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Poey ME, de los Santos E, Aznarez D, García-Laviña CX, Laviña M. Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes. Front Microbiol 2024; 15:1395953. [PMID: 38946902 PMCID: PMC11213556 DOI: 10.3389/fmicb.2024.1395953] [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: 03/04/2024] [Accepted: 05/27/2024] [Indexed: 07/02/2024] Open
Abstract
Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.
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Affiliation(s)
- María Eloísa Poey
- Sección Fisiología & Genética Bacterianas, Facultad de Ciencias, Montevideo, Uruguay
| | - Eliana de los Santos
- Sección Fisiología & Genética Bacterianas, Facultad de Ciencias, Montevideo, Uruguay
| | - Diego Aznarez
- Sección Fisiología & Genética Bacterianas, Facultad de Ciencias, Montevideo, Uruguay
| | | | - Magela Laviña
- Sección Fisiología & Genética Bacterianas, Facultad de Ciencias, Montevideo, Uruguay
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Traglia GM, Betancor L, Yim L, Iriarte A, Chabalgoity JA. Genotypic and phenotypic analysis of Salmonella enterica serovar Derby, looking for clues explaining the impairment of egg isolates to cause human disease. Front Microbiol 2024; 15:1357881. [PMID: 38903793 PMCID: PMC11186997 DOI: 10.3389/fmicb.2024.1357881] [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: 12/18/2023] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
Salmonella enterica serovar Derby causes foodborne disease (FBD) outbreaks worldwide, mainly from contaminated pork but also from chickens. During a major epidemic of FBD in Uruguay due to S. enteritidis from poultry, we conducted a large survey of commercially available eggs, where we isolated many S. enteritidis strains but surprisingly also a much larger number (ratio 5:1) of S. Derby strains. No single case of S. Derby infection was detected in that period, suggesting that the S. Derby egg strains were impaired for human infection. We sequenced fourteen of these egg isolates, as well as fifteen isolates from pork or human infection that were isolated in Uruguay before and after that period, and all sequenced strains had the same sequence type (ST40). Phylogenomic analysis was conducted using more than 3,500 genomes from the same sequence type (ST), revealing that Uruguayan isolates clustered into four distantly related lineages. Population structure analysis (BAPS) suggested the division of the analyzed genomes into nine different BAPS1 groups, with Uruguayan strains clustering within four of them. All egg isolates clustered together as a monophyletic group and showed differences in gene content with the strains in the other clusters. Differences included variations in the composition of mobile genetic elements, such as plasmids, insertion sequences, transposons, and phages, between egg isolates and human/pork isolates. Egg isolates showed an acid susceptibility phenotype, reduced ability to reach the intestine after oral inoculation of mice, and reduced induction of SPI-2 ssaG gene, compared to human isolates from other monophyletic groups. Mice challenge experiments showed that mice infected intraperitoneally with human/pork isolates died between 1-7 days p.i., while all animals infected with the egg strain survived the challenge. Altogether, our results suggest that loss of genes functions, the insertion of phages and the absence of plasmids in egg isolates may explain why these S. Derby were not capable of producing human infection despite being at that time, the main serovar recovered from eggs countrywide.
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Affiliation(s)
| | | | | | - Andrés Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Alejandro Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Rodrigues RDS, Araujo NFD, Viana C, Yamatogi RS, Nero LA. In Silico Detection of Integrons and Their Relationship with Resistance Phenotype of Salmonella Isolates from a Brazilian Pork Production Chain. Foodborne Pathog Dis 2024; 21:395-402. [PMID: 38917456 DOI: 10.1089/fpd.2023.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024] Open
Abstract
The pork production chain is an important reservoir of antimicrobial resistant bacteria. This study identified and characterized integrons in Salmonella isolates from a Brazilian pork production chain and associate them with their antibiotic resistance pattern. A total of 41 whole-genome sequencing data of nontyphoidal Salmonella were analyzed using PlasmidSPAdes and IntegronFinder software. Nine isolates (21.9%) had some integrons identified (complete and/or incomplete). Six complete class 1 integrons were found, with streptomycin resistance genes (aadA1, aadA2) alone or downstream of a trimethoprim resistance gene (dfrA1, dfrA12), and some also containing resistance genes for sulfonamides (sul1, sul3) and chloramphenicol (cmlA1). Class 2 integron was detected in only one isolate, containing dfrA1-sat2-aadA1 gene cassettes. Five isolates harbored CALINs-clusters attC but lacking integrases-with antimicrobial resistance genes typically found in integron structures. In all, integrons were observed among four serotypes: Derby, Bredeney, Panama, and monophasic var. Typhimurium I 4,[5],12:i:-. The association of integrons with antibiotic resistance phenotype showed that these elements were predominantly identified in multidrug resistance isolates, and six of the seven gentamicin-resistant isolates had integrons. So, surveillance of integrons in Salmonella should be performed to identify the potential for the spread of antimicrobial resistance genes among bacteria.
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Affiliation(s)
- Rafaela da Silva Rodrigues
- InsPOA - Laboratory of Food Inspection, Department of Veterinary Medicine, Federal University of Viçosa, Campus Universitário, Viçosa, Brazil
| | - Natália Ferreira de Araujo
- InsPOA - Laboratory of Food Inspection, Department of Veterinary Medicine, Federal University of Viçosa, Campus Universitário, Viçosa, Brazil
| | - Cibeli Viana
- InsPOA - Laboratory of Food Inspection, Department of Veterinary Medicine, Federal University of Viçosa, Campus Universitário, Viçosa, Brazil
| | - Ricardo Seiti Yamatogi
- InsPOA - Laboratory of Food Inspection, Department of Veterinary Medicine, Federal University of Viçosa, Campus Universitário, Viçosa, Brazil
| | - Luís Augusto Nero
- InsPOA - Laboratory of Food Inspection, Department of Veterinary Medicine, Federal University of Viçosa, Campus Universitário, Viçosa, Brazil
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Sequino G, Cobo-Diaz JF, Valentino V, Tassou C, Volpe S, Torrieri E, Nychas GJ, Álvarez Ordóñez A, Ercolini D, De Filippis F. Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features. Food Res Int 2024; 186:114318. [PMID: 38729711 DOI: 10.1016/j.foodres.2024.114318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.
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Affiliation(s)
- Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - José F Cobo-Diaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Chrysoula Tassou
- Hellenic Agricultural Organization - DIMITRA, Institute of Technology of Agricultural Products, Sofokli Venizelou 1, 14123 Lycovrissi, Attica, Greece
| | - Stefania Volpe
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Elena Torrieri
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | | | - Avelino Álvarez Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy.
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Li X, Brejnrod A, Trivedi U, Russel J, Thorsen J, Shah SA, Vestergaard GA, Rasmussen MA, Nesme J, Bisgaard H, Stokholm J, Sørensen SJ. Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition. MICROBIOME 2024; 12:87. [PMID: 38730321 PMCID: PMC11084089 DOI: 10.1186/s40168-024-01800-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/25/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age. RESULTS We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs. CONCLUSIONS We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.
