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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [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: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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Li XY, Yu R, Xu C, Shang Y, Li D, Du XD. A Small Multihost Plasmid Carrying erm(T) Identified in Enterococcus faecalis. Front Vet Sci 2022; 9:850466. [PMID: 35711812 PMCID: PMC9197182 DOI: 10.3389/fvets.2022.850466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine the mobile genetic elements involved in the horizontal transfer of erm(T) in Enterococcus faecalis, and its transmission ability in heterologous hosts. A total of 159 erythromycin-resistant enterococci isolates were screened for the presence of macrolide resistance genes by PCR. Whole genome sequencing for erm(T)-carrying E. faecalis E165 was performed. The transmission ability in heterologous hosts was explored by conjugation, transformation, and fitness cost. The erm(T) gene was detected only in an E. faecalis isolate E165 (1/159), which was located on a 4,244-bp small plasmid, designed pE165. Using E. faecalis OG1RF as the recipient strain, pE165 is transferable. Natural transformation experiments using Streptococcus suis P1/7 and Streptococcus mutans UA159 as the recipients indicated it is transmissible, which was also observed by electrotransformation using Staphylococcus aureus RN4220 as a recipient. The erm(T)-carrying pE165 can replicate in the heterologous host including E. faecalis OG1RF, S. suis P1/7, S. mutans UA159, and S. aureus RN4220 and conferred resistance to erythromycin and clindamycin to all hosts. Although there is no disadvantage of pE165 in the recipient strains in growth curve experiments, all the pE165-carrying recipients had a fitness cost compared to the corresponding original recipients in growth competition experiments. In brief, an erm(T)-carrying plasmid was for the first time described in E. faecalis and as transmissible to heterologous hosts.
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Cerar Kišek T, Pogačnik N, Godič Torkar K. Genetic diversity and the presence of circular plasmids in Bacillus cereus isolates of clinical and environmental origin. Arch Microbiol 2021; 203:3209-3217. [PMID: 33830284 DOI: 10.1007/s00203-021-02302-w] [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: 01/21/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The diversity of 61 Bacillus cereus strains isolated from different clinical specimens, food including raw milk and milk products, and water was evaluated. PFGE analysis could discriminate 61 distinct pulsotypes with similarity levels from 25 to 82%, which were divided into 13 clonal complexes. The similarity between clonal complexes was at least 40%. Clinical strains were divided into 10 clonal complexes, while the strains, isolated from milk, food and water were included in 9, 6 and 6 clonal complexes, respectively. Three clonal complexes were dominated by clinical isolates, while they were absent in two complexes. Bacterial isolates from food, being a probable source of alimentary toxoinfection, showed low similarity to isolates from stool specimens. The isolates from both sources were classified together in only 4 out of 13 clonal complexes. The large circular and linear plasmids with the sizes between 50 and 200 kb were detected in 24 (39.3%) and 14 (23%) B. cereus strains, respectively. Thirteen (21.3%) strains contained only one plasmid, two plasmids were found in 6 (9.8%) of strains, and three or more plasmids were obtained in 5 (8.2%) of tested strains. The plasmids were confirmed in 30.8% and 40% of isolates from clinical specimens and food and milk samples, respectively. No clear correlation between the PFGE profiles, the source as well as plasmid content among all tested strains was observed.
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Affiliation(s)
- Tjaša Cerar Kišek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nežka Pogačnik
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, 1000, Ljubljana, Slovenia
| | - Karmen Godič Torkar
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, 1000, Ljubljana, Slovenia.
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Glibota N, Grande MJ, Galvez A, Ortega E. Genetic Determinants for Metal Tolerance and Antimicrobial Resistance Detected in Bacteria Isolated from Soils of Olive Tree Farms. Antibiotics (Basel) 2020; 9:antibiotics9080476. [PMID: 32756388 PMCID: PMC7459592 DOI: 10.3390/antibiotics9080476] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/18/2020] [Accepted: 08/01/2020] [Indexed: 12/12/2022] Open
Abstract
Copper-derived compounds are often used in olive tree farms. In a previous study, a collection of bacterial strains isolated from olive tree farms were identified and tested for phenotypic antimicrobial resistance and heavy metal tolerance. The aim of this work was to study the genetic determinants of resistance and to evaluate the co-occurrence of metal tolerance and antibiotic resistance genes. Both metal tolerance and antibiotic resistance genes (including beta-lactamase genes) were detected in the bacterial strains from Cu-treated soils. A high percentage of the strains positive for metal tolerance genes also carried antibiotic resistance genes, especially for genes involved in resistances to beta-lactams and tetracycline. Significant associations were detected between genes involved in copper tolerance and genes coding for beta-lactamases or tetracycline resistance mechanisms. A significant association was also detected between zntA (coding for a Zn(II)-translocating P-type ATPase) and tetC genes. In conclusion, bacteria from soils of Cu-treated olive farms may carry both metal tolerance and antibiotic resistance genes. The positive associations detected between metal tolerance genes and antibiotic resistance genes suggests co-selection of such genetic traits by exposure to metals.
