMCID: PMC11081280 DOI: 10.1371/journal.pntd.0012116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
Diagnosing infectious diseases significantly influences patient care, aiding in outbreak identification, response, and public health monitoring. However, the range of FDA-approved molecular tests remains notably limited, especially concerning neglected tropical diseases (NTDs). Drawing upon our experience as one of the largest healthcare networks in the greater New York metropolitan area, this viewpoint manuscript aims to spotlight the existing diagnostic landscape and unmet clinical needs for 4 emerging NTDs increasingly prevalent in the United States, additionally, it delves into the possible adverse effects of the FDA's Proposed Rule on Laboratory-Developed Tests for these clinical conditions and the broader spectrum of NTDs.
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Affiliation(s)
- Alberto E. Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Juan David Ramírez
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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6
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Sabat AJ, Durfee T, Baldwin S, Akkerboom V, Voss A, Friedrich AW, Bathoorn E. The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing. Front Cell Infect Microbiol 2024; 14:1368923. [PMID: 38694516 PMCID: PMC11062135 DOI: 10.3389/fcimb.2024.1368923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements. Methods This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing. Results Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination. Conclusion This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.
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Affiliation(s)
- Artur J. Sabat
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tim Durfee
- DNASTAR, Inc., Madison, WI, United States
| | | | - Viktoria Akkerboom
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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7
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Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. FRONTIERS IN BIOINFORMATICS 2024; 4:1278228. [PMID: 38560517 PMCID: PMC10978663 DOI: 10.3389/fbinf.2024.1278228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.
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8
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Craney A, Miller S. Present and Future Non-Culture-Based Diagnostics: Stewardship Potentials and Considerations. Clin Lab Med 2024; 44:109-122. [PMID: 38280793 DOI: 10.1016/j.cll.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
The medical microbiologist plays a key role in the transition from culture-based to molecular test methods for diagnosis of infectious diseases. They must understand the scientific and technical bases underlying these tests along with their associated benefits and limitations and be able to educate administrators and patient providers on their proper use. Coordination of testing practices between clinical departments and the spectrum of public health and research laboratories is essential to optimize health care delivery.
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Affiliation(s)
- Arryn Craney
- Center for Infectious Disease Diagnostics and Research, Diagnostic Medicine Institute, Geisinger Health System, 100 North Academy Avenue, Danville, PA 17822, USA
| | - Steve Miller
- Delve Bio, Inc. and Department of Laboratory Medicine, University of California San Francisco, 953 Indiana Street, San Francisco, CA 94107, USA.
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9
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Mandal PK, Cleanthous A, Rigas V, Kleinecke M, Lawrence K, Leach AJ, Smith-Vaughan H, Morris PS, Beissbarth J, Marsh RL. Complete genome sequence of Oligella urethralis MSHR-50412PR, isolated from an ear discharge swab of a child with chronic suppurative otitis media. Microbiol Resour Announc 2024; 13:e0107123. [PMID: 38275301 PMCID: PMC10868213 DOI: 10.1128/mra.01071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Oligella urethralis are opportunistic pathogens typically associated with genitourinary infections. Here, we report the complete genome for an Oligella urethralis isolate recovered from ear discharge of a child with chronic suppurative otitis media (strain MSHR-50412PR). The genome comprises 2.58 Mb, with 2,448 coding sequences and 46.26% average GC content.
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Affiliation(s)
- Pappu K. Mandal
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Alexander Cleanthous
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Vanessa Rigas
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mariana Kleinecke
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Katrina Lawrence
- Health and Human Science, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Amanda J. Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Peter S. Morris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Robyn L. Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
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10
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Mizzi R, Plain KM, Timms VJ, Marsh I, Whittington RJ. Characterisation of IS1311 in Mycobacterium avium subspecies paratuberculosis genomes: Typing, continental clustering, microbial evolution and host adaptation. PLoS One 2024; 19:e0294570. [PMID: 38349924 PMCID: PMC10863896 DOI: 10.1371/journal.pone.0294570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/04/2023] [Indexed: 02/15/2024] Open
Abstract
Johne's disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP) is a global burden for livestock producers and has an association with Crohn's disease in humans. Within MAP there are two major lineages, S/Type I/TypeIII and C/Type II, that vary in phenotype including culturability, host preference and virulence. These lineages have been identified using the IS1311 element, which contains a conserved, single nucleotide polymorphism. IS1311 and the closely related IS1245 element belong to the IS256 family of insertion sequences, are dispersed throughout M. avium taxa but remain poorly characterised. To investigate the distribution and diversity of IS1311 in MAP, 805 MAP genomes were collated from public databases. IS1245 was absent, while IS1311 sequence, copy number and insertion loci were conserved between MAP S lineages and varied within the MAP C lineage. One locus was specific to the S strains, which contained nine IS1311 copies. In contrast, C strains contained either seven or eight IS1311 loci. Most insertion loci were associated with the boundaries of homologous regions that had undergone genome rearrangement between the MAP lineages, suggesting that this sequence may be a driver of recombination. Phylogenomic geographic clustering of MAP subtypes was demonstrated for the first time, at continental scale, and indicated that there may have been recent MAP transmission between Europe and North America, in contrast to Australia where importation of live ruminants is generally prohibited. This investigation confirmed the utility of IS1311 typing in epidemiological studies and resolved anomalies in past studies. The results shed light on potential mechanisms of niche/host adaptation, virulence of MAP and global transmission dynamics.
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Affiliation(s)
- Rachel Mizzi
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Karren M. Plain
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Verlaine J. Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, New South Wales, Australia
| | - Ian Marsh
- Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Richard J. Whittington
- School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
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11
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Reding C, Satapoomin N, Avison MB. Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo. Brief Bioinform 2024; 25:bbae057. [PMID: 38385882 PMCID: PMC10883467 DOI: 10.1093/bib/bbae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Increasing evidence suggests that microbial species have a strong within species genetic heterogeneity. This can be problematic for the analysis of prokaryote genomes, which commonly relies on a reference genome to guide the assembly process. Differences between reference and sample genomes will therefore introduce errors in final assembly, jeopardizing the detection from structural variations to point mutations-critical for genomic surveillance of antibiotic resistance. Here we present Hound, a pipeline that integrates publicly available tools to assemble prokaryote genomes de novo, detect user-given genes by similarity to report mutations found in the coding sequence, promoter, as well as relative gene copy number within the assembly. Importantly, Hound can use the query sequence as a guide to merge contigs, and reconstruct genes that were fragmented by the assembler. To showcase Hound, we screened through 5032 bacterial whole-genome sequences isolated from farmed animals and human infections, using the amino acid sequence encoded by blaTEM-1, to detect and predict resistance to amoxicillin/clavulanate which is driven by over-expression of this gene. We believe this tool can facilitate the analysis of prokaryote species that currently lack a reference genome, and can be scaled either up to build automated systems for genomic surveillance or down to integrate into antibiotic susceptibility point-of-care diagnostics.