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Affiliation(s)
- Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Asker Brejnrod
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Gisle Alberg Vestergaard
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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6
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Ghaly TM, Gillings MR, Rajabal V, Paulsen IT, Tetu SG. Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange. Front Microbiol 2024; 15:1338026. [PMID: 38741746 PMCID: PMC11089894 DOI: 10.3389/fmicb.2024.1338026] [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: 11/14/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
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Blanco P, Hipólito A, García-Pastor L, Trigo da Roza F, Toribio-Celestino L, Ortega A, Vergara E, San Millán Á, Escudero J. Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons. Nucleic Acids Res 2024; 52:2961-2976. [PMID: 38214222 PMCID: PMC11014356 DOI: 10.1093/nar/gkad1252] [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: 04/18/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encode promoterless genes, whose expression relies on the platform-associated Pc promoter, with the cassette array functioning as an operon-like structure regulated by the distance to the Pc. This is relevant in large sedentary chromosomal integrons (SCIs) carrying hundreds of ICs, like those in Vibrio species. We selected 29 gene-less cassettes in four Vibrio SCIs, and explored whether their function could be related to the transcription regulation of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Additionally, we identified the transcription start sites of gene-less ICs through 5'-RACE. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Furthermore, one cassette with an antisense promoter can reduce trimethoprim resistance when cloned downstream. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in SCIs and their clinical importance if captured by mobile integrons.
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Affiliation(s)
- Paula Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
| | - Alba Cristina Ortega
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid 28222, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [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: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. mSystems 2024; 9:e0006724. [PMID: 38380923 PMCID: PMC10949469 DOI: 10.1128/msystems.00067-24] [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: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.
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Affiliation(s)
- Juntao Zhong
- Carleton College, Northfield, Minnesota, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Troy Osborn
- Carleton College, Northfield, Minnesota, USA
| | - Thais Del Rosario Hernández
- Carleton College, Northfield, Minnesota, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Oleksandr Kyrysyuk
- Carleton College, Northfield, Minnesota, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Benjamin J. Tully
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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10
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Richard E, Darracq B, Littner E, Vit C, Whiteway C, Bos J, Fournes F, Garriss G, Conte V, Lapaillerie D, Parissi V, Rousset F, Skovgaard O, Bikard D, Rocha EPC, Mazel D, Loot C. Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems. SCIENCE ADVANCES 2024; 10:eadj3498. [PMID: 38215203 DOI: 10.1126/sciadv.adj3498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Integrons are adaptive bacterial devices that rearrange promoter-less gene cassettes into variable ordered arrays under stress conditions, thereby sampling combinatorial phenotypic diversity. Chromosomal integrons often carry hundreds of silent gene cassettes, with integrase-mediated recombination leading to rampant DNA excision and integration, posing a potential threat to genome integrity. How this activity is regulated and controlled, particularly through selective pressures, to maintain such large cassette arrays is unknown. Here, we show a key role of promoter-containing toxin-antitoxin (TA) cassettes as systems that kill the cell when the overall cassette excision rate is too high. These results highlight the importance of TA cassettes regulating the cassette recombination dynamics and provide insight into the evolution and success of integrons in bacterial genomes.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, F-75005 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
- DGA CBRN Defence, 91710 Vert-le-Petit, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Clémence Whiteway
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Julia Bos
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Florian Fournes
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Geneviève Garriss
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Delphine Lapaillerie
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Vincent Parissi
- University of Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS, UMR 5234, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - François Rousset
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Ole Skovgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde DK-4000, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, 75015 Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
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11
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Jia J, Lu SE. Comparative Genome Analyses Provide Insight into the Antimicrobial Activity of Endophytic Burkholderia. Microorganisms 2024; 12:100. [PMID: 38257926 PMCID: PMC10821513 DOI: 10.3390/microorganisms12010100] [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: 12/12/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Endophytic bacteria are endosymbionts that colonize a portion of plants without harming the plant for at least a part of its life cycle. Bacterial endophytes play an essential role in promoting plant growth using multiple mechanisms. The genus Burkholderia is an important member among endophytes and encompasses bacterial species with high genetic versatility and adaptability. In this study, the endophytic characteristics of Burkholderia species are investigated via comparative genomic analyses of several endophytic Burkholderia strains with pathogenic Burkholderia strains. A group of bacterial genes was identified and predicted as the putative endophytic behavior genes of Burkholderia. Multiple antimicrobial biosynthesis genes were observed in these endophytic bacteria; however, certain important pathogenic and virulence genes were absent. The majority of resistome genes were distributed relatively evenly among the endophytic and pathogenic bacteria. All known types of secretion systems were found in the studied bacteria. This includes T3SS and T4SS, which were previously thought to be disproportionately represented in endophytes. Additionally, questionable CRISPR-Cas systems with an orphan CRISPR array were prevalent, suggesting that intact CRISPR-Cas systems may not exist in symbiotes of Burkholderia. This research not only sheds light on the antimicrobial activities that contribute to biocontrol but also expands our understanding of genomic variations in Burkholderia's endophytic and pathogenic bacteria.
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Affiliation(s)
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA;
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12
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Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [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: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
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13
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Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D. Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites. Nat Microbiol 2024; 9:228-240. [PMID: 38172619 DOI: 10.1038/s41564-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France.
| | - Gael A Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Eloi Littner
- Sorbonne Université, Collège Doctoral, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Jean Cury
- Université Paris-Saclay, Inria, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Orsay, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Théophile Niault
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Delphine Lapaillerie
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
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14
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [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: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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15
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Alvarez-Molina A, Cobo-Díaz JF, Alexa EA, Crispie F, Prieto M, López M, Cotter PD, Alvarez-Ordóñez A. Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes. Food Res Int 2023; 173:113442. [PMID: 37803768 DOI: 10.1016/j.foodres.2023.113442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/08/2023]
Abstract
In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.
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Affiliation(s)
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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16
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Veloso M, Arros P, Acosta J, Rojas R, Berríos-Pastén C, Varas M, Araya P, Hormazábal JC, Allende ML, Chávez FP, Lagos R, Marcoleta AE. Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in Chile: high-risk ST25 clones and novel mobile elements. Microbiol Spectr 2023; 11:e0039923. [PMID: 37707451 PMCID: PMC10581085 DOI: 10.1128/spectrum.00399-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/26/2023] [Indexed: 09/15/2023] Open
Abstract
Multidrug- and carbapenem-resistant Klebsiella pneumoniae (CR-Kp) are critical threats to global health and key traffickers of resistance genes to other pathogens. Despite the sustained increase in CR-Kp infections in Chile, few strains have been described at the genomic level, lacking details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial susceptibility and performed a comparative genomic analysis of 10 CR-Kp isolates from the Chilean surveillance of carbapenem-resistant Enterobacteriaceae. High resistance was observed among the isolates (five ST25, three ST11, one ST45, and one ST505), which harbored 44 plasmids, most carrying genes for conjugation and resistance to several antibiotics and biocides. Ten plasmids encoding carbapenemases were characterized, including novel plasmids or variants with additional resistance genes, a novel genetic environment for blaKPC-2, and plasmids widely disseminated in South America. ST25 K2 isolates belonging to CG10224, a clone traced back to 2012 in Chile, which recently acquired blaNDM-1, blaNDM-7, or blaKPC-2 plasmids stood out as high-risk clones. Moreover, this corresponds to the first report of ST25 and ST45 Kp producing NDM-7 in South America and ST505 CR-Kp producing both NDM-7 and KPC-2 worldwide. Also, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for a detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence of CR-Kp in Chile and South America. IMPORTANCE In the ongoing antimicrobial resistance crisis, carbapenem-resistant strains of Klebsiella pneumoniae are critical threats to public health. Besides globally disseminated clones, the burden of local problem clones remains substantial. Although genomic analysis is a powerful tool for improving pathogen and antimicrobial resistance surveillance, it is still restricted in low- to middle-income countries, including Chile, causing them to be underrepresented in genomic databases and epidemiology surveys. This study provided the first 10 complete genomes of the Chilean surveillance for carbapenem-resistant K. pneumoniae in healthcare settings, unveiling their resistance and virulence determinants and the mobile genetic elements mediating their dissemination, placed in the South American and global K. pneumoniae epidemiological context. We found ST25 with K2 capsule as an emerging high-risk clone, along with other lineages producing two carbapenemases and several other resistance and virulence genes encoded in novel plasmids and genomic islands.
