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Meléndez-Sánchez D, Hernández L, Ares M, Méndez Tenorio A, Flores-Luna L, Torres J, Camorlinga-Ponce M. Genomic and phenotypic studies among Clostridioides difficile isolates show a high prevalence of clade 2 and great diversity in clinical isolates from Mexican adults and children with healthcare-associated diarrhea. Microbiol Spectr 2024; 12:e0394723. [PMID: 38864670 PMCID: PMC11218462 DOI: 10.1128/spectrum.03947-23] [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: 12/18/2023] [Accepted: 04/30/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridioides difficile (C. difficile) is widely distributed in the intestinal tract of humans, animals, and in the environment. It is the most common cause of diarrhea associated with the use of antimicrobials in humans and among the most common healthcare-associated infections worldwide. Its pathogenesis is mainly due to the production of toxin A (TcdA), toxin B (TcdB), and a binary toxin (CDT), whose genetic variants may be associated with disease severity. We studied genetic diversity in 39 C. difficile isolates from adults and children attended at two Mexican hospitals, using different gene and genome typing methods and investigated their association with in vitro expression of toxins. Whole-genome sequencing in 39 toxigenic C. difficile isolates were used for multilocus sequence typing, tcdA, and tcdB typing sequence type, and phylogenetic analysis. Strains were grown in broth media, and expression of toxin genes was measured by real-time PCR and cytotoxicity in cell-culture assays. Clustering of strains by genome-wide phylogeny matched clade classification, forming different subclusters within each clade. The toxin profile tcdA+/tcdB+/cdt+ and clade 2/ST1 were the most prevalent among isolates from children and adults. Isolates presented two TcdA and three TcdB subtypes, of which TcdA2 and TcdB2 were more prevalent. Prevalent clades and toxin subtypes in strains from children differed from those in adult strains. Toxin gene expression or cytotoxicity was not associated with genotyping or toxin subtypes. In conclusion, genomic and phenotypic analysis shows high diversity among C. difficile isolates from patients with healthcare-associated diarrhea. IMPORTANCE Clostridioides difficile is a toxin-producing bacterial pathogen recognized as the most common cause of diarrhea acquired primarily in healthcare settings. This bacterial species is diverse; its global population has been divided into five different clades using multilocus sequence typing, and strains may express different toxin subtypes that may be related to the clades and, importantly, to the severity and progression of disease. Genotyping of children strains differed from adults suggesting toxins might present a reduced toxicity. We studied extensively cytotoxicity, expression of toxins, whole genome phylogeny, and toxin typing in clinical C. difficile isolates. Most isolates presented a tcdA+/ tcdB+/cdt+ pattern, with high diversity in cytotoxicity and clade 2/ST1 was the most prevalent. However, they all had the same TcdA2/TcdB2 toxin subtype. Advances in genomics and bioinformatics tools offer the opportunity to understand the virulence of C. difficile better and find markers for better clinical use.
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Affiliation(s)
- D. Meléndez-Sánchez
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Laura Hernández
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
| | - Miguel Ares
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - A. Méndez Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Lourdes Flores-Luna
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - M. Camorlinga-Ponce
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, Instituto Mexicano del Seguro Social, México City, México
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Garzon A, Basbas C, Schlesener C, Silva-del-Rio N, Karle BM, Lima FS, Weimer BC, Pereira RV. WGS of intrauterine E. coli from cows with early postpartum uterine infection reveals a non-uterine specific genotype and virulence factors. mBio 2024; 15:e0102724. [PMID: 38742889 PMCID: PMC11237492 DOI: 10.1128/mbio.01027-24] [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: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli has been attributed to playing a major role in a cascade of events that affect the prevalence and severity of uterine disease in cattle. The objectives of this project were to (i) define the association between the prevalence of specific antimicrobial resistance and virulence factor genes in E. coli with the clinical status related to uterine infection, (ii) identify the genetic relationship between E. coli isolates from cows with diarrhea, with mastitis, and with and without metritis, and (iii) determine the association between the phenotypic and genotypic antimicrobial resistance identified on the E. coli isolated from postpartum cattle. Bacterial isolates (n = 148) were obtained from a larger cross-sectional study. Cows were categorized into one of three clinical groups before enrollment: metritis, cows with purulent discharge, and control cows. For genomic comparison, public genomes (n = 130) from cows with diarrhea, mastitis, and metritis were included in a genome-wide association study, to evaluate differences between the drug classes or the virulence factor category among clinical groups. A distinct E. coli genotype associated with metritis could not be identified. Instead, a high genetic diversity among the isolates from uterine sources was present. A virulence factor previously associated with metritis (fimH) using PCR was not associated with metritis. There was moderate accuracy for whole-genome sequencing to predict phenotypic resistance, which varied depending on the antimicrobial tested. Findings from this study contradict the traditional pathotype classification and the unique intrauterine E. coli genotype associated with metritis in dairy cows.IMPORTANCEMetritis is a common infectious disease in dairy cattle and the second most common reason for treating a cow with antimicrobials. The pathophysiology of the disease is complex and is not completely understood. Specific endometrial pathogenic Escherichia coli have been reported to be adapted to the endometrium and sometimes lead to uterine disease. Unfortunately, the specific genomic details of the endometrial-adapted isolates have not been investigated using enough genomes to represent the genomic diversity of this organism to identify specific virulence genes that are consistently associated with disease development and severity. Results from this study provide key microbial ecological advances by elucidating and challenging accepted concepts for the role of Intrauterine E. coli in metritis in dairy cattle, especially contradicting the existence of a unique intrauterine E. coli genotype associated with metritis in dairy cows, which was not found in our study.