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Affiliation(s)
- Carlos Reding
- University of Bristol School of Cellular and Molecular Medicine, University Walk, Bristol, BS8 1TD Bristol, UK
| | - Naphat Satapoomin
- University of Bristol School of Cellular and Molecular Medicine, University Walk, Bristol, BS8 1TD Bristol, UK
| | - Matthew B Avison
- University of Bristol School of Cellular and Molecular Medicine, University Walk, Bristol, BS8 1TD Bristol, UK
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12
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Charalampous T, Alcolea-Medina A, Snell LB, Alder C, Tan M, Williams TGS, Al-Yaakoubi N, Humayun G, Meadows CIS, Wyncoll DLA, Paul R, Hemsley CJ, Jeyaratnam D, Newsholme W, Goldenberg S, Patel A, Tucker F, Nebbia G, Wilks M, Chand M, Cliff PR, Batra R, O'Grady J, Barrett NA, Edgeworth JD. Routine Metagenomics Service for ICU Patients with Respiratory Infection. Am J Respir Crit Care Med 2024; 209:164-174. [PMID: 37938162 PMCID: PMC10806431 DOI: 10.1164/rccm.202305-0901oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/08/2023] [Indexed: 11/09/2023] Open
Abstract
Rationale: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Objectives: Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. Methods: RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy's and St Thomas' NHS Foundation Trust, London. Measurements and Main Results: During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1-7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes (n = 12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. Conclusions: This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.
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Affiliation(s)
- Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Infection Sciences, Synnovis, London, United Kingdom
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Department of Infectious Diseases and
| | - Christopher Alder
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Department of Infectious Diseases and
| | - Mark Tan
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
| | | | - Noor Al-Yaakoubi
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
| | - Gul Humayun
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
| | - Christopher I S Meadows
- Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Critical Care Directorate, Guy's and St Thomas' NHS Foundation Trust, London, England
| | - Duncan L A Wyncoll
- Critical Care Directorate, Guy's and St Thomas' NHS Foundation Trust, London, England
| | - Richard Paul
- Critical Care Directorate, Guy's and St Thomas' NHS Foundation Trust, London, England
| | | | | | | | | | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Department of Infectious Diseases and
| | | | | | - Mark Wilks
- London School of Medicine and Dentistry, Queen Mary University, London, United Kingdom
| | - Meera Chand
- UK Health Security Agency, London, United Kingdom; and
| | | | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Department of Infectious Diseases and
| | | | - Nicholas A Barrett
- Critical Care Directorate, Guy's and St Thomas' NHS Foundation Trust, London, England
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences and
- Department of Infectious Diseases and
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Isidro J, Escudero R, Luque-Larena JJ, Pinto M, Borges V, González-Martín-Niño R, Duarte S, Vieira L, Mougeot F, Vidal D, Herrera-Rodríguez D, Rodríguez-Pastor R, Herrero-Cófreces S, Jubete-Tazo F, Gomes JP, Lopes de Carvalho I. Strengthening the genomic surveillance of Francisella tularensis by using culture-free whole-genome sequencing from biological samples. Front Microbiol 2024; 14:1277468. [PMID: 38249473 PMCID: PMC10797068 DOI: 10.3389/fmicb.2023.1277468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability of strains and subsequently WGS data is still limited. Methods To surpass these constraints, we aimed to implement a culture-free approach to capture and sequence F. tularensis genomes directly from complex samples. Biological samples obtained from 50 common voles and 13 Iberian hares collected in Spain were confirmed as positive for F. tularensis subsp. holarctica and subjected to a WGS target capture and enrichment protocol, using RNA oligonucleotide baits designed to cover F. tularensis genomic diversity. Results We obtained full genome sequences of F. tularensis from 13 animals (20.6%), two of which had mixed infections with distinct genotypes, and achieved a higher success rate when compared with culture-dependent WGS (only successful for two animals). The new genomes belonged to different clades commonly identified in Europe (B.49, B.51 and B.262) and subclades. Despite being phylogenetically closely related to other genomes from Spain, the detected clusters were often found in other countries. A comprehensive phylogenetic analysis, integrating 599 F. tularensis subsp. holarctica genomes, showed that most (sub)clades are found in both humans and animals and that closely related strains are found in different, and often geographically distant, countries. Discussion Overall, we show that the implemented culture-free WGS methodology yields timely, complete and high-quality genomic data of F. tularensis, being a highly valuable approach to promote and potentiate the genomic surveillance of F. tularensis and ultimately increase the knowledge on the genomics, ecology and epidemiology of this highly infectious pathogen.
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Affiliation(s)
- Joana Isidro
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Raquel Escudero
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Juan José Luque-Larena
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rosa González-Martín-Niño
- Reference and Research Laboratory on Special Pathogens, National Centre for Microbiology (CNM), Carlos II Health Institute (ISCIII), Madrid, Spain
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - François Mougeot
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Dolors Vidal
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Daniel Herrera-Rodríguez
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
- Área de Microbiología, Facultad de Medicina, Universidad de Catilla-La Mancha (UCLM), Ciudad Real, Spain
| | - Ruth Rodríguez-Pastor
- Department of Parasitology, Veterinary Faculty, University of Zaragoza, Zaragoza, Spain, Zaragoza, Spain
- Departamento de Parasitología, Facultad de Veterinaria, Universidad de Zaragoza, Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Silvia Herrero-Cófreces
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - Fernando Jubete-Tazo
- Departamento de Ciencias Agroforestales, Instituto Universitario de Investigación en Gestión Forestal Sostenible (iuFOR), E.T.S. Ingenierías Agrarias, Universidad de Valladolid, Palencia, Spain
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Center (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Isabel Lopes de Carvalho
- Emergency and Biopreparedness Unit, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Hauser S, Lazarevic V, Tournoud M, Ruppé E, Santiago Allexant E, Guigon G, Schicklin S, Lanet V, Girard M, Mirande C, Gervasi G, Schrenzel J. A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia. Microbiol Spectr 2023; 11:e0129423. [PMID: 37889000 PMCID: PMC10715005 DOI: 10.1128/spectrum.01294-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.
