1
|
Song H, Yoo JS, Unno T. Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172068. [PMID: 38554973 DOI: 10.1016/j.scitotenv.2024.172068] [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: 01/22/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.
Collapse
Affiliation(s)
- Hokyung Song
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Jung Sik Yoo
- Division of Antimicrobial Resistance Research, National Institute of Health, Korea Disease Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea
| | - Tatsuya Unno
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea.
| |
Collapse
|
2
|
Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies. Microb Genom 2024; 10:001244. [PMID: 38717808 PMCID: PMC11165638 DOI: 10.1099/mgen.0.001244] [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: 01/08/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
Collapse
Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| |
Collapse
|
3
|
Nhu NTK, Phan MD, Hancock SJ, Peters KM, Alvarez-Fraga L, Forde BM, Andersen SB, Miliya T, Harris PNA, Beatson SA, Schlebusch S, Bergh H, Turner P, Brauner A, Westerlund-Wikström B, Irwin AD, Schembri MA. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 2024; 12:RP91853. [PMID: 38622998 PMCID: PMC11021048 DOI: 10.7554/elife.91853] [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] [Indexed: 04/17/2024] Open
Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
Collapse
Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of QueenslandBrisbaneAustralia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
| | - Patrick NA Harris
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Sanmarie Schlebusch
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers PlainsBrisbaneAustralia
| | - Haakon Bergh
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Infection Management Prevention Service, Queensland Children's HospitalBrisbaneAustralia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| |
Collapse
|
4
|
Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571215. [PMID: 38168369 PMCID: PMC10760025 DOI: 10.1101/2023.12.12.571215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
Collapse
Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| |
Collapse
|
5
|
Kikuchi-Ueda T, Maeno S, Gotoh Y, Ogura Y, Fujisaki R, Hayashi T. Complete genome sequences of 11 Streptococcus pneumoniae strains isolated from acute infectious purpura fulminans, sepsis, and pneumonia. Microbiol Resour Announc 2024; 13:e0077323. [PMID: 38132669 PMCID: PMC10868184 DOI: 10.1128/mra.00773-23] [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: 08/21/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
The complete genome sequences of 11 Japanese Streptococcus pneumoniae isolates were determined by hybrid assembly of long and short reads, including two strains isolated from patients with acute infectious purpura fulminans, six strains from patients with sepsis, and three strains from patients with pneumonia.
Collapse
Affiliation(s)
- Takane Kikuchi-Ueda
- Department of Microbiology and Immunology, Teikyo University School of Medicine, Itabashi, Tokyo, Japan
| | - Shintaro Maeno
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Ryuichi Fujisaki
- Department of Sport and Medical Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| |
Collapse
|
6
|
Wang S, Suluku R, Jalloh MB, Samba AF, Jiang B, Xie Y, Harding D, Zhang M, Sahr F, Sesay ME, Squire JS, Vandi MA, Kallon MN, Zhang S, Hu R, Zhao Y, Mi Z. Molecular characterization of an outbreak-involved Bacillus anthracis strain confirms the spillover of anthrax from West Africa. Infect Dis Poverty 2024; 13:6. [PMID: 38221635 PMCID: PMC10788998 DOI: 10.1186/s40249-023-01172-2] [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: 09/25/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Anthrax, a zoonotic disease caused by the spore-forming bacterium Bacillus anthracis, remains a major global public health concern, especially in countries with limited resources. Sierra Leone, a West African country historically plagued by anthrax, has almost been out of report on this disease in recent decades. In this study, we described a large-scale anthrax outbreak affecting both animals and humans and attempted to characterize the pathogen using molecular techniques. METHODS The causative agent of the animal outbreak in Port Loko District, Sierra Leone, between March and May 2022 was identified using the nanopore sequencing technique. A nationwide active surveillance was implemented from May 2022 to June 2023 to monitor the occurrence of anthrax-specific symptoms in humans. Suspected cases were subsequently verified using quantitative polymerase chain reaction. Full-genome sequencing was accomplished by combining long-read and short-read sequencing methods. Subsequent phylogenetic analysis was performed based on the full-chromosome single nucleotide polymorphisms. RESULTS The outbreak in Port Loko District, Sierra Leone, led to the death of 233 animals between March 26th and May 16th, 2022. We ruled out the initial suspicion of Anaplasma species and successfully identified B. anthracis as the causative agent of the outbreak. As a result of the government's prompt response, out of the 49 suspected human cases identified during the one-year active surveillance, only 6 human cases tested positive, all within the first month after the official declaration of the outbreak. The phylogenetic analysis indicated that the BaSL2022 isolate responsible for the outbreak was positioned in the A.Br.153 clade within the TransEuroAsian group of B. anthracis. CONCLUSIONS We successfully identified a large-scale anthrax outbreak in Sierra Leone. The causative isolate of B. anthracis, BaSL2022, phylogenetically bridged other lineages in A.Br.153 clade and neighboring genetic groups, A.Br.144 and A.Br.148, eventually confirming the spillover of anthrax from West Africa. Given the wide dissemination of B. anthracis spores, it is highly advisable to effectively monitor the potential reoccurrence of anthrax outbreaks and to launch campaigns to improve public awareness regarding anthrax in Sierra Leone.
