High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs
The genus <i>Herbaspirillum</i> is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the <i>Herbaspirillum</i> genus have frequently been isolated from clinical samples. Understanding the genomic cha...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Antibiotics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-6382/10/11/1409 |
| _version_ | 1797511426430992384 |
|---|---|
| author | Willian Klassen Oliveira Hugo Leonardo Ávila Michelle Zibeti Tadra Rodrigo Luiz Cardoso Cyntia Maria Teles Fadel-Pichet Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Helisson Faoro |
| author_facet | Willian Klassen Oliveira Hugo Leonardo Ávila Michelle Zibeti Tadra Rodrigo Luiz Cardoso Cyntia Maria Teles Fadel-Pichet Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Helisson Faoro |
| author_sort | Willian Klassen Oliveira |
| collection | DOAJ |
| description | The genus <i>Herbaspirillum</i> is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the <i>Herbaspirillum</i> genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of <i>H. frisingense</i> AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16–41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that <i>H. frisingense</i> has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts. |
| first_indexed | 2024-03-10T05:45:06Z |
| format | Article |
| id | doaj.art-586435a6f39c41dbbd8115c0e3b97261 |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-10T05:45:06Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-586435a6f39c41dbbd8115c0e3b972612023-11-22T22:11:14ZengMDPI AGAntibiotics2079-63822021-11-011011140910.3390/antibiotics10111409High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple DrugsWillian Klassen Oliveira0Hugo Leonardo Ávila1Michelle Zibeti Tadra2Rodrigo Luiz Cardoso3Cyntia Maria Teles Fadel-Pichet4Emanuel Maltempi de Souza5Fábio de Oliveira Pedrosa6Helisson Faoro7Laboratory for Applied Science and Technology in Health, Instituto Carlos Chagas, FIOCRUZ Paraná, Algacyr Munhoz Mader Street, 3775, Curitiba 81350-010, BrazilLaboratory for Applied Science and Technology in Health, Instituto Carlos Chagas, FIOCRUZ Paraná, Algacyr Munhoz Mader Street, 3775, Curitiba 81350-010, BrazilDepartment of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba 81531-980, BrazilDepartment of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba 81531-980, BrazilDepartment of Clinical Analyses, Universidade Federal do Paraná, Curitiba 80060-240, BrazilDepartment of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba 81531-980, BrazilDepartment of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba 81531-980, BrazilLaboratory for Applied Science and Technology in Health, Instituto Carlos Chagas, FIOCRUZ Paraná, Algacyr Munhoz Mader Street, 3775, Curitiba 81350-010, BrazilThe genus <i>Herbaspirillum</i> is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the <i>Herbaspirillum</i> genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of <i>H. frisingense</i> AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16–41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that <i>H. frisingense</i> has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts.https://www.mdpi.com/2079-6382/10/11/1409<i>H. frisingense</i>AMRhost–pathogen interactiongenome comparison |
| spellingShingle | Willian Klassen Oliveira Hugo Leonardo Ávila Michelle Zibeti Tadra Rodrigo Luiz Cardoso Cyntia Maria Teles Fadel-Pichet Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Helisson Faoro High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs Antibiotics <i>H. frisingense</i> AMR host–pathogen interaction genome comparison |
| title | High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs |
| title_full | High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs |
| title_fullStr | High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs |
| title_full_unstemmed | High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs |
| title_short | High Genomic Identity between Clinical and Environmental Strains of <i>Herbaspirillum frisingense</i> Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs |
| title_sort | high genomic identity between clinical and environmental strains of i herbaspirillum frisingense i suggests pre adaptation to different hosts and intrinsic resistance to multiple drugs |
| topic | <i>H. frisingense</i> AMR host–pathogen interaction genome comparison |
| url | https://www.mdpi.com/2079-6382/10/11/1409 |
| work_keys_str_mv | AT willianklassenoliveira highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT hugoleonardoavila highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT michellezibetitadra highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT rodrigoluizcardoso highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT cyntiamariatelesfadelpichet highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT emanuelmaltempidesouza highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT fabiodeoliveirapedrosa highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs AT helissonfaoro highgenomicidentitybetweenclinicalandenvironmentalstrainsofiherbaspirillumfrisingenseisuggestspreadaptationtodifferenthostsandintrinsicresistancetomultipledrugs |