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Affiliation(s)
- Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Joaquin Acosta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Roberto Rojas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | | | - Miguel L. Allende
- Millennium Institute Center for Genome Regulation (CGR), Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P. Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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17
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Kneis D, Lemay-St-Denis C, Cellier-Goetghebeur S, Elena AX, Berendonk TU, Pelletier JN, Heß S. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. THE ISME JOURNAL 2023; 17:1455-1466. [PMID: 37369703 PMCID: PMC10432401 DOI: 10.1038/s41396-023-01460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.
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Affiliation(s)
- David Kneis
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany.
| | - Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stella Cellier-Goetghebeur
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Alan X Elena
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany
| | | | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
- Chemistry Department, University of Montréal, Montréal, QC, H2V 0B3, Canada
| | - Stefanie Heß
- TU Dresden, Institute of Microbiology, 01062, Dresden, Germany
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18
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Bhat BA, Mir RA, Qadri H, Dhiman R, Almilaibary A, Alkhanani M, Mir MA. Integrons in the development of antimicrobial resistance: critical review and perspectives. Front Microbiol 2023; 14:1231938. [PMID: 37720149 PMCID: PMC10500605 DOI: 10.3389/fmicb.2023.1231938] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.
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Affiliation(s)
- Basharat Ahmad Bhat
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India
| | - Hafsa Qadri
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Rohan Dhiman
- Department of Life Sciences, National Institute of Technology (NIT), Rourkela, Odisha, India
| | - Abdullah Almilaibary
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Mustfa Alkhanani
- Department of Biology, College of Science, Hafr Al Batin University of Hafr Al-Batin, Hafar Al Batin, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, India
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Syed Abu Thahir S, Rajendiran S, Shaharudin R, Veloo Y. Multidrug-Resistant Salmonella Species and Their Mobile Genetic Elements from Poultry Farm Environments in Malaysia. Antibiotics (Basel) 2023; 12:1330. [PMID: 37627750 PMCID: PMC10451245 DOI: 10.3390/antibiotics12081330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
The prevalence and persistent outbreaks of multidrug-resistant (MDR) Salmonella in low-income countries have received growing attention among the public and scientific community. Notably, the excessive use of antibiotics in chicken feed for the purpose of treatment or as prophylaxis in the poultry industry have led to a rising rate of antimicrobial resistance. Therefore, this study aimed to determine the presence of antimicrobial-resistant Salmonella species and its mobile genetic elements from soil and effluent samples of 33 randomly selected poultry farms in Selangor, Malaysia. Salmonella species were isolated on selective media (CHROMagar™ Salmonella). VITEK® 2 system was used to identify the isolates and their antimicrobial susceptibility. Subsequently, eight isolates were subjected to the whole genome sequencing (WGS). Based on the results, Salmonella spp. was detected in 38.1% (24/63) of samples, with the highest resistance to ampicillin (62.5%), followed by ampicillin/sulbactam (50.0%) and ciprofloxacin (45.8%). Meanwhile, the identified serovars were Salmonella enterica subspecies enterica serovar Weltevreden (S. Weltevreden), S. Jedburgh, and S. Brancaster. The most prevalent resistance genes detected include qnrS1, blaTEM-176, dfrA14, and tet(A). The IncX1 plasmid, with encoded resistance genes, was also detected in four isolates. Furthermore, mutations in the quinolone resistant-determining regions (QRDR) were discovered, specifically in the gyrA, gyrB, and parC genes. In short, surveillance such as continuous monitoring of antimicrobial resistance and emerging trends in resistance patterns through farm environmental samples could provide information to formulate public health interventions for effective infection prevention and disease control.
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Affiliation(s)
- Syahidiah Syed Abu Thahir
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Rafiza Shaharudin
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Yuvaneswary Veloo
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
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20
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Lund D, Coertze RD, Parras-Moltó M, Berglund F, Flach CF, Johnning A, Larsson DGJ, Kristiansson E. Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens. Commun Biol 2023; 6:812. [PMID: 37537271 PMCID: PMC10400643 DOI: 10.1038/s42003-023-05174-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.
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Affiliation(s)
- David Lund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roelof Dirk Coertze
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
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21
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Ivanova O, Blumenkrants D, Krylova E, Soltynskaya I, Goncharova A, Chaikin E, Akhmetzyanova A, Panin A. Founding of the culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation. Vet World 2023; 16:1451-1460. [PMID: 37621551 PMCID: PMC10446724 DOI: 10.14202/vetworld.2023.1451-1460] [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: 11/14/2022] [Accepted: 05/29/2023] [Indexed: 08/26/2023] Open
Abstract
Background and Aim The main purpose of a national bioresource center is to standardize, centralize, preserve, and ensure accessibility of microbial bioresources that accumulate there because of state research programs. The establishment of national bioresource centers for antibiotic-resistant microorganisms allows to solve practical problems in the field of veterinary service, as well as to develop effective chemotherapeutic and disinfectant drugs to overcome the mechanisms of resistance. This study aimed to outline the process of forming a national culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation using two microbial strains. Materials and Methods The object of research was isolates of Salmonella spp., Escherichia coli, Enterococcus spp., Campylobacter spp., Listeria monocytogenes, and Staphylococcus spp., all of which were obtained from biomaterials of farm animals, feed samples, bedding, water from livestock buildings, washouts from environmental objects, and food products. The resistance of bacterial isolates was determined using microbiological and molecular-genetic research methods. Results During monitoring studies, 1489 bacterial isolates were isolated. In total, 408 bacterial isolates were tested for sensitivity to antimicrobial agents, including E. coli (47.6%), Salmonella spp. (30.4%), Enterococcus spp. (11.3%), and Campylobacter spp. (10.8%). For genetic characterization, 95 isolates of Salmonella enterica, E. coli, Campylobacter spp., L. monocytogenes, Staphylococcus spp., Enterococcus spp. were chosen from the research collection, which was formed as part of the monitoring program for antibiotic resistance. Conclusion Deposited isolates that underwent whole-genome analysis can be used as positive control samples both in the development and use of methods or test systems for the detection of various resistance genes in zoonotic bacteria. In addition, such isolates can also be used for microbiological studies related to determining the sensitivity of microorganisms to antibacterial drugs, for phenotypic studies in the diagnosis of various bacterial infections in animals and birds, and retrospective analysis of strains from numerous collections.