Collapse
Affiliation(s)
- Shuchao Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Roland Suluku
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone.
| | - Mohamed B Jalloh
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Ahmed F Samba
- Ministry of Agriculture and Food Sciences, Freetown, Sierra Leone
| | - Baogui Jiang
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China
| | - Yubiao Xie
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Doris Harding
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Foday Sahr
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Mahmud E Sesay
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone
| | - James S Squire
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Moinina N Kallon
- Department of Animal Sciences, School of Agriculture and Food Sciences, Njala University, Njala, Sierra Leone
| | - Shoufeng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Rongliang Hu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yuee Zhao
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China.
| | - Zhiqiang Mi
- Beijing Institute of Microbiology and Epidemiology, 20 East Street, Fengtai District, Beijing, China.
| |
Collapse
|
7
|
Gould AL, Henderson JB. Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences. Microb Genom 2023; 9:001161. [PMID: 38112751 PMCID: PMC10763503 DOI: 10.1099/mgen.0.001161] [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: 07/26/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.
Collapse
Affiliation(s)
- Alison L. Gould
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
| | - James B. Henderson
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
| |
Collapse
|
8
|
Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3-A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms 2023; 11:2440. [PMID: 37894099 PMCID: PMC10609609 DOI: 10.3390/microorganisms11102440] [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: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacteria, contributing significantly to the establishment and constitution of infant gut microbiota. In light of this, our study attempted to conduct an initial investigation encompassing both genomic and phenotypic aspects of the L. plantarum PU3 strain, that holds potential as a probiotic agent. By employing the cutting-edge third-generation Nanopore sequencing technology, L. plantarum PU3 revealed a circular chromosome of 3,180,940 bp and nine plasmids of various lengths. The L. plantarum PU3 genome has a total of 2962 protein-coding and non-coding genes. Our in-depth investigations revealed more than 150 probiotic gene markers that unfold the genetic determinants for acid tolerance, bile resistance, adhesion, and oxidative and osmotic stress. The in vivo analysis showed the strain's proficiency in utilizing various carbohydrates as growth substrates, complementing the in silico analysis of the genes involved in metabolic pathways. Notably, the strain demonstrated a pronounced affinity for D-sorbitol, D-mannitol, and D-Gluconic acid, among other carbohydrate sources. The in vitro experimental verification of acid, osmotic and bile tolerance validated the robustness of the strain in challenging environments. Encouragingly, no virulence factors were detected in the genome of PU3, suggesting its safety profile. In search of beneficial properties, we found potential bacteriocin biosynthesis clusters, suggesting its capability for antimicrobial activity. The characteristics exhibited by L. plantarum PU3 pave the way for promising strain potential, warranting further investigations to unlock its full capacity and contributions to probiotic and therapeutic avenues.
