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Alkorta I, Garbisu C. Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance. REVIEWS ON ENVIRONMENTAL HEALTH 2024; 0:reveh-2024-0013. [PMID: 38815132 DOI: 10.1515/reveh-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/26/2024] [Indexed: 06/01/2024]
Abstract
The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.
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Affiliation(s)
- Itziar Alkorta
- Department of Biochemistry and Molecular Biology, 16402 University of the Basque Country (UPV/EHU) , Bilbao, Spain
| | - Carlos Garbisu
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
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Summer M, Ali S, Tahir HM, Abaidullah R, Fiaz U, Mumtaz S, Fiaz H, Hassan A, Mughal TA, Farooq MA. Mode of Action of Biogenic Silver, Zinc, Copper, Titanium and Cobalt Nanoparticles Against Antibiotics Resistant Pathogens. J Inorg Organomet Polym Mater 2024; 34:1417-1451. [DOI: 10.1007/s10904-023-02935-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/02/2023] [Indexed: 08/04/2024]
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Costa TRD, Patkowski JB, Macé K, Christie PJ, Waksman G. Structural and functional diversity of type IV secretion systems. Nat Rev Microbiol 2024; 22:170-185. [PMID: 37814112 PMCID: PMC11290344 DOI: 10.1038/s41579-023-00974-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
Considerable progress has been made in recent years in the structural and molecular biology of type IV secretion systems in Gram-negative bacteria. The latest advances have substantially improved our understanding of the mechanisms underlying the recruitment and delivery of DNA and protein substrates to the extracellular environment or target cells. In this Review, we aim to summarize these exciting structural and molecular biology findings and to discuss their functional implications for substrate recognition, recruitment and translocation, as well as the biogenesis of extracellular pili. We also describe adaptations necessary for deploying a breadth of processes, such as bacterial survival, host-pathogen interactions and biotic and abiotic adhesion. We highlight the functional and structural diversity that allows this extremely versatile secretion superfamily to function under different environmental conditions and in different bacterial species. Additionally, we emphasize the importance of further understanding the mechanism of type IV secretion, which will support us in combating antimicrobial resistance and treating type IV secretion system-related infections.
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Affiliation(s)
- Tiago R D Costa
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK.
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College, London, UK
| | - Kévin Macé
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK
- Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes and CNRS, Rennes, France
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA.
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Birkbeck and UCL, London, UK.
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Yang C, Jiang S, Wei C, Li C, Wang J, Li X, Zeng L, Hu K, Yang Y, Zhang J, Zhang X. Mechanism for transmission and pathogenesis of carbapenem-resistant Enterobacterales harboring the carbapenemase IMP and clinical countermeasures. Microbiol Spectr 2024; 12:e0231823. [PMID: 38197660 PMCID: PMC10846200 DOI: 10.1128/spectrum.02318-23] [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: 06/05/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are some of the most important pathogens causing infections, which can be challenging to treat. We identified four blaIMP-carrying CRE isolates and collected clinical data. The transferability and stability of the plasmid were verified by conjugation, successive passaging, and plasmid elimination assays. The IncC blaIMP-4-carrying pIMP4-ECL42 plasmid was successfully transferred into the recipient strain, and the high expression of traD may have facilitated the conjugation transfer of the plasmid. Interestingly, the plasmid showed strong stability in clinical isolates. Whole-genome sequencing was performed on all isolates. We assessed the sequence similarity of blaIMP -harboring plasmid from our institution and compared it to plasmids for which sequence data are publicly available. We found that four blaIMP-carrying CRE belonged to four different sequence types. The checkerboard technique and time-kill assays were used to investigate the best antimicrobial therapies for blaIMP-carrying CRE. The time-kill assay showed that the imipenem of 1× minimum inhibitory concentration (MIC) alone had the bactericidal or bacteriostatic effect against IMP-producing strains at 4-12 h in vitro. Moreover, the combination of tigecycline (0.5/1/2 × MIC) and imipenem (0.5/1 × MIC) showed a bactericidal effect against the blaIMP-26-carrying CRECL60 strain.IMPORTANCECarbapenem-resistant Enterobacterales (CRE) are an urgent public health threat, and infections caused by these microorganisms are often associated with high mortality and limited treatment options. This study aimed to determine the clinical features, molecular characteristics, and plasmid transmissible mechanisms of blaIMP carriage as well as to provide a potential treatment option. Here, we demonstrated that conjugated transfer of the IncC blaIMP-4-carrying plasmid promotes plasmid stability, so inhibition of conjugated transfer and enhanced plasmid loss may be potential ways to suppress the persistence of this plasmid. The imipenem alone or tigecycline-imipenem combination showed a good bactericidal effect against IMP-producing strains. In particular, our study revealed that imipenem alone or tigecycline-imipenem combination may be a potential therapeutic option for patients who are infected with IMP-producing strains. Our study supports further trials of appropriate antibiotics to determine optimal treatment and emphasizes the importance of continued monitoring of IMP-producing strains in the future.