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Affiliation(s)
| | - V. Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - E. Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - V. Lanet
- bioMérieux, Marcy-l'Étoile, France
| | - M. Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - C. Mirande
- bioMérieux, La Balme-les-Grottes, France
| | | | - J. Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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15
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Constantinides B, Hunt M, Crook DW. Hostile: accurate decontamination of microbial host sequences. Bioinformatics 2023; 39:btad728. [PMID: 38039142 PMCID: PMC10749771 DOI: 10.1093/bioinformatics/btad728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/11/2023] [Accepted: 11/29/2023] [Indexed: 12/03/2023] Open
Abstract
MOTIVATION Microbial sequences generated from clinical samples are often contaminated with human host sequences that must be removed for ethical and legal reasons. Care must be taken to excise host sequences without inadvertently removing target microbial sequences to the detriment of downstream analyses such as variant calling and de novo assembly. RESULTS To facilitate accurate host decontamination of both short and long sequencing reads, we developed Hostile, a tool capable of accurate host read removal using a laptop. We demonstrate that our approach removes at least 99.6% of real human reads and retains at least 99.989% of simulated bacterial reads. Using Hostile with a masked reference genome further increases bacterial read retention (≥99.997%) with negligible (≤0.001%) reduction in human read removal performance. Compared with an existing tool, Hostile removes 21%-23% more human short reads and 21-43 times fewer bacterial reads, typically in less time. AVAILABILITY AND IMPLEMENTATION Hostile is implemented as an MIT-licensed Python package available from https://github.com/bede/hostile together with supplementary material.
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Affiliation(s)
- Bede Constantinides
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
| | - Martin Hunt
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
- EMBL-EBI, Wellcome Genome Campus, Cambridgeshire CB10 1SD, United Kingdom
| | - Derrick W Crook
- NDM Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxfordshire OX3 9DU, United Kingdom
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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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17
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Heitz M, Levrat A, Lazarevic V, Barraud O, Bland S, Santiago-Allexant E, Louis K, Schrenzel J, Hauser S. Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study. Respir Res 2023; 24:285. [PMID: 37968636 PMCID: PMC10648381 DOI: 10.1186/s12931-023-02597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise. METHODS This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients. RESULTS A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test. CONCLUSIONS This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.
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Affiliation(s)
- Morgane Heitz
- Intensive Care Unit, Annecy-Genevois Hospital, Site d'Annecy, 1 Avenue de L'hôpital, 74370, Metz Tessy, France.
| | - Albrice Levrat
- Intensive Care Unit, Annecy-Genevois Hospital, Site d'Annecy, 1 Avenue de L'hôpital, 74370, Metz Tessy, France
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olivier Barraud
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Bland
- Bacteriology Laboratory, Annecy-Genevois Hospital, Metz Tessy, France
| | | | - Karen Louis
- BIOASTER Microbiology Technology Institute, 40 Avenue Tony Garnier, 69007, Lyon, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sébastien Hauser
- bioMérieux Grenoble, Centre Christophe Mérieux, 5 Rue Des Berges, 38024, Grenoble Cedex 01, France
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18
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Ma J, Zhao H, Mo S, Li J, Ma X, Tang Y, Li H, Liu Z. Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii. Microb Genom 2023; 9:001107. [PMID: 37754275 PMCID: PMC10569733 DOI: 10.1099/mgen.0.001107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.
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Affiliation(s)
- Jiayue Ma
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Honghao Zhao
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Shuangyi Mo
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, PR China
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Scott NE, Edwin Erayil S, Kline SE, Selmecki A. Rapid Evolution of Multidrug Resistance in a Candida lusitaniae Infection during Micafungin Monotherapy. Antimicrob Agents Chemother 2023; 67:e0054323. [PMID: 37428075 PMCID: PMC10433866 DOI: 10.1128/aac.00543-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Candida (Clavispora) lusitaniae is a rare, emerging non-albicans Candida species that can cause life-threatening invasive infections, spread within hospital settings, and rapidly acquire antifungal drug resistance, including multidrug resistance. The frequency and spectrum of mutations causing antifungal drug resistance in C. lusitaniae are poorly understood. Analyses of serial clinical isolates of any Candida species are uncommon and often analyze a limited number of samples collected over months of antifungal therapy with multiple drug classes, limiting the ability to understand relationships between drug classes and specific mutations. Here, we performed comparative genomic and phenotypic analysis of 20 serial C. lusitaniae bloodstream isolates collected daily from an individual patient treated with micafungin monotherapy during a single 11-day hospital admission. We identified isolates with decreased micafungin susceptibility 4 days after initiation of antifungal therapy and a single isolate with increased cross-resistance to micafungin and fluconazole, despite no history of azole therapy in this patient. Only 14 unique single nucleotide polymorphisms (SNPs) were identified between all 20 samples, including three different FKS1 alleles among isolates with decreased micafungin susceptibility and an ERG3 missense mutation found only in the isolate with increased cross-resistance to both micafungin and fluconazole. This is the first clinical evidence of an ERG3 mutation in C. lusitaniae that occurred during echinocandin monotherapy and is associated with cross-resistance to multiple drug classes. Overall, the evolution of multidrug resistance in C. lusitaniae is rapid and can emerge during treatment with only first-line antifungal therapy.