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Affiliation(s)
- Olga Ivanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Dmitry Blumenkrants
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Ekaterina Krylova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Irina Soltynskaya
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anastasia Goncharova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Evgeny Chaikin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anna Akhmetzyanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Alexander Panin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
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22
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Mazumder R, Hussain A, Bhadra B, Phelan J, Campino S, Clark TG, Mondal D. Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh. Front Med (Lausanne) 2023; 10:1206756. [PMID: 37435536 PMCID: PMC10330784 DOI: 10.3389/fmed.2023.1206756] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Klebsiella aerogenes, a nosocomial pathogen, is increasingly associated with extensive drug resistance and virulence profiles. It is responsible for high morbidity and mortality. This report describes the first successfully treated case of community-acquired urinary tract infection (UTI) caused by Klebsiella aerogenes in an elderly housewife with Type-2 diabetes (T2D) from Dhaka, Bangladesh. The patient was empirically treated with intravenous ceftriaxone (500 mg/8 h). However, she did not respond to the treatment. The urine culture and sensitivity tests, coupled with bacterial whole-genome sequencing (WGS) and analysis, revealed the bacteria to be K. aerogenes which was extensively drug-resistant but was susceptible to carbapenems and polymyxins. Based on these findings, meropenem (500 mg/8 h) was administered to the patient, who then responded to the treatment and recovered successfully without having a relapse. This case raises awareness of the importance of diagnosis of not-so-common etiological agents, correct identification of the pathogens, and targeted antibiotic therapy. In conclusion, correctly identifying etiological agents of UTI using WGS approaches that are otherwise difficult to diagnose could help improve the identification of infectious agents and improve the management of infectious diseases.
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Affiliation(s)
- Razib Mazumder
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Arif Hussain
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Bithika Bhadra
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dinesh Mondal
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
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23
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Prasolova O, Krylova E, Bogomazova A, Soltynskaya I, Sklyarov O, Gordeeva V, Timofeeva I, Motorygin A, Panin A. Russian collection of Brucella abortus vaccine strains: annotation, implementation and genomic analysis. Front Vet Sci 2023; 10:1154520. [PMID: 37415963 PMCID: PMC10322197 DOI: 10.3389/fvets.2023.1154520] [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: 01/30/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
Over the past 10 years, immunization of cattle in Russia has been performed using vaccines from Brucella abortus strains 82, 19 and 75/79. To prevent brucellosis in small ruminants, two vaccines have been used, from the Brucella melitensis strain REV-1 and the B. abortus strain 19; note that twice as many animals have been immunized with the former vaccine than with the latter vaccine. The disadvantage of using these preparations is the formation of prolonged post-vaccination seropositivity, which is especially pronounced in animals after immunization with vaccines from B. abortus strain 19 and B. melitensis strain REV-1. This study aims to perform the whole genome sequencing of Brucella vaccine strains from the Russian collection. A bioinformatics analysis of the genomic data proved that the vaccine strains 75/79AB, 82, R-1096, and the KV 17/100 belong to ST-2, 104 M to ST-1, KV 13/100 to ST-5. This analysis allowed us to characterize vaccine strains's phylogenetic relationships and to prove the close relation of vaccine strains 75/79AB, 82, R-1096. Also, we defined candidate mutations in genes pmm, wbdA, wbkA, wboA, and eryB, which could be responsible for the attenuated virulence of vaccine strains. The complete genomic sequences of B. abortus strains make further studies of bacterial pathogenicity determinants and virulence phenotype feasible, as well as their use in quality control of animal medicines.
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Affiliation(s)
- Olga Prasolova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Ekaterina Krylova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Alexandra Bogomazova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
- The Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia, Moscow, Russia
| | - Irina Soltynskaya
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Oleg Sklyarov
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Veronika Gordeeva
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
- The Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia, Moscow, Russia
| | - Irina Timofeeva
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Anton Motorygin
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - Alexander Panin
- The Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
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24
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Kim JJ, Seong HJ, Johnson TA, Cha CJ, Sul WJ, Chae JC. Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131761. [PMID: 37290355 DOI: 10.1016/j.jhazmat.2023.131761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.
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Affiliation(s)
- Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea; Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea.
| | - Jong-Chan Chae
- Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea.
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25
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Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
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26
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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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27
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Zhou K, Xue CX, Xu T, Shen P, Wei S, Wyres KL, Lam MMC, Liu J, Lin H, Chen Y, Holt KE, Xiao Y. A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. Nat Commun 2023; 14:2464. [PMID: 37117217 PMCID: PMC10147710 DOI: 10.1038/s41467-023-38061-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Adaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019. We uncovered a subclonal replacement in the predominant clone ST11, where the previously prevalent subclone OL101:KL47 was replaced by O2v1:KL64 over time in a stepwise manner. O2v1:KL64 carried a higher load of mobile genetic elements, and a point mutation exclusively detected in the recC of O2v1:KL64 significantly promotes recombination proficiency. The epidemic success of O2v1:KL64 was further associated with a hypervirulent sublineage with enhanced resistance to phagocytosis, sulfamethoxazole-trimethoprim, and tetracycline. The phenotypic alterations were linked to the overrepresentation of hypervirulence determinants and antibiotic genes conferred by the acquisition of an rmpA-positive pLVPK-like virulence plasmid and an IncFII-type multidrug-resistant plasmid, respectively. The dissemination of the sublineage was further promoted by more frequent inter-hospital transmission. The results collectively demonstrate that the expansion of O2v1:KL64 is correlated to a repertoire of genomic alterations convergent in a subpopulation with evolutionary advantages.
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Affiliation(s)
- Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China.
| | - Chun-Xu Xue
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Sha Wei
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Jinquan Liu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Haoyun Lin
- Department of Clinical Laboratory, Shenzhen People's Hospital, Shenzhen, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Fraenkel CJ, Starlander G, Tano E, Sütterlin S, Melhus Å. The First Swedish Outbreak with VIM-2-Producing Pseudomonas aeruginosa, Occurring between 2006 and 2007, Was Probably Due to Contaminated Hospital Sinks. Microorganisms 2023; 11:microorganisms11040974. [PMID: 37110397 PMCID: PMC10143745 DOI: 10.3390/microorganisms11040974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa is an increasing clinical problem worldwide. The aim of this study was to describe the first outbreak of a Verona integron-borne metallo-ß-lactamase (VIM)-2-producing P. aeruginosa strain in Sweden and its expansion in the region. A cluster of multidrug-resistant P. aeruginosa appeared at two neighbouring hospitals in 2006. The isolates were characterized by PCR, pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing. Patient charts, laboratory records, and hygiene routines were reviewed, and patients, staff, and the environment were screened. The investigation revealed a clonal outbreak of a VIM-2-producing P. aeruginosa strain belonging to the high-risk clonal complex 111, susceptible only to gentamicin and colistin. No direct contact between patients could be established, but most of them had stayed in certain rooms/wards weeks to months apart. Cultures from two sinks yielded growth of the same strain. The outbreak ended when control measures against the sinks were taken, but new cases occurred in a tertiary care hospital in the region. In conclusion, when facing prolonged outbreaks with this bacterium, sinks and other water sources in the hospital environment should be considered. By implementing proactive control measures to limit the bacterial load in sinks, the waterborne transmission of P. aeruginosa may be reduced.