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Affiliation(s)
- Chengru Yang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Shan Jiang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, Jiangyou People’s Hospital, Jiangyou, China
| | - Chunli Wei
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjiang Li
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Jianmin Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xinhui Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Lingyi Zeng
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Kewang Hu
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Yang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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Arbé-Carton K, Rey-Sogo A, Santos-Fernández N, Altube O, Garbisu C, Arana L, Alkorta I. Development of a high-throughput platform to measure plasmid transfer frequency. Front Cell Infect Microbiol 2023; 13:1269732. [PMID: 37886666 PMCID: PMC10598849 DOI: 10.3389/fcimb.2023.1269732] [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: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.
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Affiliation(s)
- Kepa Arbé-Carton
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Ana Rey-Sogo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Nagore Santos-Fernández
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Oihane Altube
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Lide Arana
- Department of Applied Chemistry, University of the Basque Country (UPV/EHU), Donostia, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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Bravo A, Moreno-Blanco A, Espinosa M. One Earth: The Equilibrium between the Human and the Bacterial Worlds. Int J Mol Sci 2023; 24:15047. [PMID: 37894729 PMCID: PMC10606248 DOI: 10.3390/ijms242015047] [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: 08/17/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.
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Affiliation(s)
- Alicia Bravo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
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Beltrán de Heredia I, Garbisu C, Alkorta I, Urra J, González-Gaya B, Ruiz-Romera E. Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120883. [PMID: 36572269 DOI: 10.1016/j.envpol.2022.120883] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.
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Affiliation(s)
- Irene Beltrán de Heredia
- Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Plaza Ingeniero Torres Quevedo 1, 48013, Bilbao, Spain.
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, P812, 48160, Derio, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain
| | - Julen Urra
- Department of Conservation of Natural Resources, NEIKER-Basque Institute of Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, P812, 48160, Derio, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, University of the Basque Country (UPV/EHU), Campus of Leioa, 48940, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Areatza Pasealekua 47, 48620, Plentzia, Spain
| | - Estilita Ruiz-Romera
- Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Plaza Ingeniero Torres Quevedo 1, 48013, Bilbao, Spain
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Chen H, Tao S, Li N, Zhu Q, Liu L, Fang Y, Xu Y, Liang W. Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism. J Antimicrob Chemother 2023; 78:521-530. [PMID: 36575565 DOI: 10.1093/jac/dkac423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/20/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria. OBJECTIVES To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread. METHODS We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro. RESULTS We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P < 0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules. CONCLUSIONS These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.
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Affiliation(s)
- Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Na Li
- Laboratory Medical School, Bengbu Medical College, Bengbu, Anhui, China
| | - Qing Zhu
- School of Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Liping Liu
- School of Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yeiwei Fang
- School of medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yao Xu
- School of medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, No. 59, Liuting Street, Ningbo City, Zhejiang 315010, China
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Zhang F, Ye X, Yin Z, Hu M, Wang B, Liu W, Li B, Ren H, Jin Y, Yue J. Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids. Front Microbiol 2022; 13:1045314. [PMID: 36466664 PMCID: PMC9709138 DOI: 10.3389/fmicb.2022.1045314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 06/13/2024] Open
Abstract
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.
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Affiliation(s)
- Fengwei Zhang
- Medical College of Guizhou University, Guiyang, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xianwei Ye
- Medical College of Guizhou University, Guiyang, China
- Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, China
| | - Mingda Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Boqian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wenting Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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Al Mamun AAM, Kissoon K, Kishida K, Shropshire WC, Hanson B, Christie PJ. IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems. Plasmid 2022; 123-124:102652. [PMID: 36228885 PMCID: PMC10018792 DOI: 10.1016/j.plasmid.2022.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 12/04/2022]
Abstract
Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.
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Affiliation(s)
- Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
| | - Kimberly Kissoon
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - Kouhei Kishida
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America
| | - William C Shropshire
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Fannin St, Houston, TX 77030, United States of America.
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Gurinovich AS, Titok MA. Molecular Genetic and Functional Analysis of the Conjugation System of the pBS72 Plasmid from Bacillus subtilis Environmental Isolates. Microbiology (Reading) 2022. [DOI: 10.1134/s002626172230018x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Belloso Daza MV, Milani G, Cortimiglia C, Pietta E, Bassi D, Cocconcelli PS. Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. Front Microbiol 2022; 13:894241. [PMID: 35814695 PMCID: PMC9262338 DOI: 10.3389/fmicb.2022.894241] [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: 03/11/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.