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Affiliation(s)
- Nancy E. Scott
- University of Minnesota, Bioinformatics and Computational Biology Program, Minneapolis, Minnesota, USA
- University of Minnesota, Department of Microbiology and Immunology, Minneapolis, Minnesota, USA
| | - Serin Edwin Erayil
- University of Minnesota Medical School, Department of Medicine, Division of Infectious Diseases and International Medicine, Minneapolis, Minnesota, USA
| | - Susan E. Kline
- University of Minnesota Medical School, Department of Medicine, Division of Infectious Diseases and International Medicine, Minneapolis, Minnesota, USA
| | - Anna Selmecki
- University of Minnesota, Bioinformatics and Computational Biology Program, Minneapolis, Minnesota, USA
- University of Minnesota, Department of Microbiology and Immunology, Minneapolis, Minnesota, USA
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20
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Qiu J, Shi Y, Zhao F, Xu Y, Xu H, Dai Y, Cao Y. The Pan-Genomic Analysis of Corynebacterium striatum Revealed its Genetic Characteristics as an Emerging Multidrug-Resistant Pathogen. Evol Bioinform Online 2023; 19:11769343231191481. [PMID: 37576785 PMCID: PMC10422898 DOI: 10.1177/11769343231191481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
Corynebacterium striatum is a Gram-positive bacterium that is straight or slightly curved and non-spore-forming. Although it was originally believed to be a part of the normal microbiome of human skin, a growing number of studies have identified it as a cause of various chronic diseases, bacteremia, and respiratory infections. However, despite its increasing importance as a pathogen, the genetic characteristics of the pathogen population, such as genomic characteristics and differences, the types of resistance genes and virulence factors carried by the pathogen and their distribution in the population are poorly understood. To address these knowledge gaps, we conducted a pan-genomic analysis of 314 strains of C. striatum isolated from various tissues and geographic locations. Our analysis revealed that C. striatum has an open pan-genome, comprising 5692 gene families, including 1845 core gene families, 2362 accessory gene families, and 1485 unique gene families. We also found that C. striatum exhibits a high degree of diversity across different sources, but strains isolated from skin tissue are more conserved. Furthermore, we identified 53 drug resistance genes and 42 virulence factors by comparing the strains to the drug resistance gene database (CARD) and the pathogen virulence factor database (VFDB), respectively. We found that these genes and factors are widely distributed among C. striatum, with 77.7% of strains carrying 2 or more resistance genes and displaying primary resistance to aminoglycosides, tetracyclines, lincomycin, macrolides, and streptomycin. The virulence factors are primarily associated with pathogen survival within the host, iron uptake, pili, and early biofilm formation. In summary, our study provides insights into the population diversity, resistance genes, and virulence factors ofC. striatum from different sources. Our findings could inform future research and clinical practices in the diagnosis, prevention, and treatment of C. striatum-associated diseases.
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Affiliation(s)
- Junhui Qiu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yulan Shi
- Wound Treatment Center of West China Hospital of Sichuan University, West China College of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Fei Zhao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yan Dai
- Wound Treatment Center of West China Hospital of Sichuan University, West China College of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Anscome C, Zuza A, Roberts AP, Heinz E, Thomson NR, Feasey NA. Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity. Microb Genom 2023; 9:mgen001035. [PMID: 37314322 PMCID: PMC10327512 DOI: 10.1099/mgen.0.001035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/15/2023] [Indexed: 06/15/2023] Open
Abstract
Escherichia coli is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicrobials may not be available. A large number of E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli colonising adults in Blantyre, Malawi to assess bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli genomes and sequence type (ST)-specific collections for our three most commonly identified STs. These were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were bla CTX-M, mirroring global trends. However, 37 % of Malawian isolates did not cluster with any isolates in the curated multicountry collection and phylogenies were consistent with locally spreading monophyletic clades, including within the globally distributed, carbapenemase-associated B4/H24RxC ST410 lineage. A single ST2083 isolate in this collection harboured a carbapenemase gene. Long read sequencing demonstrated the presence of a globally distributed ST410-associated carbapenemase carrying plasmid in this isolate, which was absent from the ST410 strains in our collection. We conclude there is a risk that carbapenem resistance in E. coli could proliferate rapidly in Malawi under increasing selection pressure, and that both ongoing antimicrobial stewardship and genomic surveillance are critical as local carbapenem use increases.
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Affiliation(s)
- Joseph M. Lewis
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Madalitso Mphasa
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Rachel Banda
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Jane Mallewa
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscome
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Allan Zuza
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- London School of Hygiene and Tropical Medicine, London, UK
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23
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Everhart J, Henshaw NG. Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients. Infect Dis Clin North Am 2023:S0891-5520(23)00038-7. [PMID: 37244805 DOI: 10.1016/j.idc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.
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Affiliation(s)
- James Everhart
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA.
| | - Nancy G Henshaw
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA
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24
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Botts RT, Page DM, Bravo JA, Brown ML, Castilleja CC, Guzman VL, Hall S, Henderson JD, Kenney SM, Lensink ME, Paternoster MV, Pyle SL, Ustick L, Walters-Laird CJ, Top EM, Cummings DE. Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases. Plasmid 2023; 126:102682. [PMID: 37023995 PMCID: PMC10213127 DOI: 10.1016/j.plasmid.2023.102682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10-3 transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.
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Affiliation(s)
- Ryan T Botts
- Department of Mathematics, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Dawne M Page
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Joseph A Bravo
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Madelaine L Brown
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Claudia C Castilleja
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Victoria L Guzman
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Samantha Hall
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Jacob D Henderson
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Shelby M Kenney
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Mariele E Lensink
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Megan V Paternoster
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Sarah L Pyle
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Lucas Ustick
- Department of Mathematics, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America; Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Chara J Walters-Laird
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America
| | - Eva M Top
- Department of Biological Sciences, Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, 875 Perimeter Dr., Moscow, ID 83844, United States of America
| | - David E Cummings
- Department of Biology, Point Loma Nazarene University, 3900 Lomaland Dr., San Diego, CA 92106, United States of America.
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25
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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26
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Qin G, Ai X, Xu J, Yang Y. Dual RNA-seq of spleens extracted from channel catfish infected with Aeromonas veronii reveals novel insights into host-pathogen interactions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114609. [PMID: 36739739 DOI: 10.1016/j.ecoenv.2023.114609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Interactions between host and pathogen are involving various dynamic changes in transcript expression and critical for understanding host immunity against infections and its associated pathogenesis. Herein, we established a model of channel catfish infected with Aeromonas veronii. The infected fish had prominent body surface bleeding, and the spleen showed hyperemia and swelling. Then, the spleen of channel catfish infected with A. veronii was analyzed by dual RNA sequencing (RNA-seq), and the transcriptome data were compared with uninfected channel catfish spleen or bacteria cultured in vitro. The transcript expression profile of pathogen-host interaction between A. veronii and channel catfish was successfully studied. During infection, the host was enriched for multiple immune-related signaling pathways, such as the Toll-like receptor signaling pathway, Cytokine-cytokine receptor interaction, and T cell receptor signaling pathway; and significantly upregulated for many innate immune-related genes, including IL-8. At the same time, we found that A. veronii mainly harmed the host spleen through hemolysin. Our current findings are of great significance in clarifying the pathogenesis of channel catfish induced by A. veronii and provide gene targets for developing preventive measures.
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Affiliation(s)
- Gaixiao Qin
- College of Animal Science and Technology, Henan university of animal husbandry and Economy, Zhengzhou 450046, China
| | - Xiaohui Ai
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Jin Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Yibin Yang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
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27
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A case for investment in clinical metagenomics in low-income and middle-income countries. THE LANCET. MICROBE 2023; 4:e192-e199. [PMID: 36563703 DOI: 10.1016/s2666-5247(22)00328-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.