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Affiliation(s)
- Adriana Garzon
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Noelia Silva-del-Rio
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Tulare, California, USA
| | - Betsy M. Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, California, USA
| | - Fabio S. Lima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Richard V. Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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Depenbrock S, Schlesener C, Aly S, Williams D, ElAshmawy W, McArthur G, Clothier K, Wenz J, Fritz H, Chigerwe M, Weimer B. Antimicrobial Resistance Genes in Respiratory Bacteria from Weaned Dairy Heifers. Pathogens 2024; 13:300. [PMID: 38668255 PMCID: PMC11053459 DOI: 10.3390/pathogens13040300] [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: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Bovine respiratory disease (BRD) is the leading cause of mortality and antimicrobial drug (AMD) use in weaned dairy heifers. Limited information is available regarding antimicrobial resistance (AMR) in respiratory bacteria in this population. This study determined AMR gene presence in 326 respiratory isolates (Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni) from weaned dairy heifers using whole genome sequencing. Concordance between AMR genotype and phenotype was determined. Twenty-six AMR genes for 8 broad classes of AMD were identified. The most prevalent, medically important AMD classes used in calf rearing, to which these genes predict AMR among study isolates were tetracycline (95%), aminoglycoside (94%), sulfonamide (94%), beta-lactam (77%), phenicol (50%), and macrolide (44%). The co-occurrence of AMR genes within an isolate was common; the largest cluster of gene co-occurrence encodes AMR to phenicol, macrolide, elfamycin, β-lactam (cephalosporin, penam cephamycin), aminoglycoside, tetracycline, and sulfonamide class AMD. Concordance between genotype and phenotype varied (Matthew's Correlation Coefficient ranged from -0.57 to 1) by bacterial species, gene, and AMD tested, and was particularly poor for fluoroquinolones (no AMR genes detected) and ceftiofur (no phenotypic AMR classified while AMR genes present). These findings suggest a high genetic potential for AMR in weaned dairy heifers; preventing BRD and decreasing AMD reliance may be important in this population.
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Affiliation(s)
- Sarah Depenbrock
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA;
| | - Sharif Aly
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
| | - Deniece Williams
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
| | - Wagdy ElAshmawy
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
- Department of Internal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12613, Egypt
| | - Gary McArthur
- Swinging Udders Veterinarian Services, Galt, CA 95632, USA
| | - Kristin Clothier
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - John Wenz
- Field Disease Investigation Unit, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA
| | - Heather Fritz
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Munashe Chigerwe
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Bart Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA;
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Prentice MB, Gilbertson MLJ, Storm DJ, Turner WC, Walsh DP, Pinkerton ME, Kamath PL. Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer ( Odocoileus virginianus). Microb Genom 2024; 10:001214. [PMID: 38536208 PMCID: PMC10995629 DOI: 10.1099/mgen.0.001214] [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: 10/10/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024] Open
Abstract
With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.
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Affiliation(s)
| | - Marie L. J. Gilbertson
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Wendy C. Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Wisconsin, USA
| | - Daniel P. Walsh
- U.S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Montana, USA
| | - Marie E. Pinkerton
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Wisconsin, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Maine, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, Maine, USA
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Genomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico. Microorganisms 2023; 11:microorganisms11020340. [PMID: 36838305 PMCID: PMC9962129 DOI: 10.3390/microorganisms11020340] [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: 01/16/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Rodents and bats are the most diverse mammal group that host Bartonella species. In the Americas, they were described as harboring Bartonella species; however, they were mostly characterized to the genotypic level. We describe here Bartonella isolates obtained from blood samples of one rodent (Peromyscus yucatanicus from San José Pibtuch, Yucatan) and two bat species (Desmodus rotundus from Progreso, and Pteronotus parnellii from Chamela-Cuitzmala) from Mexico. We sequenced and described the genomic features of three Bartonella strains and performed phylogenomic and pangenome analyses to decipher their phylogenetic relationships. The mouse-associated genome was closely related to Bartonella vinsonii. The two bat-associated genomes clustered into a single distinct clade in between lineages 3 and 4, suggesting to be an ancestor of the rodent-associated Bartonella clade (lineage 4). These three genomes showed <95% OrthoANI values compared to any other Bartonella genome, and therefore should be considered as novel species. In addition, our analyses suggest that the B. vinsonii complex should be revised, and all B. vinsonii subspecies need to be renamed and considered as full species. The phylogenomic clustering of the bat-associated Bartonella strains and their virulence factor profile (lack of the Vbh/TraG conjugation system remains of the T4SS) suggest that it should be considered as a new lineage clade (L5) within the Bartonella genus.