Collapse
Affiliation(s)
- Daniela Mollova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Ilia Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| |
Collapse
|
9
|
de Almeida FM, de Campos TA, Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. F1000Res 2023; 12:1205. [PMID: 37970066 PMCID: PMC10646344 DOI: 10.12688/f1000research.139488.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 11/17/2023] Open
Abstract
Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago. However, transforming raw reads into a complete genome model is a significant computational challenge due to the varying quality and quantity of data obtained from different sequencing instruments, as well as intrinsic characteristics of the genome and desired analyses. To address this issue, we have developed a set of container-based pipelines using Nextflow, offering both common workflows for inexperienced users and high levels of customization for experienced ones. Their processing strategies are adaptable based on the sequencing data type, and their modularity enables the incorporation of new components to address the community's evolving needs. Methods: These pipelines consist of three parts: quality control, de novo genome assembly, and bacterial genome annotation. In particular, the genome annotation pipeline provides a comprehensive overview of the genome, including standard gene prediction and functional inference, as well as predictions relevant to clinical applications such as virulence and resistance gene annotation, secondary metabolite detection, prophage and plasmid prediction, and more. Results: The annotation results are presented in reports, genome browsers, and a web-based application that enables users to explore and interact with the genome annotation results. Conclusions: Overall, our user-friendly pipelines offer a seamless integration of computational tools to facilitate routine bacterial genomics research. The effectiveness of these is illustrated by examining the sequencing data of a clinical sample of Klebsiella pneumoniae.
Collapse
Affiliation(s)
- Felipe Marques de Almeida
- Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Brasília, FD, 70910-900, Brazil
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Tatiana Amabile de Campos
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Georgios Joannis Pappas Jr
- Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Brasília, FD, 70910-900, Brazil
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| |
Collapse
|
10
|
Aurich S, Schneider J, Brangsch H, Koets A, Melzer F, Ewers C, Prenger-Berninghoff E. Brucella suis biovar 1 infection in a dog with orchitis in Germany. Front Vet Sci 2023; 10:1233118. [PMID: 37601758 PMCID: PMC10435866 DOI: 10.3389/fvets.2023.1233118] [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: 06/01/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
In 2021, a case of canine brucellosis diagnosed in a dog with orchitis was presented to a veterinary practice in Germany. Serological testing excluded Brucella (B.) canis as a causative agent, but molecular analysis revealed the presence of B. suis biovar 1. Since biovar 1 is not endemic in Europe and the dog had no history of travel to endemic areas, a comprehensive epidemiological investigation was conducted using whole genome sequence data to determine the source of infection. We describe the clinical progress of the animal and the potential infection of a veterinary clinic employee. The findings highlight the importance of considering less common Brucella species as possible causes of canine brucellosis. The data also emphasize that it is quite challenging to identify Brucella species in a routine diagnostic laboratory and to conduct epidemiological investigations to unveil possible transmission routes.
Collapse
Affiliation(s)
- Sophie Aurich
- Department of Veterinary Science, Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University, Giessen, Germany
| | - Juliane Schneider
- Tierärztliche Klinik für Kleintiere am Kaiserberg, Duisburg, Germany
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Jena, Germany
| | - Ad Koets
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Jena, Germany
| | - Christa Ewers
- Department of Veterinary Science, Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University, Giessen, Germany
| | - Ellen Prenger-Berninghoff
- Department of Veterinary Science, Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University, Giessen, Germany
| |
Collapse
|
11
|
Thomas C, Methner U, Marz M, Linde J. Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella. Front Vet Sci 2023; 10:1178922. [PMID: 37323838 PMCID: PMC10267320 DOI: 10.3389/fvets.2023.1178922] [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: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.
Collapse
Affiliation(s)
- Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| |
Collapse
|
12
|
Linde J, Brangsch H, Hölzer M, Thomas C, Elschner MC, Melzer F, Tomaso H. Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis. BMC Genomics 2023; 24:258. [PMID: 37173617 PMCID: PMC10182678 DOI: 10.1186/s12864-023-09343-z] [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: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. RESULTS As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. CONCLUSIONS In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.
Collapse
Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Mandy C Elschner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| |
Collapse
|
13
|
Yano B, Taniguchi I, Gotoh Y, Hayashi T, Nakamura K. Dynamic changes in Shiga toxin (Stx) 1 transducing phage throughout the evolution of O26:H11 Stx-producing Escherichia coli. Sci Rep 2023; 13:4935. [PMID: 36973327 PMCID: PMC10042803 DOI: 10.1038/s41598-023-32111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Shiga toxin (Stx) is the key virulence factor of Stx-producing Escherichia coli (STEC). All known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages). Although the genetic diversity of Stx phages has frequently been described, systematic analyses of Stx phages in a single STEC lineage are limited. In this study, focusing on the O26:H11 STEC sequence type 21 (ST21) lineage, where the stx1a gene is highly conserved, we analysed the Stx1a phages in 39 strains representative of the entire ST21 lineage and found a high level of variation in Stx1a phage genomes caused by various mechanisms, including replacement by a different Stx1a phage at the same or different locus. The evolutionary timescale of events changing Stx1a phages in ST21 was also determined. Furthermore, by using an Stx1 quantification system developed in this study, we found notable variations in the efficiency of Stx1 production upon prophage induction, which sharply contrasted with the conserved iron regulated Stx1 production. These variations were associated with the Stx1a phage alteration in some cases but not in other cases; thus, Stx1 production in this STEC lineage was determined by differences not only in Stx1 phages but also in host-encoded factors.