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28
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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0339222. [PMID: 36445077 PMCID: PMC9769990 DOI: 10.1128/spectrum.03392-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M. avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.
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29
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Gan L, Zheng J, Xu WH, Lin J, Liu J, Zhang Y, Wu Z, Lv Z, Jia Y, Guo Q, Chen S, Liu C, Defoirdt T, Qin Q, Liu Y. Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei. Sci Rep 2022; 12:16296. [PMID: 36175476 PMCID: PMC9522882 DOI: 10.1038/s41598-022-20565-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
The muscle of aquatic crustaceans is perishable and susceptible to environmental contamination. Vibrio harveyi is a widely occurring pathogen in aquatic animals. Here, bath treatment with a virulent V. harveyi strain (which was added directly in the rearing water to imitate environmental contamination) isolated from the muscle of the whiteleg shrimp, Litopenaeus vannamei, caused the muscle of Li. vannamei to display a whitish-opaque appearance due to microscopic changes including muscle lysis, muscle fiber damage and microbial colonization. When administered orally by incorporating this isolate in feed (which is an imitation of infection via natural route), rather than direct invasion followed by colonization in the muscle, this isolate indirectly stimulated severe muscle necrosis in Li. vannamei via steering the enrichment of two important (human) pathogens, V. cholerae and V. vulnificus, and one environmental bacterium Pseudomonas oleovorans, based on the meta-taxonomic analyses. In addition to the scientifically proven viral diseases, our research proved that bacterial agents are also capable of causing muscle spoilage in crustaceans via changing the microbial composition, and that the crustaceans might be exploited as the wide-spectrum sensitive bio-detector to indicate the extent of microbial contamination.
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Affiliation(s)
- Lian Gan
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Jianwei Zheng
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wei-Hua Xu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianhao Lin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jingshu Liu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yu Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zizhan Wu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaolin Lv
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Youming Jia
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Qingqi Guo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shijun Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Chuanhe Liu
- Instrumental Analysis and Research Center, South China Agricultural University, Guangzhou, China
| | - Tom Defoirdt
- Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium
| | - Qiwei Qin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yiying Liu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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30
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In Silico Study of Cell Surface Structures of Parabacteroides distasonis Involved in Its Maintenance within the Gut Microbiota. Int J Mol Sci 2022; 23:ijms23169411. [PMID: 36012685 PMCID: PMC9409006 DOI: 10.3390/ijms23169411] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
The health-promoting Parabacteroides distasonis, which is part of the core microbiome, has recently received a lot of attention, showing beneficial properties for its host and potential as a new biotherapeutic product. However, no study has yet investigated the cell surface molecules and structures of P. distasonis that allow its maintenance within the gut microbiota. Moreover, although P. distasonis is strongly recognized as an intestinal commensal species with benefits for its host, several works displayed controversial results, showing it as an opportunistic pathogen. In this study, we reported gene clusters potentially involved in the synthesis of capsule, fimbriae-like and pili-like cell surface structures in 26 P. distasonis genomes and applied the new RfbA-typing classification in order to better understand and characterize the beneficial/pathogenic behavior related to P. distasonis strains. Two different types of fimbriae, three different types of pilus and up to fourteen capsular polysaccharide loci were identified over the 26 genomes studied. Moreover, the addition of data to the rfbA-type classification modified the outcome by rearranging rfbA genes and adding a fifth group to the classification. In conclusion, the strain variability in terms of external proteinaceous structure could explain the inter-strain differences previously observed of P. distasonis adhesion capacities and its potential pathogenicity, but no specific structure related to P. distasonis beneficial or detrimental activity was identified.
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31
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Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt. Microorganisms 2022; 10:microorganisms10081585. [PMID: 36014003 PMCID: PMC9415397 DOI: 10.3390/microorganisms10081585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.
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32
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Damas MSF, Ferreira RL, Campanini EB, Soares GG, Campos LC, Laprega PM, Soares da Costa A, Freire CCDM, Pitondo-Silva A, Cerdeira LT, da Cunha AF, Pranchevicius MCDS. Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. Front Med (Lausanne) 2022; 9:931379. [PMID: 35966843 PMCID: PMC9366087 DOI: 10.3389/fmed.2022.931379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.
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Affiliation(s)
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | - Pedro Mendes Laprega
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Andrea Soares da Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - André Pitondo-Silva
- Programa de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, Brazil
- *Correspondence: Maria-Cristina da Silva Pranchevicius,
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Versoza CJ, Howell AA, Aftab T, Blanco M, Brar A, Chaffee E, Howell N, Leach W, Lobatos J, Luca M, Maddineni M, Mirji R, Mitra C, Strasser M, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages. Viruses 2022; 14:v14081647. [PMID: 36016269 PMCID: PMC9413003 DOI: 10.3390/v14081647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.
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Affiliation(s)
- Cyril J. Versoza
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Abigail A. Howell
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Tanya Aftab
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Madison Blanco
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Akarshi Brar
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Elaine Chaffee
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Nicholas Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Willow Leach
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Jackelyn Lobatos
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Michael Luca
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Meghna Maddineni
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Ruchira Mirji
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Corinne Mitra
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Maria Strasser
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Correspondence:
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Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units. Microbiol Spectr 2022; 10:e0074622. [PMID: 35861525 PMCID: PMC9430677 DOI: 10.1128/spectrum.00746-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of metagenomic next-generation sequencing (mNGS) was evaluated and compared with that of conventional culture testing in patients with sepsis. Prospective blood and bronchoalveolar lavage fluid (BALF) samples from 50 patients with sepsis were tested using cultures (bacterial, fungal, and viral) and mNGS of microbial DNA (blood and BALF) and RNA (BALF). mNGS had higher detection rates than blood culture (88.0% versus 26.0%, P < 0.001) and BALF culture (92.0% versus 76.0%, P = 0.054). RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. The number of multiple detections per specimen was higher in BALF (92.0%) than in blood (78.0%) samples, and the highest number of pathogens detected in a single specimen was 32. Among blood samples, compared to cultures, mNGS detected significantly more bacteria (P < 0.001), fungi (P = 0.012), and viruses (P < 0.001), whereas BALF mNGS had a higher detection rate for bacteria (P < 0.001) and viruses (P < 0.001). The percentage of mNGS-positive samples was significantly higher than that of culture-positive samples for several Gram-negative bacteria, some Gram-positive bacteria, and viruses, but not fungi. Mycobacteria had a higher detection rate by culture than by mNGS, but the difference was not significant due to the small sample size. The positive and negative agreements with 95% confidence intervals of mNGS and culture were 62.0% (50.4 to 72.7) and 96.8% (96.5 to 97.1), respectively. mNGS offers a sensitive diagnostic method for patients with sepsis and is promising for the detection of multipathogen infections. Clinical correlation is advised to interpret mNGS data due to the lack of unified diagnostic criteria. IMPORTANCE Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms. Among patients with sepsis, we showed that mNGS methods had higher positive rates than culture methods, especially for bacteria, viruses, and multipathogen infections, which are difficult to culture and detect in patients treated with antibiotics. RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. mNGS also showed a high negative percent agreement with cultures. However, the interpretation of mNGS data should be combined with clinical data and conventional methods considering the lack of unified diagnostic criteria.