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Seabolt EE, Nayar G, Krishnareddy H, Agarwal A, Beck KL, Terrizzano I, Kandogan E, Kunitomi M, Roth M, Mukherjee V, Kaufman JH. Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:940-952. [PMID: 32877338 DOI: 10.1109/tcbb.2020.3021231] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks to gain insight from the data. To address these challenges, we pre-computed important relationships between biological entities spanning the Central Dogma of Molecular Biology and captured this information in a relational database. The database can be queried across hundreds of millions of entities and returns results in a fraction of the time required by traditional methods. In this paper, we describe Functional Genomics Platform (formerly known as OMXWare), a comprehensive database relating genotype to phenotype for bacterial life. Continually updated, the Functional Genomics Platform today contains data derived from 200,000 curated, self-consistently assembled genomes. The database stores functional data for over 68 million genes, 52 million proteins, and 239 million domains with associated biological activity annotations from Gene Ontology, KEGG, MetaCyc, and Reactome. The Functional Genomics Platform maps all of the many-to-many connections between each biological entity including the originating genome, gene, protein, and protein domain. Various microbial studies, from infectious disease to environmental health, can benefit from the rich data and connections. We describe the data selection, the pipeline to create and update the Functional Genomics Platform, and the developer tools (Python SDK and REST APIs)which allow researchers to efficiently study microbial life at scale.
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Anuntakarun S, Sawaswong V, Jitvaropas R, Praianantathavorn K, Poomipak W, Suputtamongkol Y, Chirathaworn C, Payungporn S. Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients. Genomics Inform 2021; 19:e31. [PMID: 34638178 PMCID: PMC8510873 DOI: 10.5808/gi.21037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/12/2021] [Indexed: 11/20/2022] Open
Abstract
Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. For better understanding the difference between Leptospira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotypes. DNA of Leptospira isolated from two patients, one with mild and another with severe symptoms, were included in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using SPAdes. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched in EggNOG and David gene ontology database to characterize gene ontology. In addition, Leptospira from mild and severe patients, that passed the criteria e-value < 10e-5 from blastP against virulence factor database, were used to analyze with Venn diagram. From this study, we found 13 and 12 genes that were unique in the isolates from mild and severe patients, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.
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Affiliation(s)
- Songtham Anuntakarun
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rungrat Jitvaropas
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand
| | | | - Witthaya Poomipak
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yupin Suputtamongkol
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chintana Chirathaworn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok 10330, Thailand
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Li IC, Wu HH, Chen ZW, Chou CH. Prevalence of IncFIB Plasmids Found among Salmonella enterica Serovar Schwarzengrund Isolates from Animal Sources in Taiwan Using Whole-Genome Sequencing. Pathogens 2021; 10:pathogens10081024. [PMID: 34451486 PMCID: PMC8399590 DOI: 10.3390/pathogens10081024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/22/2022] Open
Abstract
Salmonella enterica serovar Schwarzengrund is one of the most frequently isolated Salmonella serotypes responsible for human and poultry infections in Taiwan, and it has raised public health concerns. To better facilitate the understanding of transmission patterns and the dynamics of epidemics, sharing molecular data on pathogen profiles is urgently needed. The objectives of the current study were to determine and establish baseline data of S. enterica serovar Schwarzengrund isolates from 23 epidemiologically unrelated sources from year 2000 to 2018 and examine their phenotypic and genotypic characteristics. Genomic DNA of the Salmonella isolates was extracted and subjected to whole-genome sequencing using an Illumina platform. Results showed that all selected isolates exhibited multidrug resistance, and six of those were resistant to ciprofloxacin phenotypically. Genotypically, these isolates carried genes resistant to aminoglycoside (100%), phenicol (91.3%), β-lactams (69.5%), folate pathway antagonist (100%), tetracycline (82.6%), and fluoroquinolone (4.3%). Moreover, these isolates harbor integrons with five different gene cassettes identified for the first time, which are associated with resistance to trimethoprim, streptomycin, tetracycline, sulfonamide, chloramphenicol, and gentamicin. Furthermore, prevalence of IncFIB plasmid was found among studied isolates, which may increase its ability to colonize the chicken cecum and cause extra-intestinal disease. Salmonella pathogenicity islands SPI-1 to SPI-5, SPI-13, and SPI-14, as well as C63PI locus, were also detected in all isolates. This study demonstrated that a considerable high antimicrobial resistance with high virulence levels of Salmonella were found from animal sources. Sharing data on these pathogen profiles can not only help increase the reproducibility and accessibility of genomic analysis but can also support surveillance and epidemiological investigations for salmonellosis in the region.
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Affiliation(s)
- I-Chen Li
- Zoonoses Research Center, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei City 106, Taiwan;
| | - Hsiu-Hui Wu
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Road, Zhunan Township, Miaoli County 350, Taiwan;
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Road, Zhunan Township, Miaoli County 350, Taiwan;
- Correspondence: (Z.-W.C.); (C.-H.C.); Tel.: +886-37-585-851 (Z.-W.C.); +886-2-3366-3861 (C.-H.C.); Fax: +886-2-2364-9154 (C.-H.C.)
| | - Chung-Hsi Chou
- Zoonoses Research Center, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei City 106, Taiwan;
- Correspondence: (Z.-W.C.); (C.-H.C.); Tel.: +886-37-585-851 (Z.-W.C.); +886-2-3366-3861 (C.-H.C.); Fax: +886-2-2364-9154 (C.-H.C.)