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Affiliation(s)
- Carl-Johan Fraenkel
- Department of Infectious Diseases and Hospital Infection Control, Lund University Hospital, SE-22185 Lund, Sweden
| | - Gustaf Starlander
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Eva Tano
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
| | - Susanne Sütterlin
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
- Department of Women's and Children's Health, Uppsala University, SE-75185 Uppsala, Sweden
| | - Åsa Melhus
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, SE-75185 Uppsala, Sweden
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Qi Q, Ghaly TM, Penesyan A, Rajabal V, Stacey JA, Tetu SG, Gillings MR. Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4870-4879. [PMID: 36912846 DOI: 10.1021/acs.est.2c09739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeremy Ac Stacey
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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Inda-Díaz JS, Lund D, Parras-Moltó M, Johnning A, Bengtsson-Palme J, Kristiansson E. Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. MICROBIOME 2023; 11:44. [PMID: 36882798 PMCID: PMC9993715 DOI: 10.1186/s40168-023-01479-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants. RESULTS A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs. CONCLUSIONS Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.
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Affiliation(s)
- Juan Salvador Inda-Díaz
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - David Lund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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Abstract
Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.
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Off-Target Integron Activity Leads to Rapid Plasmid Compensatory Evolution in Response to Antibiotic Selection Pressure. mBio 2023; 14:e0253722. [PMID: 36840554 PMCID: PMC10127599 DOI: 10.1128/mbio.02537-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. Under stress, the integron can generate combinatorial variation in resistance cassette expression by cassette reshuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here, we test this hypothesis by selecting for increased-piperacillin-resistance populations of Pseudomonas aeruginosa with a mobile integron containing a difficult-to-mobilize β-lactamase cassette to minimize the potential for adaptive cassette reshuffling. We found that integron activity can decrease the overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations albeit at the cost of a reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes. IMPORTANCE Tackling the public health challenge created by antibiotic resistance requires understanding the mechanisms driving its evolution. Mobile integrons are widespread genetic platforms heavily involved in the spread of antibiotic resistance. Through the action of the integrase enzyme, integrons allow bacteria to capture, excise, and shuffle antibiotic resistance gene cassettes. This integrase enzyme is characterized by its ability to recognize a wide range of recombination sites, which allows it to easily capture diverse resistance cassettes but which may also lead to off-target reactions with the rest of the genome. Using experimental evolution, we tested the off-target impact of integron activity. We found that integrons increased the fitness of the surviving bacteria through extensive genomic rearrangements of the plasmids carrying the integrons, reducing their ability to spread horizontally. These results show that integrons not only accelerate resistance evolution but also can generate extensive structural variation, driving bacterial evolution beyond antibiotic resistance.
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Pradier L, Bedhomme S. Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes. eLife 2023; 12:77015. [PMID: 36785930 PMCID: PMC9928423 DOI: 10.7554/elife.77015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Antibiotic consumption and its abuses have been historically and repeatedly pointed out as the major driver of antibiotic resistance emergence and propagation. However, several examples show that resistance may persist despite substantial reductions in antibiotic use, and that other factors are at stake. Here, we study the temporal, spatial, and ecological distribution patterns of aminoglycoside resistance, by screening more than 160,000 publicly available genomes for 27 clusters of genes encoding aminoglycoside-modifying enzymes (AME genes). We find that AME genes display a very ubiquitous pattern: about 25% of sequenced bacteria carry AME genes. These bacteria were sequenced from all the continents (except Antarctica) and terrestrial biomes, and belong to a wide number of phyla. By focusing on European countries between 1997 and 2018, we show that aminoglycoside consumption has little impact on the prevalence of AME-gene-carrying bacteria, whereas most variation in prevalence is observed among biomes. We further analyze the resemblance of resistome compositions across biomes: soil, wildlife, and human samples appear to be central to understand the exchanges of AME genes between different ecological contexts. Together, these results support the idea that interventional strategies based on reducing antibiotic use should be complemented by a stronger control of exchanges, especially between ecosystems.
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Affiliation(s)
- Léa Pradier
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
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34
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Orlek A, Anjum MF, Mather AE, Stoesser N, Walker AS. Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. Sci Rep 2023; 13:2500. [PMID: 36781908 PMCID: PMC9925765 DOI: 10.1038/s41598-023-29530-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Plasmids are major vectors of bacterial antibiotic resistance, but understanding of factors associated with plasmid antibiotic resistance gene (ARG) carriage is limited. We curated > 14,000 publicly available plasmid genomes and associated metadata. Duplicate and replicate plasmids were excluded; where possible, sample metadata was validated externally (BacDive database). Using Generalised Additive Models (GAMs) we assessed the influence of 12 biotic/abiotic factors (e.g. plasmid genetic factors, isolation source, collection date) on ARG carriage, modelled as a binary outcome. Separate GAMs were built for 10 major ARG types. Multivariable analysis indicated that plasmid ARG carriage patterns across time (collection years), isolation sources (human/livestock) and host bacterial taxa were consistent with antibiotic selection pressure as a driver of plasmid-mediated antibiotic resistance. Only 0.42% livestock plasmids carried carbapenem resistance (compared with 12% human plasmids); conversely, tetracycline resistance was enriched in livestock vs human plasmids, reflecting known prescribing practices. Interpreting results using a timeline of ARG type acquisition (determined by literature review) yielded additional novel insights. More recently acquired ARG types (e.g. colistin and carbapenem) showed increases in plasmid carriage during the date range analysed (1994-2019), potentially reflecting recent onset of selection pressure; they also co-occurred less commonly with ARGs of other types, and virulence genes. Overall, this suggests that following acquisition, plasmid ARGs tend to accumulate under antibiotic selection pressure and co-associate with other adaptive genes (other ARG types, virulence genes), potentially re-enforcing plasmid ARG carriage through co-selection.