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Biofilm cultivation facilitates coexistence and adaptive evolution in an industrial bacterial community. NPJ Biofilms Microbiomes 2022; 8:59. [PMID: 35858930 PMCID: PMC9300721 DOI: 10.1038/s41522-022-00323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
The majority of ecological, industrial and medical impacts of bacteria result from diverse communities containing multiple species. This diversity presents a significant challenge as co-cultivation of multiple bacterial species frequently leads to species being outcompeted and, with this, the possibility to manipulate, evolve and improve bacterial communities is lost. Ecological theory predicts that a solution to this problem will be to grow species in structured environments, which reduces the likelihood of competitive exclusion. Here, we explored the ability of cultivation in a structured environment to facilitate coexistence, evolution, and adaptation in an industrially important community: Lactococcus lactis and Leuconostoc mesenteroides frequently used as dairy starter cultures. As commonly occurs, passaging of these two species together in a liquid culture model led to the loss of one species in 6 of 20 lineages (30%). By contrast, when we co-cultured the two species as biofilms on beads, a stable coexistence was observed in all lineages studied for over 100 generations. Moreover, we show that the co-culture drove evolution of new high-yield variants, which compared to the ancestor grew more slowly, yielded more cells and had enhanced capability of biofilm formation. Importantly, we also show that these high-yield biofilm strains did not evolve when each species was passaged in monoculture in the biofilm model. Therefore, both co-culture and the biofilm model were conditional for these high-yield strains to evolve. Our study underlines the power of ecological thinking—namely, the importance of structured environments for coexistence—to facilitate cultivation, evolution, and adaptation of industrially important bacterial communities.
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Barker DF. A synergistic arrangement of two unrelated IS elements facilitates adjacent deletion in Micrococcus luteus ATCC49732. FEMS Microbiol Lett 2022; 369:6646518. [DOI: 10.1093/femsle/fnac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/07/2022] [Accepted: 07/15/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Mutants of M. luteus strain ATCC49732 lacking the yellow pigment sarcinaxanthin were observed at an unexpectedly high frequency and the molecular basis was investigated. PCR probing revealed complete deletion of the crt biosynthetic operon in 11/14 mutants. Inverse PCR was used to identify a common breakpoint 35 kb downstream from crt precisely at the end of the right inverted repeat (IRR) of a partial ISMlu8 element that lies between two inversely oriented full-length ISMlu2. Three different breakpoints 5′ to crt were found with the sequence CTAG one bp 5′ to each novel junction. Analysis of 35 genomic sites with single ISMlu8 insertions showed that ISMlu8 transposase has high specificity for CTAG, implicating its key role in formation of the Δcrt deletions. No downstream deletion endpoints were observed at an immediately adjacent ISMlu8 with a nearly identical IRR in the same orientation and slightly closer to the crt operon, indicating that access of ISMlu8 transposase to the ISMlu2-flanked ISMlu8 IRR is greatly enhanced by the surrounding inverted repeat arrangement. The association of high frequency genomic rearrangement with this distinctive natural configuration of ISs from two different IS families offers a new insight into IS element evolutionary potential.
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Affiliation(s)
- David F Barker
- Department of Medical Laboratory Science, Bellarmine University , 2001 Newburg Road, Louisville, KY 40205 , USA
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Ellena V, Steiger MG. The importance of complete and high-quality genome sequences in Aspergillus niger research. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:935993. [PMID: 37746178 PMCID: PMC10512394 DOI: 10.3389/ffunb.2022.935993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/27/2022] [Indexed: 09/26/2023]
Abstract
The possibility to sequence the entire genome of an organism revolutionized the fields of biology and biotechnology. The first genome sequence of the important filamentous fungus Aspergillus niger was obtained in 2007, 11 years after the release of the first eukaryotic genome sequence. From that moment, genomics of A. niger has seen major progresses, facilitated by the advances in the sequencing technologies and in the methodologies for gene function prediction. However, there are still challenges to face when trying to obtain complete genomes, equipped with all the repetitive sequences that they contain and without omitting the mitochondrial sequences. The aim of this perspective article is to discuss the current status of A. niger genomics and draw attention to the open challenges that the fungal community should address to move research of this important fungus forward.
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Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
| | - Matthias G. Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology (TU Wien), Vienna, Austria
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Abstract
The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI’s RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI’s RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI’s core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an “elephant in the room” for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. IMPORTANCE The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI’s RefSeq database. We present a comparative analysis of de novo-assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.