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Santos-Medellín C, Liechty Z, Edwards J, Nguyen B, Huang B, Weimer BC, Sundaresan V. Prolonged drought imparts lasting compositional changes to the rice root microbiome. NATURE PLANTS 2021; 7:1065-1077. [PMID: 34294907 DOI: 10.1038/s41477-021-00967-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
Microbial symbioses can mitigate drought stress in crops but harnessing these beneficial interactions will require an in-depth understanding of root microbiome responses to drought cycles. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during drought stress and recovery, we find that endosphere communities remained compositionally altered after rewatering, with prolonged droughts leading to decreased resilience. Several endospheric Actinobacteria were significantly enriched during drought and for weeks after rewatering. Notably, the most abundant endosphere taxon during this period was a Streptomyces, and a corresponding isolate promoted root growth. Additionally, drought stress disrupted the temporal dynamics of late-colonizing microorganisms, permanently altering the normal successional trends of root microbiota. These findings reveal that severe drought results in enduring impacts on rice root microbiomes, including enrichment of taxonomic groups that could shape the recovery response of the host, and have implications relevant to drought protection strategies using root microbiota.
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Affiliation(s)
- Christian Santos-Medellín
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Zachary Liechty
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Microbiology and Environmental Toxicology Department, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Bihua Huang
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.
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Bandoy DJDR, Weimer BC. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Sci Rep 2021; 11:7380. [PMID: 33795722 PMCID: PMC8016908 DOI: 10.1038/s41598-021-86265-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found mutational variations in the viral genome; however, previous comparisons failed to show a direct relationship between viral genome diversity, transmission, and the epidemic severity. COVID-19 incidences from different countries were modeled over the epidemic curve. Estimates of the instantaneous R (Wallinga and Teunis method) with a short and standard serial interval were done. WGS were used to determine the populations genomic variation and that underpinned creation of the pathogen genome identity (GENI) score, which was merged with the outbreak curve in four distinct phases. Inference of transmission time was based on a mutation rate of 2 mutations/month. R estimates revealed differences in the transmission and variable infection dynamics between and within outbreak progression for each country examined. Outside China, our R estimates observed propagating dynamics indicating that other countries were poised to move to the takeoff and exponential stages. Population density and local temperatures had no clear relationship to the outbreak progression. Integration of incidence data with the GENI score directly predicted increases in cases as the genome variation increased that led to new variants. Integrating the outbreak curve, dynamic R, and SNP variation found a direct association between increasing cases and transmission genome evolution. By defining the epidemic curve into four stages and integrating the instantaneous country-specific R with the GENI score, we directly connected changes in individual outbreaks based on changes in the virus genome via SNPs. This resulted in the ability to forecast potential increases in cases as well as mutations that may defeat PCR screening and the infection process. By using instantaneous R estimations and WGS, outbreak dynamics were defined to be linked to viral mutations, indicating that WGS, as a surveillance tool, is required to predict shifts in each outbreak that will provide actionable decision making information. Integrating epidemiology with genome sequencing and modeling allows for evidence-based disease outbreak tracking with predictive therapeutically valuable insights in near real time.
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Affiliation(s)
- D J Darwin R Bandoy
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.,Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Bart C Weimer
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.
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11
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Camorlinga-Ponce M, Gómez-Delgado A, Aguilar-Zamora E, Torres RC, Giono-Cerezo S, Escobar-Ogaz A, Torres J. Phenotypic and Genotypic Antibiotic Resistance Patterns in Helicobacter pylori Strains From Ethnically Diverse Population in México. Front Cell Infect Microbiol 2021; 10:539115. [PMID: 33643927 PMCID: PMC7905308 DOI: 10.3389/fcimb.2020.539115] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori strains carry a range of mutations in genes that confer antimicrobial resistance and restrict the available options to treat the infection. Latin America is a region that conserve a large number of indigenous communities relatively isolated that practice a traditional medicine without consumption of drugs. We hypothesized that rates of antibiotic resistance are lower in these communities. Recent progress in whole-genome sequencing has allowed the study of drug susceptibility by searching for the known mutations associated with antibiotic resistance. The aim of this work was to study trends of antibiotic resistance over a 20-year period in Mexican H. pylori strains and to compare susceptibility between strains from Mexican mestizos and from indigenous population; we also aimed to learn the prevalence of mutational patterns in genes gyrA, gyrB, rdxA, frxA, rpsU, omp11, dppA, and 23S rRNA and its association with phenotypic tests. Resistance to clarithromycin, metronidazole, amoxicillin and levofloxacin was determined in167 H. pylori isolates by E-test, and the occurrence of mutational patterns in specific genes was determined by whole genome sequencing (WGS). The trend of resistance over 20 years in mestizo isolates showed significant resistant increase for clarithromycin and levofloxacin to frequencies that banned its clinical use. Resistance in H. pylori isolates of native communities was lower for all antibiotics tested. Phenotypic resistance showed good to moderate correlation with genotypic tests. Genetic methods for characterizing antibiotic resistance require further validation in each population.