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Affiliation(s)
- Alex Orlek
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
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Chukamnerd A, Pomwised R, Chusri S, Singkhamanan K, Chumtong S, Jeenkeawpiam K, Sakunrang C, Saroeng K, Saengsuwan P, Wonglapsuwan M, Surachat K. Antimicrobial Susceptibility and Molecular Features of Colonizing Isolates of Pseudomonas aeruginosa and the Report of a Novel Sequence Type (ST) 3910 from Thailand. Antibiotics (Basel) 2023; 12:antibiotics12010165. [PMID: 36671367 PMCID: PMC9854967 DOI: 10.3390/antibiotics12010165] [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: 12/19/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an important pathogen as it can cause hospital-acquired infections. Additionally, it can also colonize in patients and in other various environments. Hence, this study aimed to investigate the antimicrobial susceptibility, and to study the molecular features, of colonizing isolates of P. aeruginosa from Songklanagarind Hospital, Thailand. Genomic DNA extraction, whole-genome sequencing (WGS), and bioinformatics analysis were performed in all studied isolates. The findings demonstrated that the majority of isolates were non-susceptible to colistin and carbapenem. For in silico study, multilocus sequence typing (MLST) revealed one novel sequence type (ST) 3910 and multiple defined STs. The isolates carried several antimicrobial resistance genes (blaOXA-50, aph(3')-IIb, etc.) and virulence-associated genes (fleN, waaA, etc.). CRISPR-Cas sequences with different spacers and integrated bacteriophage sequences were also identified in these isolates. Very high SNPs were found in the alignments of the novel ST-3910 isolate with other isolates. A comparative genomic analysis exhibited phylogenetic clustering of our colonizing isolates with clinical isolates from many countries. Interestingly, ST-3981, ST-3982, ST-3983, ST-3984, ST-3985, ST-3986, ST-3986, ST-3986, ST-3987, and ST-3988, the new STs from published genomes, were assigned in this study. In conclusion, this WGS data might be useful for tracking the spread of P. aeruginosa colonizing isolates.
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Affiliation(s)
- Arnon Chukamnerd
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kamonnut Singkhamanan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Sanicha Chumtong
- Division of Animal Production Innovation and Management, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kongpop Jeenkeawpiam
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kuwanhusna Saroeng
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Phanvasri Saengsuwan
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
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36
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Filipić B, Malešević M, Vasiljević Z, Novović K, Kojić M, Jovčić B. Comparative genomics of trimethoprim-sulfamethoxazole-resistant Achromobacter xylosoxidans clinical isolates from Serbia reveals shortened variant of class 1 integron integrase gene. Folia Microbiol (Praha) 2022; 68:431-440. [PMID: 36567375 DOI: 10.1007/s12223-022-01026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/12/2022] [Indexed: 12/27/2022]
Abstract
Trimethoprim-sulfamethoxazole (SXT) is the preferable treatment option of the infections caused by Achromobacter spp. Our study aimed to analyze the SXT resistance of 98 Achromobacter spp. isolates from pediatric patients, among which 33 isolates were SXT-resistant. The presence of intI1 was screened by PCR and genome sequence analyses. The intI1 gene was detected in 10 of SXT-resistant isolates that had shorter intI1 PCR fragments named intI1S. Structural changes in intI1S were confirmed by genome sequencing and analyses which revealed 86 amino acids deletion in IntI1S protein compared to canonical IntI1 protein. All IntI1S isolates were of non-CF origin. Pan-genome analysis of intI1S bearing A. xylosoxidans isolates comprised 9052 genes, with the core genome consisting of 5455 protein-coding genes. Results in this study indicate that IntI1S isolates were derived from clinical settings and that cystic fibrosis (CF) patients were potential reservoirs for healthcare-associated infections that occurred in non-CF patients.
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Affiliation(s)
| | - Milka Malešević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Katarina Novović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milan Kojić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branko Jovčić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia. .,Faculty of Biology, University of Belgrade, Belgrade, Serbia.
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Mencía-Ares O, Borowiak M, Argüello H, Cobo-Díaz JF, Malorny B, Álvarez-Ordóñez A, Carvajal A, Deneke C. Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production Systems. Microbiol Spectr 2022; 10:e0289622. [PMID: 36377950 PMCID: PMC9769681 DOI: 10.1128/spectrum.02896-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a threat to public health due to long-term antimicrobial use (AMU), which promotes the bacterial acquisition of antimicrobial resistance determinants (ARDs). Within food-producing animals, organic and extensive Iberian swine production is based on sustainable and eco-friendly management systems, providing an excellent opportunity to evaluate how sustained differences in AMU impact the development and spread of AMR. Here, through a whole-genome sequencing approach, we provide an in-depth characterization of the resistome and mobilome and their interaction in 466 sentinel bacteria, namely, Escherichia coli, Enterococcus spp., Campylobacter coli, and Staphylococcus spp., recovered from 37 intensive and organic-extensive pig farms. Both ARDs and mobile genetic elements (MGEs) were primarily taxon-associated, with higher similarities among bacteria which were closely phylogenetically related. E. coli exhibited the most diverse resistome and mobilome, with 85.4% mobilizable ARDs, 50.3% of which were plasmid-associated. Staphylococcus spp. exhibited a broad repertoire of ARDs and MGEs, with 52.3% of its resistome being mobilizable. Although Enterococcus spp. carried the highest number of ARDs per isolate and its plasmidome was similar in size to that of E. coli, 43.7% of its resistome was mobilizable. A narrow spectrum of ARDs constituted the C. coli resistome, with point mutations as its main AMR driver. A constrained AMU, as observed in organic-extensive herds, determined a reduction in the quantitative composition of the resistome and the complexity of the resistome-mobilome interaction. These results demonstrate taxon-associated AMR-MGE interactions and evidence that responsible AMU can contribute to reducing AMR pressure in the food chain. IMPORTANCE This study provides the first integral genomic characterization of the resistome and mobilome of sentinel microorganisms for antimicrobial resistance (AMR) surveillance from two different swine production systems. Relevant differences were observed among taxa in the resistomes and mobilomes they harbored, revealing their distinctive risk in AMR dissemination and spread. Thus, Escherichia coli and, to a lesser extent, Staphylococcus spp. constituted the main reservoirs of mobilizable antimicrobial resistance genes, which were predominantly plasmid-associated; in contrast to Campylobacter coli, whose resistome was mainly determined by point mutations. The reduced complexity of mobilome-resistome interaction in Enterococcus spp. suggested its limited role in AMR dissemination from swine farms. The significant differences in antimicrobial use among the studied farms allowed us to assess the suitability of whole-genome sequencing as a rapid and efficient technique for the assessment of mid- to long-term on-farm interventions for the reduction of antimicrobial use and the evaluation of AMR status.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Héctor Argüello
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Ana Carvajal
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Abstract
The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread. IMPORTANCE Antimicrobial resistance (AMR) has proven to be a global public health concern. To conquer this increasingly worrying trend, an overarching, One Health approach has been used that brings together different sectors, but the fundamental knowledge of the relationship between humans, food animals, and their environments is not mature yet or is lacking in some aspect. With swine and chicken as examples of food animals, a large global data set of over 1,000 human and food animal gut metagenomes was analyzed with a focus on acquired antibiotic resistance genes (ARGs) associated with mobile genetic elements (MGEs) to answer this question. Outputs from this work open a new avenue to further our understanding of ARG transferability in food animals. It is a necessary milestone to better equip governmental agencies to monitor and pre-empt antibiotic resistance hot spots. This work will assist and give guidance on how to decipher other links within any One Health initiatives with expected positive feedback to human health.