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Abstract
The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect Neisseria species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2022; 10:80. [PMID: 35847383 PMCID: PMC9243550 DOI: 10.12688/f1000research.39214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Affiliation(s)
| | - Marco Fabbri
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Guy Van den Eede
- European Commission Joint Research Centre, Ispra, Italy
- European Commission Joint Research Centre, Geel, Belgium
| | - Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Catherine Carrillo
- Ottawa Laboratory – Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | | | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teresa Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, Madrid, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul Hammer
- BIOMES. NGS GmbH c/o Technische Hochschule Wildau, Wildau, Germany
| | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, Lyon, France
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Thierry Naas
- French-NRC for CPEs, Service de Bactériologie-Hygiène, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | | | - John Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Lukas M. Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Present address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Chen F, Wang P, Yin Z, Yang H, Hu L, Yu T, Jing Y, Guan J, Wu J, Zhou D. VIM-encoding Inc pSTY plasmids and chromosome-borne integrative and mobilizable elements (IMEs) and integrative and conjugative elements (ICEs) in Pseudomonas. Ann Clin Microbiol Antimicrob 2022; 21:10. [PMID: 35264204 PMCID: PMC8905914 DOI: 10.1186/s12941-022-00502-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The carbapenem-resistance genes blaVIM are widely disseminated in Pseudomonas, and frequently harbored within class 1 integrons that reside within various mobile genetic elements (MGEs). However, there are few reports on detailed genetic dissection of blaVIM-carrying MGEs in Pseudomonas. METHODS This study presented the complete sequences of five blaVIM-2/-4-carrying MGEs, including two plasmids, two chromosomal integrative and mobilizable elements (IMEs), and one chromosomal integrative and conjugative element (ICE) from five different Pseudomonas isolates. RESULTS The two plasmids were assigned to a novel incompatibility (Inc) group IncpSTY, which included only seven available plasmids with determined complete sequences and could be further divided into three subgroups IncpSTY-1/2/3. A detailed sequence comparison was then applied to a collection of 15 MGEs belonging to four different groups: three representative IncpSTY plasmids, two Tn6916-related IMEs, two Tn6918-related IMEs, and eight Tn6417-related ICEs and ten of these 15 MGEs were first time identified. At least 22 genes involving resistance to seven different categories of antibiotics and heavy metals were identified within these 15 MGEs, and most of these resistance genes were located within the accessory modules integrated as exogenous DNA regions into these MGEs. Especially, eleven of these 15 MGEs carried the blaVIM genes, which were located within 11 different concise class 1 integrons. CONCLUSION These blaVIM-carrying integrons were further integrated into the above plasmids, IMEs/ICEs with intercellular mobility. These MGEs could transfer between Pseudomonas isolates, which resulted in the accumulation and spread of blaVIM among Pseudomonas and thus was helpful for the bacteria to survival from the stress of antibiotics. Data presented here provided a deeper insight into the genetic diversification and evolution of VIM-encoding MGEs in Pseudomonas.
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Affiliation(s)
- Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,Basic Medical College, Guizhou Medical University, Guiyang, 550025, China.,Guangzhou Medical University, Guangzhou, 511436, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ting Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jiayao Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jiahong Wu
- Basic Medical College, Guizhou Medical University, Guiyang, 550025, China.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,Guangzhou Medical University, Guangzhou, 511436, China.
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Bank NC, Singh V, Rodriguez-Palacios A. Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and hypothesis for pathogenic vs. probiotic strain differentiation. Gut Microbes 2022; 14:1997293. [PMID: 35090379 PMCID: PMC8803095 DOI: 10.1080/19490976.2021.1997293] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus, and a gut commensal of the Bacteroidetes phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen Pdis is a probiotic. We posit there is an urgent need to characterize the pathogenicity of Pdis strain-strain variability. Unfortunately, no methods/insights exist to classify Bacteroidetes for this purpose. Herein, we developed a virulence gene-based classification system for Pdis and Bacteroidetes to facilitate pathogenic-vs-probiotic characterization. We used DNA in silico methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) 'rfbA O-antigen-synthesis gene'. We then performed phylogenetic analysis of rfbA from fourteen Pdis complete genomes (21 genes), other Parabacteroides, Bacteroidetes, and Enterobacteriaceae; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that Pdis can be classified into four lineages (based on gene gaps/insertions) which we designated rfbA-Types I, II, III, and IV. In context, we found 14 additional rfbA-types (I-XVIII) interspersed with numerous Bacteroidetes and pathogenic Enterobacteriaceae forming three major "rfbA-superclusters." For laboratory rfbA-Typing implementation, we developed a PCR-primer strategy to amplify Pdis rfbA genes (100%-specificity) to conduct MboII-RFLP and sub-classify Pdis. In-silico primers for other Bacteroidetes are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene lpxK confirmed rfbA as highly discriminant. In conclusion, rfbA-Typing classifies Bacteroidetes/Pdis into unique clusters/superclusters given rfbA copy/sequence variability. Analysis revealed that most pathogenic Pdis strains are single-copy rfbA-Type I . The relevance of the rfbA strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.
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Affiliation(s)
- Nicholas C. Bank
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States,School of Medicine, Digestive Health Research Institute, Case Western Reserve University, Cleveland, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, United States,CONTACT Alex Rodriguez-Palacios Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, United States; School of Medicine, Digestive Health Research Institute, Case Western Reserve University, Cleveland, United States; University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, United States
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Butler J, Kelly SD, Muddiman KJ, Besinis A, Upton M. Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1. J Med Microbiol 2022; 71. [PMID: 35113779 PMCID: PMC8941954 DOI: 10.1099/jmm.0.001501] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Introduction.Cupriavidus pauculus is historically found in soil and water but has more recently been reported to cause human infection and death. Hospital sink traps can serve as a niche for bacterial persistence and a platform for horizontal gene transfer, with evidence of dissemination of pathogens in hospital plumbing systems driving nosocomial infection. Gap Statement. This paper presents the first C. pauculus strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for C. pauculus; two of these are PacBio/Illumina hybrids. This paper presents the first ONT/Illumina hybrid assembly, with five contigs. The other assemblies available consist of 37, 38, 111 and 227 contigs. This paper also presents data on biofilm formation and lethal dose in Galleria mellonella; there is little published information describing these aspects of virulence. Aim. The aims were to identify the isolate found in a hospital sink trap, characterize its genome, and assess whether it could pose a risk to human health. Methodology. The genome was sequenced, and a hybrid assembly of short and long reads produced. Antimicrobial susceptibility was determined by the broth microdilution method. Virulence was assessed by measuring in vitro biofilm formation compared to Pseudomonas aeruginosa and in vivo lethality in Galleria mellonella larvae. Results. The isolate was confirmed to be a strain of C. pauculus, with a 6.8 Mb genome consisting of 6468 coding sequences and an overall G+C content of 63.9 mol%. The genome was found to contain 12 antibiotic resistance genes, 8 virulence factor genes and 33 metal resistance genes. The isolate can be categorized as resistant to meropenem, amoxicillin, amikacin, gentamicin and colistin, but susceptible to cefotaxime, cefepime, imipenem and ciprofloxacin. Clear biofilm formation was seen in all conditions over 72 h and exceeded that of P. aeruginosa when measured at 37 °C in R2A broth. Lethality in G. mellonella larvae over 48 h was relatively low. Conclusion. The appearance of a multidrug-resistant strain of C. pauculus in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and in vivo virulence between clinical and environmental strains, to determine how easily environmental strains may establish human infection. Infection control teams and clinicians should be aware of the emerging nature of this pathogen and further work is needed to minimize the impact of contaminated hospital plumbing systems on patient outcomes.