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Affiliation(s)
- Margarita Camorlinga-Ponce
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Alejandro Gómez-Delgado
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Emmanuel Aguilar-Zamora
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico.,Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto C Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Silvia Giono-Cerezo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Antonio Escobar-Ogaz
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
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12
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Beck KL, Haiminen N, Chambliss D, Edlund S, Kunitomi M, Huang BC, Kong N, Ganesan B, Baker R, Markwell P, Kawas B, Davis M, Prill RJ, Krishnareddy H, Seabolt E, Marlowe CH, Pierre S, Quintanar A, Parida L, Dubois G, Kaufman J, Weimer BC. Monitoring the microbiome for food safety and quality using deep shotgun sequencing. NPJ Sci Food 2021; 5:3. [PMID: 33558514 PMCID: PMC7870667 DOI: 10.1038/s41538-020-00083-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 11/24/2020] [Indexed: 01/30/2023] Open
Abstract
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species' viability from total RNA sequencing.
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Affiliation(s)
- Kristen L. Beck
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Niina Haiminen
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481554.9IBM T.J. Watson Research Center, Yorktown Heights, Ossining, NY USA
| | - David Chambliss
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Stefan Edlund
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Mark Kunitomi
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - B. Carol Huang
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.27860.3b0000 0004 1936 9684University of California Davis, School of Veterinary Medicine, 100 K Pathogen Genome Project, Davis, CA 95616 USA
| | - Nguyet Kong
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.27860.3b0000 0004 1936 9684University of California Davis, School of Veterinary Medicine, 100 K Pathogen Genome Project, Davis, CA 95616 USA
| | - Balasubramanian Ganesan
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,Mars Global Food Safety Center, Beijing, China ,grid.507690.dWisdom Health, A Division of Mars Petcare, Vancouver, WA USA
| | - Robert Baker
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,Mars Global Food Safety Center, Beijing, China
| | - Peter Markwell
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,Mars Global Food Safety Center, Beijing, China
| | - Ban Kawas
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Matthew Davis
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Robert J. Prill
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Harsha Krishnareddy
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Ed Seabolt
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Carl H. Marlowe
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.418312.d0000 0001 2187 1663Bio-Rad Laboratories, Hercules, CA USA
| | - Sophie Pierre
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481801.40000 0004 0623 3323Bio-Rad, Food Science Division, MArnes-La-Coquette, France
| | - André Quintanar
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481801.40000 0004 0623 3323Bio-Rad, Food Science Division, MArnes-La-Coquette, France
| | - Laxmi Parida
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481554.9IBM T.J. Watson Research Center, Yorktown Heights, Ossining, NY USA
| | - Geraud Dubois
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - James Kaufman
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.481551.cIBM Almaden Research Center, San Jose, CA USA
| | - Bart C. Weimer
- Consortium for Sequencing the Food Supply Chain, San Jose, CA USA ,grid.27860.3b0000 0004 1936 9684University of California Davis, School of Veterinary Medicine, 100 K Pathogen Genome Project, Davis, CA 95616 USA
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13
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Miller JJ, Weimer BC, Timme R, Lüdeke CHM, Pettengill JB, Bandoy DJD, Weis AM, Kaufman J, Huang BC, Payne J, Strain E, Jones JL. Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data. Appl Environ Microbiol 2021; 87:e01403-20. [PMID: 33187991 PMCID: PMC7848924 DOI: 10.1128/aem.01403-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. The draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from multiple locations. There was population structure along the Gulf and Atlantic Coasts of North America, with what seemed to be a hub of genetic variability along the Gulf Coast, with some of the same STs occurring along the Atlantic Coast and one shared between the coastal waters of the Gulf and those of Washington State. Phylogenetic analyses found nine well-supported clades. Two clades were composed of isolates from both clinical and oyster sources. Four were composed of isolates entirely from clinical sources, and three were entirely from oyster sources. Each single-source clade consisted of one ST. Some human isolates lack tdh, trh, and some type III secretion system (T3SS) genes, which are established virulence genes of V. parahaemolyticus Thus, these genes are not essential for pathogenicity. However, isolates in the monophyletic groups from clinical sources were enriched in several categories of genes compared to those from monophyletic groups of oyster isolates. These functional categories include cell signaling, transport, and metabolism. The identification of genes in these functional categories provides a basis for future in-depth pathogenicity investigations of V. parahaemolyticusIMPORTANCEVibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States and is frequently associated with shellfish consumption. This study contributes to our knowledge of the biogeography and functional genomics of this species around North America. STs shared between the Gulf Coast and the Atlantic seaboard as well as Pacific waters suggest possible transport via oceanic currents or large shipping vessels. STs frequently isolated from humans but rarely, if ever, isolated from the environment are likely more competitive in the human gut than other STs. This could be due to additional functional capabilities in areas such as cell signaling, transport, and metabolism, which may give these isolates an advantage in novel nutrient-replete environments such as the human gut.