Collapse
Affiliation(s)
- Bungo Yano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan.
| |
Collapse
|
14
|
Miyata T, Taniguchi I, Nakamura K, Gotoh Y, Yoshimura D, Itoh T, Hirai S, Yokoyama E, Ohnishi M, Iyoda S, Ogura Y, Hayashi T. Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microb Genom 2023; 9:mgen000935. [PMID: 36821793 PMCID: PMC9997748 DOI: 10.1099/mgen.0.000935] [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: 02/25/2023] Open
Abstract
Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n=510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.
Collapse
Affiliation(s)
- Tatsuya Miyata
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan.,Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| |
Collapse
|
15
|
Bonenfant Q, Noé L, Touzet H. Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. BIOINFORMATICS ADVANCES 2022; 3:vbac085. [PMID: 36698762 PMCID: PMC9869717 DOI: 10.1093/bioadv/vbac085] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/07/2022] [Indexed: 11/23/2022]
Abstract
Motivation Oxford Nanopore Technologies (ONT) sequencing has become very popular over the past few years and offers a cost-effective solution for many genomic and transcriptomic projects. One distinctive feature of the technology is that the protocol includes the ligation of adapters to both ends of each fragment. Those adapters should then be removed before downstream analyses, either during the basecalling step or by explicit trimming. This basic task may be tricky when the definition of the adapter sequence is not well documented. Results We have developed a new method to scan a set of ONT reads to see if it contains adapters, without any prior knowledge on the sequence of the potential adapters, and then trim out those adapters. The algorithm is based on approximate k-mers and is able to discover adapter sequences based on their frequency alone. The method was successfully tested on a variety of ONT datasets with different flowcells, sequencing kits and basecallers. Availability and implementation The resulting software, named Porechop_ABI, is open-source and is available at https://github.com/bonsai-team/Porechop_ABI. Supplementary information Supplementary data are available at Bioinformatics advances online.
Collapse
Affiliation(s)
- Quentin Bonenfant
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL—Centre de Recherche en Informatique Signal et Automatique de Lille, Lille F-59000, France
| | - Laurent Noé
- Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL—Centre de Recherche en Informatique Signal et Automatique de Lille, Lille F-59000, France
| | | |
Collapse
|
16
|
Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism. Int J Mol Sci 2022; 23:ijms23158569. [PMID: 35955702 PMCID: PMC9369328 DOI: 10.3390/ijms23158569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022] Open
Abstract
Nanopore sequencing (ONT) is a new and rapidly developing method for determining nucleotide sequences in DNA and RNA. It serves the ability to obtain long reads of thousands of nucleotides without assembly and amplification during sequencing compared to next-generation sequencing. Nanopore sequencing can help for determination of genetic changes leading to antibiotics resistance. This study presents the application of ONT technology in the assembly of an E. coli genome characterized by a deletion of the tolC gene and known single-nucleotide variations leading to antibiotic resistance, in the absence of a reference genome. We performed benchmark studies to determine minimum coverage depth to obtain a complete genome, depending on the quality of the ONT data. A comparison of existing programs was carried out. It was shown that the Flye program demonstrates plausible assembly results relative to others (Shasta, Canu, and Necat). The required coverage depth for successful assembly strongly depends on the size of reads. When using high-quality samples with an average read length of 8 Kbp or more, the coverage depth of 30× is sufficient to assemble the complete genome de novo and reliably determine single-nucleotide variations in it. For samples with shorter reads with mean lengths of 2 Kbp, a higher coverage depth of 50× is required. Avoiding of mechanical mixing is obligatory for samples preparation. Nanopore sequencing can be used alone to determine antibiotics-resistant genetic features of bacterial strains.