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Affiliation(s)
- James Butler
- School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Plymouth PL4 8AA, UK
| | - Sean D Kelly
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Katie J Muddiman
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Alexandros Besinis
- School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Plymouth PL4 8AA, UK.,Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Mathew Upton
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
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Exploring the universal healthy human gut microbiota around the World. Comput Struct Biotechnol J 2022; 20:421-433. [PMID: 35035791 PMCID: PMC8749183 DOI: 10.1016/j.csbj.2021.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 02/08/2023] Open
Abstract
The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.
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Staphylococcus ratti sp. nov. Isolated from a Lab Rat. Pathogens 2022; 11:pathogens11010051. [PMID: 35055999 PMCID: PMC8779110 DOI: 10.3390/pathogens11010051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
Staphylococci from the Staphylococcus intermedius-Staphylococcus hyicus species group include numerous animal pathogens and are an important reservoir of virulence and antimicrobial resistance determinants. Due to their pathogenic potential, they are possible causative agents of zoonoses in humans; therefore, it is important to address the properties of these strains. Here we used a polyphasic taxonomic approach to characterize the coagulase-negative staphylococcal strain NRL/St 03/464T, isolated from the nostrils of a healthy laboratory rat during a microbiological screening of laboratory animals. The 16S rRNA sequence, MALDI-TOF mass spectrometry and positive urea hydrolysis and beta-glucuronidase tests clearly distinguished it from closely related Staphylococcus spp. All analyses have consistently shown that the closest relative is Staphylococcus chromogenes; however, values of digital DNA-DNA hybridization <35.3% and an average nucleotide identity <81.4% confirmed that the analyzed strain is a distinct Staphylococcus species. Whole-genome sequencing and expert annotation of the genome revealed the presence of novel variable genetic elements, including two plasmids named pSR9025A and pSR9025B, prophages, genomic islands and a composite transposon that may confer selective advantages to other bacteria and enhance their survival. Based on phenotypic, phylogenetic and genomic data obtained in this study, the strain NRL/St 03/464T (= CCM 9025T = LMG 31873T = DSM 111348T) represents a novel species with the suggested name Staphylococcus ratti sp. nov.
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46
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Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
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47
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Gooch HCC, Kiu R, Rudder S, Baker DJ, Hall LJ, Maxwell A. Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella. Int J Syst Evol Microbiol 2021; 71:005168. [PMID: 34919037 PMCID: PMC8744253 DOI: 10.1099/ijsem.0.005168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Four bacterial strains were isolated from two different colony sources of the wax moth Galleria mellonella. They were characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), determination of G+C content, screening of antibiotic resistance genes, and various phenotypic analyses. Initial analysis of 16S rRNA gene sequence identities indicated that strain GAL7T was potentially very closely related to Enterococcus casseliflavus and Enterococcus gallinarum, having 99.5-99.9 % sequence similarity. However, further analysis of whole genome sequences revealed a genome size of 3.69 Mb, DNA G+C content of 42.35 mol%, and low dDDH and ANI values between the genomes of strain GAL7T and closest phylogenetic relative E. casseliflavus NBRC 100478T of 59.0 and 94.5 %, respectively, indicating identification of a putative new Enterococcus species. In addition, all novel strains encoded the atypical vancomycin-resistance gene vanC-4. Results of phylogenomic, physiological and phenotypic characterization confirmed that strain GAL7T represented a novel species within the genus Enterococcus, for which the name Enterococcus innesii sp. nov. is proposed. The type strain is GAL7T (=DSM 112306T=NCTC 14608T).
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Affiliation(s)
- Harriet C. C. Gooch
- Dept. Biochemisty & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Raymond Kiu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David J. Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK,School of Life Sciences, ZIEL – Institute for Food &Health, Technical University of Munich, Freising, 85354, Germany,*Correspondence: Lindsay J. Hall,
| | - Anthony Maxwell
- Dept. Biochemisty & Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK,*Correspondence: Anthony Maxwell,
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Forde BM, De Oliveira DMP, Falconer C, Graves B, Harris PNA. Strengths and caveats of identifying resistance genes from whole genome sequencing data. Expert Rev Anti Infect Ther 2021; 20:533-547. [PMID: 34852720 DOI: 10.1080/14787210.2022.2013806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Antimicrobial resistance (AMR) continues to present major challenges to modern healthcare. Recent advances in whole-genome sequencing (WGS) have made the rapid molecular characterization of AMR a realistic possibility for diagnostic laboratories; yet major barriers to clinical implementation exist. AREAS COVERED We describe and compare short- and long-read sequencing platforms, typical components of bioinformatics pipelines, tools for AMR gene detection and the relative merits of read- or assembly-based approaches. The challenges of characterizing mobile genetic elements from genomic data are outlined, as well as the complexities inherent to the prediction of phenotypic resistance from WGS. Practical obstacles to implementation in diagnostic laboratories, the critical role of quality control and external quality assurance, as well as standardized reporting standards are also discussed. Future directions, such as the application of machine-learning and artificial intelligence algorithms, linked to clinically meaningful outcomes, may offer a new paradigm for the clinical application of AMR prediction. EXPERT OPINION AMR prediction from WGS data presents an exciting opportunity to advance our capacity to comprehensively characterize infectious pathogens in a rapid manner, ultimately aiming to improve patient outcomes. Collaborative efforts between clinicians, scientists, regulatory bodies and healthcare administrators will be critical to achieve the full promise of this approach.
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Affiliation(s)
- Brian M Forde
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - David M P De Oliveira
- University of Queensland, Faculty of Science, School of Chemistry and Molecular Biosciences, St Lucia, Australia
| | - Caitlin Falconer
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - Bianca Graves
- Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia
| | - Patrick N A Harris
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia.,Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Australia
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The ATCC Genome Portal: Microbial Genome Reference Standards with Data Provenance. Microbiol Resour Announc 2021; 10:e0081821. [PMID: 34817215 PMCID: PMC8612085 DOI: 10.1128/mra.00818-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Lack of data provenance negatively impacts scientific reproducibility and the reliability of genomic data. The ATCC Genome Portal (https://genomes.atcc.org) addresses this by providing data provenance information for microbial whole-genome assemblies originating from authenticated biological materials. To date, we have sequenced 1,579 complete genomes, including 466 type strains and 1,156 novel genomes.
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Use of Metagenomic Next-Generation Sequencing in the Clinical Microbiology Laboratory: A Step Forward, but Not an End-All. J Mol Diagn 2021; 23:1415-1421. [PMID: 34756275 DOI: 10.1016/j.jmoldx.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
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