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Affiliation(s)
- John J Miller
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Bart C Weimer
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Ruth Timme
- FDA, Division of Microbiology, College Park, Maryland, USA
| | - Catharina H M Lüdeke
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
- University of Hamburg, Hamburg School of Food Science, Hamburg, Germany
| | - James B Pettengill
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
| | - DJ Darwin Bandoy
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Allison M Weis
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | | | - B Carol Huang
- University of California-Davis, Institute for Veterinary Medicine, Davis, California, USA
| | - Justin Payne
- FDA, Division of Microbiology, College Park, Maryland, USA
| | - Errol Strain
- FDA, Biostatistics and Bioinformatics Staff, College Park, Maryland, USA
| | - Jessica L Jones
- FDA, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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14
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Aguilar-Zamora E, Weimer BC, Torres RC, Gómez-Delgado A, Ortiz-Olvera N, Aparicio-Ozores G, Barbero-Becerra VJ, Torres J, Camorlinga-Ponce M. Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico. Front Microbiol 2021; 12:787451. [PMID: 35360652 PMCID: PMC8960119 DOI: 10.3389/fmicb.2021.787451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a global public health problem, which is a primary cause of antibiotic-associated diarrhea in humans. The emergence of hypervirulent and antibiotic-resistant strains is associated with the increased incidence and severity of the disease. There are limited studies on genomic characterization of C. difficile in Latin America. We aimed to learn about the molecular epidemiology and antimicrobial resistance in C. difficile strains from adults and children in hospitals of México. We studied 94 C. difficile isolates from seven hospitals in Mexico City from 2014 to 2018. Whole-genome sequencing (WGS) was used to determine the genotype and examine the toxigenic profiles. Susceptibility to antibiotics was determined by E-test. Multilocus sequence typing (MLST) was used to determine allelic profiles. Results identified 20 different sequence types (ST) in the 94 isolates, mostly clade 2 and clade 1. ST1 was predominant in isolates from adult and children. Toxigenic strains comprised 87.2% of the isolates that were combinations of tcdAB and cdtAB (tcdA+/tcdB+/cdtA+/cdtB+, followed by tcdA+/tcdB+/cdtA-/cdtB-, tcdA-/tcdB+/cdtA-/ cdtB-, and tcdA-/tcdB-/cdtA+/cdtB+). Toxin profiles were more diverse in isolates from children. All 94 isolates were susceptible to metronidazole and vancomycin, whereas a considerable number of isolates were resistant to clindamycin, fluroquinolones, rifampicin, meropenem, and linezolid. Multidrug-resistant isolates (≥3 antibiotics) comprised 65% of the isolates. The correlation between resistant genotypes and phenotypes was evaluated by the kappa test. Mutations in rpoB and rpoC showed moderate concordance with resistance to rifampicin and mutations in fusA substantial concordance with fusidic acid resistance. cfrE, a gene recently described in one Mexican isolate, was present in 65% of strains linezolid resistant, all ST1 organisms. WGS is a powerful tool to genotype and characterize virulence and antibiotic susceptibility patterns.
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Affiliation(s)
- Emmanuel Aguilar-Zamora
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
| | - Roberto C. Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Alejandro Gómez-Delgado
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Nayeli Ortiz-Olvera
- Departamento de Gastroenterología, UMAE Hospital de Especialidades, Instituto Mexicano del Seguro Social, México City, Mexico
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | | | - Javier Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- *Correspondence: Javier Torres,
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Margarita Camorlinga-Ponce,
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15
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Baines SL, da Silva AG, Carter GP, Jennison A, Rathnayake I, Graham RM, Sintchenko V, Wang Q, Rockett RJ, Timms VJ, Martinez E, Ballard S, Tomita T, Isles N, Horan KA, Pitchers W, Stinear TP, Williamson DA, Howden BP, Seemann T. Complete microbial genomes for public health in Australia and the Southwest Pacific. Microb Genom 2020; 6:mgen000471. [PMID: 33180013 PMCID: PMC8116684 DOI: 10.1099/mgen.0.000471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health laboratory activities. Here, we announce a BioProject (PRJNA556438) dedicated to sharing complete genomes chosen to represent a range of pathogenic bacteria with regional importance to Australia and the Southwest Pacific; enriching the catalogue of globally available complete genomes for public health while providing valuable strains to regional public health microbiology laboratories. In this first step, we present 26 complete high-quality bacterial genomes. Additionally, we describe here a framework for reconstructing complete microbial genomes and highlight some of the challenges and considerations for accurate and reproducible genome reconstruction.
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Affiliation(s)
- Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Amy Jennison
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Irani Rathnayake
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Rikki M. Graham
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Verlaine J. Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Nicole Isles
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Kristy A. Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - William Pitchers
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
| | - Communicable Diseases Genomics Network (CDGN)
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3001, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3001, Australia
- Public Health Microbiology, Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Queensland Department of Health, Archerfield, Queensland 4108, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital and NSW Health Pathology, Sydney, New South Wales 2145, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales 2006, Australia
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16
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DNA barcoding for the identification of mold species in bakery plants and products. Food Chem 2020; 318:126501. [PMID: 32131042 DOI: 10.1016/j.foodchem.2020.126501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 11/23/2022]
Abstract
Mold identification at the species level in environmental samples is a major challenge. Molecular techniques have been widely used for fungal classification, but as most primers are genus-specific, it is laborious to identify unknown samples. In this study, a PCR-based method for the identification of mold at the species level was developed. Therefore, common sequencing primers and combinations of them, targeting specific DNA regions, were tested. Here we present a combination of eight primer pairs to identify mold within a single PCR run. The approach correctly identified mold of unknown species from samples taken at a local bakery, including Penicillium chrysogenum, Penicillium citrinum, Cladosporium sphaerospermum, Paecilomyces formosus, Rhizopus oryzae and Aspergillus niger. Results obtained from the PCR method were successfully validated by chromatographic mycotoxin and microscopy analysis. Findings highlight DNA barcoding as an appropriate tool for mold identification; however, its efficacy is essentially dependent on DNA quality and primer selection.