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Versluis D, Rodriguez de Evgrafov M, Sommer MOA, Sipkema D, Smidt H, van Passel MWJ. Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes. Front Microbiol 2016; 7:1848. [PMID: 27909433 PMCID: PMC5112248 DOI: 10.3389/fmicb.2016.01848] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022] Open
Abstract
Wide application of antibiotics has contributed to the evolution of multi-drug resistant human pathogens, resulting in poorer treatment outcomes for infections. In the marine environment, seawater samples have been investigated as a resistance reservoir; however, no studies have methodically examined sponges as a reservoir of antibiotic resistance. Sponges could be important in this respect because they often contain diverse microbial communities that have the capacity to produce bioactive metabolites. Here, we applied functional metagenomics to study the presence and diversity of functional resistance genes in the sponges Aplysina aerophoba, Petrosia ficiformis, and Corticium candelabrum. We obtained 37 insert sequences facilitating resistance to D-cycloserine (n = 6), gentamicin (n = 1), amikacin (n = 7), trimethoprim (n = 17), chloramphenicol (n = 1), rifampicin (n = 2) and ampicillin (n = 3). Fifteen of 37 inserts harbored resistance genes that shared <90% amino acid identity with known gene products, whereas on 13 inserts no resistance gene could be identified with high confidence, in which case we predicted resistance to be mainly mediated by antibiotic efflux. One marine-specific ampicillin-resistance-conferring β-lactamase was identified in the genus Pseudovibrio with 41% global amino acid identity to the closest β-lactamase with demonstrated functionality, and subsequently classified into a new family termed PSV. Taken together, our results show that sponge microbiota host diverse and novel resistance genes that may be harnessed by phylogenetically distinct bacteria.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | | | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; National Institute for Public Health and the EnvironmentBilthoven, Netherlands
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Laport MS, Pontes PVM, Dos Santos DS, Santos-Gandelman JDF, Muricy G, Bauwens M, Giambiagi-deMarval M, George I. Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast. Braz J Microbiol 2016; 47:617-20. [PMID: 27287338 PMCID: PMC4927650 DOI: 10.1016/j.bjm.2016.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/11/2016] [Indexed: 01/27/2023] Open
Abstract
Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria.
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Affiliation(s)
- Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil; Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.
| | - Paula Veronesi Marinho Pontes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Daniela Silva Dos Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Juliana de Fátima Santos-Gandelman
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Guilherme Muricy
- Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Mathieu Bauwens
- Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Marcia Giambiagi-deMarval
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Isabelle George
- Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
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Nonaka L, Maruyama F, Suzuki S, Masuda M. Novel macrolide-resistance genes, mef(C) and mph(G), carried by plasmids from Vibrio and Photobacterium isolated from sediment and seawater of a coastal aquaculture site. Lett Appl Microbiol 2015; 61:1-6. [PMID: 25765542 DOI: 10.1111/lam.12414] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 01/10/2023]
Abstract
UNLABELLED The aim of this study was to determine whether mef(C) and mph(G), originally found on the transferable multi-drug plasmid pAQU1 from Photobacterium damselae subsp. damselae isolated from seawater of a fish farm, are responsible for conferring macrolide resistance. Since these genes are localized head-to-tail on pAQU1 and only four nucleotides exist between them, the single- and combination-effect of these genes was examined. When mph(G) alone was introduced to Escherichia coli, the minimum inhibitory concentrations (MICs) against erythromycin, clarithromycin and azithromycin increased, whereas introduction of mef(C) alone did not influence macrolide susceptibility. Introduction of both mef(C) and mph(G) dramatically increased the MICs to the same three macrolides, i.e. >512 μg ml(-1) , >512 μg ml(-1) and 128 μg ml(-1) respectively. These results suggest that the macrolide phosphotransferase encoded by mph(G) is essential for macrolide resistance, while the efflux pump encoded by mef(C) is required for high-level macrolide resistance. The tandem-pair arrangements of the mef(C) and mph(G) genes were conserved on plasmids ranging in size from 240 to 350 kb of the 22 erythromycin-resistant strains belonging to Vibrio and Photobacterium obtained from the fish farm. Sixteen of 22 plasmids ranged in size from 300 to 350 kb. This is the first report of novel macrolide resistance genes originating from a marine bacterium. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, mef(C) and mph(G) were found to be novel macrolide-resistance genes, and this is the first report of macrolide-resistance genes originating from a marine bacterium. These genes may be responsible for previously reported cases of the emergence of erythromycin-resistant bacteria in aquaculture sites by an unknown mechanism. The introduction of the tandem arrangement of the mef(C) and mph(G) genes in Escherichia coli increased the MICs to erythromycin, clarithromycin and azithromycin, suggesting a novel mechanism conferring high-level macrolide resistance via combined expression of the efflux pump and macrolide phosphotransferase.
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Affiliation(s)
- L Nonaka
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - F Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - S Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - M Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
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