Collapse
|
17
|
PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data. Viruses 2022; 14:v14061260. [PMID: 35746732 PMCID: PMC9230805 DOI: 10.3390/v14061260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and time-consuming task. As a result, we developed PIMGAVir and Vir-MinION, two metagenomics pipelines that automatically provide the user with a complete baseline analysis. The PIMGAVir and Vir-MinION pipelines work on 2nd and 3rd generation data, respectively, and provide the user with a taxonomic classification of the reads through three strategies: assembly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehensive results in graphical and textual format for future analyses. Finally, the pipelines equip the user with a stand-alone platform with dedicated and various viral databases, which is a requirement for working in field conditions without internet connection.
Collapse
|
18
|
Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains. PLoS Negl Trop Dis 2022; 16:e0009482. [PMID: 35700198 PMCID: PMC9236262 DOI: 10.1371/journal.pntd.0009482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/27/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Background Burkholderia pseudomallei is an environmental gram-negative bacterium that causes the disease melioidosis and is endemic in many countries of the Asia-Pacific region. In Australia, the mortality rate remains high at approximately 10%, despite curative antibiotic treatment being available. The bacterium is almost exclusively found in the endemic region, which spans the tropical Northern Territory and North Queensland, with clusters occasionally present in more temperate climates. Despite being endemic to North Queensland, these infections remain understudied compared to those of the Northern Territory. Methodology/Principal findings This study aimed to assess the prevalence of central nervous system (CNS) disease associated variant bimABm, identify circulating antimicrobial resistance mutations and genetically distinct strains from Queensland, via comparative genomics. From 76 clinical isolates, we identified the bimABm variant in 20 (26.3%) isolates and in 9 (45%) of the isolates with documented CNS infection (n = 18). Explorative analysis suggests a significant association between isolates carrying the bimABm variant and CNS disease (OR 2.8, 95% CI 1.3–6.0, P = 0.009) compared with isolates carrying the wildtype bimABp. Furthermore, 50% of isolates were identified as novel multi-locus sequence types, while the bimABm variant was more commonly identified in isolates with novel sequence types, compared to those with previously described. Additionally, mutations associated with acquired antimicrobial resistance were only identified in 14.5% of all genomes. Conclusions/Significance The findings of this research have provided clinically relevant genomic data of B. pseudomallei in Queensland and suggest that the bimABm variant may enable risk stratification for the development CNS complications and be a potential therapeutic target. Melioidosis is a life-threatening infection, caused by the Gram-negative bacterium Burkholderia pseudomallei, which is endemic to tropical regions in Australia. Variants of the bimA gene have been proposed as a virulence factor associated with more severe disease. In a genomic analysis of 76 clinical B. pseudomallei isolates from Queensland, Australia, we identified that the bimABm variant was associated with infection involving the central nervous system (odds ratio 2.8, 95% Confidence Interval: 1.3–6.0, P = 0.009), compared to isolates with the wild-type allele bimABp. Half of the isolates from this region were novel multi-locus sequence types, and bimABm was more commonly seen in these novel sequence types. Early genomic characterisation to identify virulence factors such as bimABm, may be useful as an early marker of more complex disease that could guide further investigation and help determine optimal treatment. Further investigation of a “genomics-guided” approach to the clinical management of this complex infectious disease are warranted.
Collapse
|
19
|
Brangsch H, Golovko A, Pinchuk N, Deriabin O, Kyselova T, Linde J, Melzer F, Elschner MC. Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques. Microorganisms 2022; 10:microorganisms10020461. [PMID: 35208915 PMCID: PMC8875922 DOI: 10.3390/microorganisms10020461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.
Collapse
Affiliation(s)
- Hanka Brangsch
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
- Correspondence:
| | - Anatolii Golovko
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Nataliia Pinchuk
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Oleg Deriabin
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Tetiana Kyselova
- Department of Bacteriological Research and Quality Control of Veterinary Immunobiological Preparations, SSCIBSM, 30, Donetskaya St., 03151 Kyiv, Ukraine; (A.G.); (N.P.); (O.D.); (T.K.)
| | - Jörg Linde
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Falk Melzer
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| | - Mandy Carolina Elschner
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (F.M.); (M.C.E.)
| |
Collapse
|