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17
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Shapiro JW, Putonti C. UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales. Virus Evol 2020; 6:veaa030. [PMID: 32607251 PMCID: PMC7307601 DOI: 10.1093/ve/veaa030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host's genome by co-opting the host's XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UPϕ901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UPϕ901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call 'UPϕ viruses', also harbors two or more novel genes of unknown function.
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Affiliation(s)
- Jason W Shapiro
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.,Department of Computer Science, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL, 60626, USA.,Bioinformatics Program, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL 60626, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, 2160 S First Ave, Maywood, IL 60153, USA
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Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017. J Clin Microbiol 2020; 58:JCM.02070-19. [PMID: 32269101 PMCID: PMC7269400 DOI: 10.1128/jcm.02070-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Results revealed a remarkably diverse population composed of at least 28 sequence types, which are mostly represented by 1 or a few strains. A comparison of our isolates with 249 clinical C. jejuni from other states showed frequent phylogenetic intermingling, suggesting a lack of geographical structure and minimal local diversification within the state. Multiple independent acquisitions of resistance genes from 5 classes of antibiotics characterize the population, with 47/52 (90.4%) of the genomes carrying at least 1 horizontally acquired resistance gene. Frequently recombining genes include those associated with heptose biosynthesis, colonization, and stress resistance. We conclude that the diversity of clinical C. jejuni in New Hampshire in 2017 was driven mainly by the coexistence of phylogenetically diverse antibiotic-resistant lineages, widespread geographical mixing, and frequent recombination. This study provides an important baseline census of the standing pangenomic variation and drug resistance to aid the development of a statewide database for epidemiological studies and clinical decision making. Continued genomic surveillance will be necessary to accurately assess how the population of C. jejuni changes over the long term.
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19
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Deorowicz S, Gudys A, Dlugosz M, Kokot M, Danek A. Kmer-db: instant evolutionary distance estimation. Bioinformatics 2019; 35:133-136. [PMID: 29986074 DOI: 10.1093/bioinformatics/bty610] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Summary Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40 715 pathogens in <7 min (on a modern workstation), 26 times faster than Mash, its main competitor. Availability and implementation https://github.com/refresh-bio/kmer-db and http://sun.aei.polsl.pl/REFRESH/kmer-db. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sebastian Deorowicz
- Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Adam Gudys
- Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Maciej Dlugosz
- Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Marek Kokot
- Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Agnieszka Danek
- Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
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Bhushan A, Egli PJ, Peters EE, Freeman MF, Piel J. Genome mining- and synthetic biology-enabled production of hypermodified peptides. Nat Chem 2019; 11:931-939. [PMID: 31501509 PMCID: PMC6763334 DOI: 10.1038/s41557-019-0323-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 08/01/2019] [Indexed: 12/12/2022]
Abstract
The polytheonamides are among the most complex and biosynthetically distinctive natural products known to date. These potent peptide cytotoxins are derived from a ribosomal precursor processed by 49 mostly non-canonical posttranslational modifications. As the producer is a 'microbial dark matter' bacterium only distantly related to any cultivated organism, >70-step chemical syntheses have been developed to access these unique compounds. Here, we mined prokaryotic diversity to establish a synthetic platform based on the new host Microvirgula aerodenitrificans that produces hypermodified peptides within two days. Using this system, we generated the aeronamides, new polytheonamide-type compounds with near-picomolar cytotoxicity. Aeronamides, as well as the polygeonamides produced from deep-rock biosphere DNA, contain the highest numbers of D-amino acids in known biomolecules. With increasing bacterial genomes being sequenced, similar host mining strategies might become feasible to access further elusive natural products from uncultivated life.
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Affiliation(s)
- Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | | | - Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota-Twin Cities, St Paul, MN, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
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21
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Boldogkői Z, Moldován N, Balázs Z, Snyder M, Tombácz D. Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research. Trends Microbiol 2019; 27:578-592. [DOI: 10.1016/j.tim.2019.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/21/2019] [Accepted: 01/30/2019] [Indexed: 12/16/2022]
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23
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Abstract
The growth of pathogen genomics shows no signs of abating. Whole-genome sequencing of clinical viral and bacterial isolates continues to grow in nearly exponential bounds. Reductions in cost driven by new technology have created a seamless environment for generating, sharing, and analyzing pathogen genomes. The high-resolution view of infectious disease transmission dynamics offered by analyzing whole genomes from pathogens, coupled with the genomicist ethic of widespread data sharing, has created a veritable Internet of pathogens, which inadvertently produces new threats to patient privacy and protected heath information. The health care system, and society more generally, have yet to explore the far-reaching privacy concerns raised by readily accessible pathogen genomic data. The recent use of human genomic databases, the existence of freely available alternative data and metadata sources, and lax regulation of collecting publicly available genomes to identify individuals in a criminal context raise concerning parallels about what is possible with pathogen genomics. The growing ability to ascertain culpability for infectious disease transmission at a nearly individual level could change our perspective on disease outbreaks from one based on public health to one based on individual liability. These technological breakthroughs in the absence of an understanding of potential privacy and liability issues lead to questions about the dominant paradigm of better living through pathogen genomics.