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Witaningrum AM, Wibisono FJ, Permatasari DA, Effendi MH, Ugbo EN. Multidrug resistance-encoding gene in Citrobacter freundii isolated from healthy laying chicken in Blitar District, Indonesia. INTERNATIONAL JOURNAL OF ONE HEALTH 2022. [DOI: 10.14202/ijoh.2022.161-166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background and Aim: The increasing prevalence of resistance (MDR) of Enterobacteriaceae in Indonesia has caused concern regarding human health. Citrobacter freundii reportedly targets the gastrointestinal tract of animals and is a common cause of foodborne diseases associated with diarrhea, peritonitis, meningitis, brain abscess, bacteremia, and urinary tract infection. This study aimed to estimate the prevalence of MDR and the presence of Class 1 integron-encoding genes in C. freundii isolates obtained from cloacal swabs of healthy laying chickens in Blitar district, Indonesia.
Materials and Methods: One hundred and sixty-five cloacal swab samples were collected from 33 farms in Blitar over a period of 4 months. Standard microbiological techniques such as bacterial culture in MacConkey agar, Simmons citrate agar, and triple sugar iron agar and biochemical tests such as the indole test were performed to identify the isolates. The antibiotic sensitivity patterns of C. freundii isolates were determined by the disk diffusion method, and MDR-encoding genes (Class 1 integron) were detected by polymerase chain reaction (PCR).
Results: Out of 165 cloacal swab samples, 7 (4.24%) were positive for C. freundii. Citrobacter freundii was highly resistant to erythromycin (71.43%) and moderately to streptomycin, tetracycline, and trimethoprim-sulfamethoxazole (all 42.86%); however, it showed low resistance to ampicillin (28.57%). All isolates were found to exhibit MDR. Only 1 (14.29%) of the seven C. freundii isolates harbored a Class 1 integron gene. This study revealed that Class 1 integron-encoding genes have a low prevalence in C. freundii isolated from healthy laying chickens in Blitar, Indonesia.
Conclusion: Poultry animals can play a role in the transmission of resistance genes to humans due to the MDR of Enterobacteriaceae, including C. freundii in the intestines.
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Affiliation(s)
- Adiana Mutamsari Witaningrum
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Kampus C Mulyorejo, Surabaya 60115, Indonesia
| | - Freshinta Jellia Wibisono
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Wijaya Kusuma Surabaya, Jl. DukuhKupang XXV No.54, Surabaya 60225, Indonesia
| | - Dian Ayu Permatasari
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Kampus C Mulyorejo, Surabaya 60115, Indonesia
| | - Mustofa Helmi Effendi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Kampus C Mulyorejo, Surabaya 60115, Indonesia
| | - Emmanuel Nnabuike Ugbo
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
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Cellier-Goetghebeur S, Lafontaine K, Lemay-St-Denis C, Tsamo P, Bonneau-Burke A, Copp JN, Pelletier JN. Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance. Antibiotics (Basel) 2022; 11:antibiotics11121768. [PMID: 36551425 PMCID: PMC9774602 DOI: 10.3390/antibiotics11121768] [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: 11/22/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression.
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Affiliation(s)
- Stella Cellier-Goetghebeur
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Kiana Lafontaine
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Princesse Tsamo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Alexis Bonneau-Burke
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
| | - Janine N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joelle N. Pelletier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
- Correspondence:
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Stephen J, Lekshmi M, Nayak BB, Kumar SH. First report of a multidrug-resistant Salmonella enterica Serovar Infantis carrying pESI megaplasmid isolated from marine shrimp in India. J Glob Antimicrob Resist 2022; 31:248-251. [PMID: 36216290 DOI: 10.1016/j.jgar.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Non-typhoidal Salmonella enterica (NTS) in seafood is an important human health concern. An emerging strain of NTS serovar Infantis carrying a megaplasmid pESI and resistant to multipe drugs has been responsible for frequent food-borne human infections worldwide. METHODS S. enterica strain JS5 was isolated from a sample of shrimp from the retail market on XLD agar after enrichment in the RV medium. The genomic DNA was isolated and sequenced using the Illumina platform. The draft whole genome sequence of Salmonella Infantis JS5 revealed the presence of a plasmid. RESULTS The genome size was 4,977,731 bp with 4663 open reading frames. The bacterium harboured a megaplasmid similar to the pESI plasmid reported in the emerging S. Infantis. The 285 kb plasmid contained the characteristic genes of the pESI plasmids, such as the mercury operon, yersiniabactin siderophore operon, fimbriae, toxin-antitoxin systems and the hypothetical protein backbone. The antibiotic resistance genes tet(A), dfrA14, aadA, qacEdelta1, and sul1 were detected. To the best of our knowledge, this is the first report on pESI plasmid carrying S. Infantis from India.
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Affiliation(s)
- Jerusha Stephen
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400061, India
| | - Manjusha Lekshmi
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400061, India
| | - Binaya Bhusan Nayak
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400061, India
| | - Sanath H Kumar
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400061, India.
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Genomic and Transcriptomic Analysis Reveal Multiple Strategies for the Cadmium Tolerance in Vibrio parahaemolyticus N10-18 Isolated from Aquatic Animal Ostrea gigas Thunberg. Foods 2022; 11:foods11233777. [PMID: 36496584 PMCID: PMC9741282 DOI: 10.3390/foods11233777] [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: 09/17/2022] [Revised: 11/05/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
The waterborne Vibrio parahaemolyticus can cause acute gastroenteritis, wound infection, and septicemia in humans. Pollution of heavy metals in aquatic environments is proposed to link high incidence of the multidrug-resistant (MDR) pathogen. Nevertheless, the genome evolution and heavy metal tolerance mechanism of V. parahaemolyticus in aquatic animals remain to be largely unveiled. Here, we overcome the limitation by characterizing an MDR V. parahaemolyticus N10-18 isolate with high cadmium (Cd) tolerance using genomic and transcriptomic techniques. The draft genome sequence (4,910,080 bp) of V. parahaemolyticus N10-18 recovered from Ostrea gigas Thunberg was determined, and 722 of 4653 predicted genes had unknown function. Comparative genomic analysis revealed mobile genetic elements (n = 11) and heavy metal and antibiotic-resistance genes (n = 38 and 7). The bacterium significantly changed cell membrane structure to resist the Cd2+ (50 μg/mL) stress (p < 0.05). Comparative transcriptomic analysis revealed seven significantly altered metabolic pathways elicited by the stress. The zinc/Cd/mercury/lead transportation and efflux and the zinc ATP-binding cassette (ABC) transportation were greatly enhanced; metal and iron ABC transportation and thiamine metabolism were also up-regulated; conversely, propanoate metabolism and ribose and maltose ABC transportation were inhibited (p < 0.05). The results of this study demonstrate multiple strategies for the Cd tolerance in V. parahaemolyticus.
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Ghaly TM, Tetu SG, Penesyan A, Qi Q, Rajabal V, Gillings MR. Discovery of integrons in Archaea: Platforms for cross-domain gene transfer. SCIENCE ADVANCES 2022; 8:eabq6376. [PMID: 36383678 PMCID: PMC9668308 DOI: 10.1126/sciadv.abq6376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Qin Qi
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
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Leigh RJ, McKenna C, McWade R, Lynch B, Walsh F. Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction.
