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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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Scicchitano D, Leuzzi D, Babbi G, Palladino G, Turroni S, Laczny CC, Wilmes P, Correa F, Leekitcharoenphon P, Savojardo C, Luise D, Martelli P, Trevisi P, Aarestrup FM, Candela M, Rampelli S. Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. Anim Microbiome 2024; 6:17. [PMID: 38555432 PMCID: PMC10981832 DOI: 10.1186/s42523-024-00305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment. RESULTS In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe. CONCLUSIONS Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.
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Affiliation(s)
- Daniel Scicchitano
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Daniela Leuzzi
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Paul Wilmes
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Pierluigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Marco Candela
- Fano Marine Center, Fano, Italy.
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Simone Rampelli
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Ulrich JU, Epping L, Pilz T, Walther B, Stingl K, Semmler T, Renard BY. Nanopore adaptive sampling effectively enriches bacterial plasmids. mSystems 2024; 9:e0094523. [PMID: 38376263 PMCID: PMC10949517 DOI: 10.1128/msystems.00945-23] [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: 09/04/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions. IMPORTANCE Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.
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Affiliation(s)
- Jens-Uwe Ulrich
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Tanja Pilz
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Bernhard Y. Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
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Sabino YNV, de Melo MD, da Silva GC, Mantovani HC. Unraveling the diversity and dissemination dynamics of antimicrobial resistance genes in Enterobacteriaceae plasmids across diverse ecosystems. J Appl Microbiol 2024; 135:lxae028. [PMID: 38323496 DOI: 10.1093/jambio/lxae028] [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: 10/08/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/08/2024]
Abstract
AIM The objective of this study was to investigate the antimicrobial resistance genes (ARGs) in plasmids of Enterobacteriaceae from soil, sewage, and feces of food-producing animals and humans. METHODS AND RESULTS The plasmid sequences were obtained from the NCBI database. For the identification of ARG, comprehensive antibiotic resistance database (CARD), and ResFinder were used. Gene conservation and evolution were investigated using DnaSP v.6. The transfer potential of the plasmids was evaluated using oriTfinder and a MOB-based phylogenetic tree was reconstructed using Fastree. We identified a total of 1064 ARGs in all plasmids analyzed, conferring resistance to 15 groups of antibiotics, mostly aminoglycosides, beta-lactams, and sulfonamides. The greatest number of ARGs per plasmid was found in enterobacteria from chicken feces. Plasmids from Escherichia coli carrying multiple ARGs were found in all ecosystems. Some of the most abundant genes were shared among all ecosystems, including aph(6)-Id, aph(3'')-Ib, tet(A), and sul2. A high level of sequence conservation was found among these genes, and tet(A) and sul2 are under positive selective pressure. Approximately 62% of the plasmids carrying at least one ARG were potentially transferable. Phylogenetic analysis indicated a potential co-evolution of Enterobacteriaceae plasmids in nature. CONCLUSION The high abundance of Enterobacteriaceae plasmids from diverse ecosystems carrying ARGs reveals their widespread distribution and importance.
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Affiliation(s)
| | - Mariana Dias de Melo
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Giarlã Cunha da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Hilario Cuquetto Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, USA
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Jiang N, Chen H, Cheng L, Fu Q, Liu R, Liang Q, Fu G, Wan C, Huang Y. Genomic analysis reveals the population structure and antimicrobial resistance of avian Pasteurella multocida in China. J Antimicrob Chemother 2024; 79:186-194. [PMID: 38019670 DOI: 10.1093/jac/dkad365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
OBJECTIVES To investigate the population structure and antimicrobial resistance (AMR) of avian Pasteurella multocida in China. METHODS Utilizing WGS analysis, we explored the phylogeny using a dataset of 546 genomes, comprising avian P. multocida isolates from China (n = 121), the USA (n = 165), Australia(n = 153), Bangladesh (n = 3) and isolates of other hosts from China (n = 104). We examined the integrative and conjugative element (ICE) structures and the distribution of their components carrying resistance genes, and reconstructed the evolutionary history of A:L1:ST129 (n = 110). RESULTS The population structure of avian P. multocida in China was dominated by the A:L1:ST129 clone with limited genetic diversity. A:L1:ST129 isolates possessed a broader spectrum of resistance genes at comparatively higher frequencies than those from other hosts and countries. The novel putative ICEs harboured complex resistant clusters that were prevalent in A:L1:ST129. Bayesian analysis predicted that the A:L1:ST129 clone emerged around 1923, and evolved slowly. CONCLUSIONS A:L1:ST129 appears to possess a host predilection towards avian species in China, posing a potential health threat to other animals. The complex AMR determinants coupled with high frequencies may strengthen the population dominance of A:L1:ST129. The extensive antimicrobial utilization in poultry farming and the mixed rearing practices could have accelerated AMR accumulation in A:L1:ST129. ICEs, together with their resistant clusters, significantly contribute to resistance gene transfer and facilitate the adaptation of A:L1:ST129 to ecological niches. Despite the genetic stability and slow evolution rate, A:L1:ST129 deserves continued monitoring due to its propensity to retain resistance genes, warranting global attention to preclude substantial economic losses.
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Affiliation(s)
- Nansong Jiang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Hongmei Chen
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Longfei Cheng
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Qiuling Fu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Rongchang Liu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Qizhang Liang
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Guanghua Fu
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Chunhe Wan
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
| | - Yu Huang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
- Fujian Key Laboratory for Prevention and Control of Avian Diseases, Fuzhou, Fujian Province, China
- Fujian Industry Technology Innovation Research Academy of Livestock and Poultry Diseases Prevention & Control, Fuzhou, Fujian Province, China
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Dwiyanto J, Huët MAL, Hussain MH, Su TT, Tan JBL, Toh KY, Lee JWJ, Rahman S, Chong CW. Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia. NPJ Biofilms Microbiomes 2023; 9:55. [PMID: 37573460 PMCID: PMC10423249 DOI: 10.1038/s41522-023-00425-0] [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: 12/27/2022] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.
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Affiliation(s)
- J Dwiyanto
- AMILI, Singapore, 118261, Singapore.
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - M A L Huët
- Faculty of Science, University of Mauritius, Reduit, 80837, Mauritius
| | - M H Hussain
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - T T Su
- South East Asia Community Observatory, Segamat, 85000, Malaysia
| | - J B L Tan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - K Y Toh
- AMILI, Singapore, 118261, Singapore
| | - J W J Lee
- AMILI, Singapore, 118261, Singapore
- Department of Medicine, National University Hospital, Singapore, 119228, Singapore
| | - S Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
- Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - C W Chong
- AMILI, Singapore, 118261, Singapore.
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia.
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Gonçalves OS, de Assis JCS, Santana MF. Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes. Funct Integr Genomics 2022; 22:1139-1145. [PMID: 36149586 DOI: 10.1007/s10142-022-00903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jessica Catarine Silva de Assis
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. Mob DNA 2022; 13:19. [PMID: 35962419 PMCID: PMC9373382 DOI: 10.1186/s13100-022-00275-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00275-1.
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