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24
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Draft Genome Sequence of Enterococcus plantarum Strain TRW2, Isolated from Lettuce. Microbiol Resour Announc 2019; 8:MRA01428-18. [PMID: 30746515 PMCID: PMC6368650 DOI: 10.1128/mra.01428-18] [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: 10/21/2018] [Accepted: 12/17/2018] [Indexed: 12/04/2022] Open
Abstract
We report the draft genome sequence for Enterococcus plantarum strain TRW2, isolated from the phyllosphere of romaine lettuce. The draft sequence consists of 3,383,441 bp, with a G+C content of 35.8% and 3,218 protein-coding genes. We report the draft genome sequence for Enterococcus plantarum strain TRW2, isolated from the phyllosphere of romaine lettuce. The draft sequence consists of 3,383,441 bp, with a G+C content of 35.8% and 3,218 protein-coding genes. None of the 22,190 known antibiotic resistance genes were detected.
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25
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Draft Genome Sequence of Bacillus velezensis CE2, Which Genetically Encodes a Novel Multicomponent Lantibiotic. Microbiol Resour Announc 2019; 8:MRA01420-18. [PMID: 30687828 PMCID: PMC6346160 DOI: 10.1128/mra.01420-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/12/2018] [Indexed: 12/03/2022] Open
Abstract
Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Whole-genome sequencing revealed that the strain genetically encodes a novel multicomponent lantibiotic, velezensicidin.
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26
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Xu GC, Xu TJ, Zhu R, Zhang Y, Li SQ, Wang HW, Li JT. LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly. Gigascience 2019; 8:5256637. [PMID: 30576505 PMCID: PMC6324547 DOI: 10.1093/gigascience/giy157] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 02/05/2023] Open
Abstract
Background Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes. Findings We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster and with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats; the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and next-generation sequencing-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was greater than 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome. Conclusions LR_Gapcloser is a fast and efficient tool that can be used to close gaps and improve the contiguity of genome assemblies. A proposed hybrid assembly including this tool promises reference-grade assemblies. The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.
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Affiliation(s)
- Gui-Cai Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China.,College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Tian-Jun Xu
- College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Rui Zhu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China.,College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Shang-Qi Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
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Xu GC, Xu TJ, Zhu R, Zhang Y, Li SQ, Wang HW, Li JT. LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly. Gigascience 2019. [PMID: 30576505 DOI: 10.5524/100540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes. FINDINGS We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster and with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats; the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and next-generation sequencing-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was greater than 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome. CONCLUSIONS LR_Gapcloser is a fast and efficient tool that can be used to close gaps and improve the contiguity of genome assemblies. A proposed hybrid assembly including this tool promises reference-grade assemblies. The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.
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Affiliation(s)
- Gui-Cai Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
- College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Tian-Jun Xu
- College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Rui Zhu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Shang-Qi Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
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28
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Xu GC, Xu TJ, Zhu R, Zhang Y, Li SQ, Wang HW, Li JT. LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly. Gigascience 2019. [PMID: 30576505 DOI: 10.1093/gigascience/giy157/5256637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes. FINDINGS We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps faster and with a lower error rate and a much lower memory usage than two existing, state-of-the art tools. This tool utilized raw reads to fill more gaps than when using error-corrected reads. It is applicable to gaps in the assemblies by different approaches and from large and complex genomes. After performing gap-closure using this tool, the contig N50 size of the human CHM1 genome was improved from 143 kb to 19 Mb, a 132-fold increase. We also closed the gaps in the Triticum urartu genome, a large genome rich in repeats; the contig N50 size was increased by 40%. Further, we evaluated the contiguity and correctness of six hybrid assembly strategies by combining the optimal TGS-based and next-generation sequencing-based assemblers with LR_Gapcloser. A proposed and optimal hybrid strategy generated a new human CHM1 genome assembly with marked contiguity. The contig N50 value was greater than 28 Mb, which is larger than previous non-reference assemblies of the diploid human genome. CONCLUSIONS LR_Gapcloser is a fast and efficient tool that can be used to close gaps and improve the contiguity of genome assemblies. A proposed hybrid assembly including this tool promises reference-grade assemblies. The software is available at http://www.fishbrowser.org/software/LR_Gapcloser/.
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Affiliation(s)
- Gui-Cai Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
- College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Tian-Jun Xu
- College of Marine Science, Zhejiang Ocean University, 1 Haida South Road, Zhoushan, 316022, China
| | - Rui Zhu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Shang-Qi Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, 150 Yongding Road, Beijing, 100141, China
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Nüesch-Inderbinen M, Cernela N, Wüthrich D, Egli A, Stephan R. Genetic characterization of Shiga toxin producing Escherichia coli belonging to the emerging hybrid pathotype O80:H2 isolated from humans 2010–2017 in Switzerland. Int J Med Microbiol 2018; 308:534-538. [DOI: 10.1016/j.ijmm.2018.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/10/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022] Open
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