Enterococcus faecium
has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.
Hypothesis/Gap statement. Vancomycin resistance rates persist amongst
E. faecium
isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.
Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.
Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of
E. faecium
persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.
Conclusions. These results highlight the evolutionary history of Irish
E. faecium
isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible
E. faecium
should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.
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Affiliation(s)
- Robert J. Leigh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Chloe McKenna
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Robert McWade
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Breda Lynch
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
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Li N, Li H, Zhu C, Liu C, Su G, Chen J. Controlling AMR in the Pig Industry: Is It Enough to Restrict Heavy Metals? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11265. [PMID: 36141538 PMCID: PMC9517514 DOI: 10.3390/ijerph191811265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Heavy metals have the potential to influence the transmission of antimicrobial resistance (AMR). However, the effect on AMR caused by heavy metals has not been clearly revealed. In this study, we used a microcosm experiment and metagenomics to examine whether common levels of Cu and Zn in pig manure influence AMR transmission in manured soil. We found that the abundance of 204 ARGs significantly increased after manure application, even though the manure did not contain antibiotic residuals. However, the combined addition of low Cu and Zn (500 and 1000 mg/kg, respectively) only caused 14 ARGs to significantly increase, and high Cu and Zn (1000 and 3000 mg/kg, respectively) caused 27 ARGs to significantly increase. The disparity of these numbers suggested that factors within the manure were the primary driving reasons for AMR transmission, rather than metal amendments. A similar trend was found for biocide and metal resistance genes (BMRGs) and mobile genetic elements (MGEs). This study offers deeper insights into AMR transmission in relation to the effects of manure application and heavy metals at commonly reported levels. Our findings recommend that more comprehensive measures in controlling AMR in the pig industry are needed apart from restricting heavy metal additions.
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Affiliation(s)
- Na Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Institute for Public Safety Research, Tsinghua University, Beijing 100084, China
| | - Hongna Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chong Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guofeng Su
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Institute for Public Safety Research, Tsinghua University, Beijing 100084, China
| | - Jianguo Chen
- Department of Engineering Physics, Tsinghua University, Beijing 100084, China
- Institute for Public Safety Research, Tsinghua University, Beijing 100084, China
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Qiu T, Huo L, Guo Y, Gao M, Wang G, Hu D, Li C, Wang Z, Liu G, Wang X. Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost. ENVIRONMENTAL MICROBIOME 2022; 17:42. [PMID: 35953830 PMCID: PMC9367140 DOI: 10.1186/s40793-022-00437-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/29/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts. RESULTS In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting. CONCLUSIONS Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.
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Affiliation(s)
- Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Linhe Huo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Guoliang Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Dong Hu
- Institute of Agro-Resources and Environment, Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, Hebei, People's Republic of China
| | - Cheng Li
- Institute of Quality Standard and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Zhanwu Wang
- Institute of Agro-Resources and Environment, Hebei Fertilizer Technology Innovation Center, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, Hebei, People's Republic of China
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Hipólito A, García-Pastor L, Blanco P, Trigo da Roza F, Kieffer N, Vergara E, Jové T, Álvarez J, Escudero J. The expression of aminoglycoside resistance genes in integron cassettes is not controlled by riboswitches. Nucleic Acids Res 2022; 50:8566-8579. [PMID: 35947699 PMCID: PMC9410878 DOI: 10.1093/nar/gkac662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
Regulation of gene expression is a key factor influencing the success of antimicrobial resistance determinants. A variety of determinants conferring resistance against aminoglycosides (Ag) are commonly found in clinically relevant bacteria, but whether their expression is regulated or not is controversial. The expression of several Ag resistance genes has been reported to be controlled by a riboswitch mechanism encoded in a conserved sequence. Yet this sequence corresponds to the integration site of an integron, a genetic platform that recruits genes of different functions, making the presence of such a riboswitch counterintuitive. We provide, for the first time, experimental evidence against the existence of such Ag-sensing riboswitch. We first tried to reproduce the induction of the well characterized aacA5 gene using its native genetic environment, but were unsuccessful. We then broadened our approach and analyzed the inducibility of all AgR genes encoded in integrons against a variety of antibiotics. We could not observe biologically relevant induction rates for any gene in the presence of several aminoglycosides. Instead, unrelated antibiotics produced mild but consistently higher increases in expression, that were the result of pleiotropic effects. Our findings rule out the riboswitch control of aminoglycoside resistance genes in integrons.
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Affiliation(s)
- Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | | | | | - Nicolas Kieffer
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Julio Álvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
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Chuprikova L, Mateo-Cáceres V, de Toro M, Redrejo-Rodríguez M. ExplorePipolin: reconstruction and annotation of piPolB-encoding bacterial mobile elements from draft genomes. BIOINFORMATICS ADVANCES 2022; 2:vbac056. [PMID: 36699382 PMCID: PMC9710591 DOI: 10.1093/bioadv/vbac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 08/06/2022] [Indexed: 01/28/2023]
Abstract
Motivation Detailed and accurate analysis of mobile genetic elements (MGEs) in bacteria is essential to deal with the current threat of multiresistant microbes. The overwhelming use of draft, contig-based genomes hinder the delineation of the genetic structure of these plastic and variable genomic stretches, as in the case of pipolins, a superfamily of MGEs that spans diverse integrative and plasmidic elements, characterized by the presence of a primer-independent DNA polymerase. Results ExplorePipolin is a Python-based pipeline that screens for the presence of the element and performs its reconstruction and annotation. The pipeline can be used on virtually any genome from diverse organisms and of diverse quality, obtaining the highest-scored possible structure and reconstructed out of different contigs if necessary. Then, predicted pipolin boundaries and pipolin encoded genes are subsequently annotated using a custom database, returning the standard file formats suitable for comparative genomics of this mobile element. Availability and implementation All code is available and can be accessed here: github.com/pipolinlab/ExplorePipolin. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - V Mateo-Cáceres
- Department of Biochemistry, School of Medicine, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (UAM-CSIC), Madrid, Spain
| | - M de Toro
- Plataforma de Genómica y Bioinformática, CIBIR (Centro de Investigación Biomédica de La Rioja), Logroño, La Rioja 26006, Spain
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Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing. Int J Med Microbiol 2022; 312:151559. [PMID: 35961233 DOI: 10.1016/j.ijmm.2022.151559] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/18/2022] [Accepted: 08/07/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited. AIM The objective of the study was to describe the resistome in cfiA-positive B. fragilis. METHODS A collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015-2017 was analysed by whole genome sequencing. RESULTS In the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0-7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, β-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient. CONCLUSION This study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.
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Nielsen TK, Browne PD, Hansen LH. Antibiotic resistance genes are differentially mobilized according to resistance mechanism. Gigascience 2022; 11:6652189. [PMID: 35906888 PMCID: PMC9338424 DOI: 10.1093/gigascience/giac072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes. RESULTS Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. CONCLUSIONS In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Patrick Denis Browne
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
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