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Jäger F, Lamy A, Sun WS, Guerini N, Berntsson RPA. Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family. Structure 2022; 30:876-885.e5. [DOI: 10.1016/j.str.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
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Jauregi L, Epelde L, González A, Lavín JL, Garbisu C. Reduction of the resistome risk from cow slurry and manure microbiomes to soil and vegetable microbiomes. Environ Microbiol 2021; 23:7643-7660. [PMID: 34792274 DOI: 10.1111/1462-2920.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
In cow farms, the interaction between animal and environmental microbiomes creates hotspots for antibiotic resistance dissemination. A shotgun metagenomic approach was used to survey the resistome risk in five dairy cow farms. To this purpose, 10 environmental compartments were sampled: 3 of them linked to productive cows (fresh slurry, stored slurry, slurry-amended pasture soil); 6 of them to non-productive heifers and dry cows (faeces, fresh manure, aged manure, aged manure-amended orchard soil, vegetables-lettuces and grazed soil); and, finally, unamended control soil. The resistome risk was assessed using MetaCompare, a computational pipeline which scores the resistome risk according to possible links between antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and human pathogens. The resistome risk decreased from slurry and manure microbiomes to soil and vegetable microbiomes. In total (sum of all the compartments), 18,157 ARGs were detected: 24% related to ansamycins, 21% to multidrugs, 14% to aminoglycosides, 12% to tetracyclines, 9% to β-lactams, and 9% to macrolide-lincosamide-streptogramin B. All but two of the MGE-associated ARGs were only found in the animal dejections (not in soil or vegetable samples). Several ARGs with potential as resistome risk markers (based on their presence in hubs of co-occurrence networks and high dissemination potential) were identified. As a precautionary principle, improved management of livestock dejections is necessary to minimize the risk of antibiotic resistance.
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Affiliation(s)
- Leire Jauregi
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Lur Epelde
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Aitor González
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - José Luis Lavín
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
| | - Carlos Garbisu
- NEIKER, Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, E-48160 Derio, Spain
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Liu Z, Liu Y, Xi W, Liu S, Liu J, Mu H, Chen B, He H, Fan Y, Ma W, Zhang W, Fu M, Wang J, Song X. Genetic Features of Plasmid- and Chromosome-Mediated mcr-1 in Escherichia coli Isolates From Animal Organs With Lesions. Front Microbiol 2021; 12:707332. [PMID: 34456890 PMCID: PMC8386294 DOI: 10.3389/fmicb.2021.707332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022] Open
Abstract
The genomic context of the mcr-1 gene in Escherichia coli from animal feces has been widely reported. However, less is known about the mcr-1-carrying plasmid characteristics and other functional regions of Escherichia coli isolates from animal organs with lesions. The present study investigated the antimicrobial resistance, population structure, and genetic features of mcr-1-positive Escherichia coli strains isolated from animal organs with lesions. The antimicrobial susceptibility testing indicated that 24 mcr-1-positive Escherichia coli isolates were resistant to at least three or all antimicrobial categories. MLST analysis suggested that the dominant clone complexes (CC) were mainly CC156, CC448, and CC10. In addition, ST10596, a newly discovered sequence type in swine, failed to be classified. Meanwhile, the mcr-1 gene located on the different plasmids was successfully transferred to the recipients, and whole-genome sequencing indicated the mcr-1 gene was embedded in mcr-1-pap2 cassette but not flanked by ISApl1. The mcr-1 gene is located on the chromosome and embedded in Tn6330. Furthermore, NDM-5 was found on the IncX3-type plasmid of J-8. The virB6 and traI gene of type IV secretion system (T4SS) were truncated by IS2 and IS100 and located on the IncX4- and the IncHI2/HI2A/N-type plasmids, respectively. The multidrug-resistant (MDR) region of IncHI2/HI2A/N-type plasmids contained two class 1 integrons (In0, In640) and four composite transposons (Tn4352, Tn6010, cn_4692_IS26, cn_6354_IS26). Overall, 24 mcr-1-positive Escherichia coli isolates in our study showed MDR, or even extensively drug resistant (XDR), and exhibited population diversity. The T4SS gene truncation by the insertion sequence may affect the efficiency of plasmid conjugative transfer. Furthermore, the class 1 integrons and composite transposons in the MDR region of IncHI2/HI2A/n-type plasmid contributed to the multireplicon plasmid formation, the acquisition, and transfer of antimicrobial resistance genes (ARGs).
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Affiliation(s)
- Zengyuan Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yingqiu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wei Xi
- Qingdao Adverse Drug Reaction Monitoring Center, China Qingdao Institute for Food and Drug Control, Qingdao, China
| | - Shuangshi Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jia Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hailong Mu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Beibei Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hao He
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yunpeng Fan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wuren Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Weimin Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Mingzhe Fu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiaoping Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
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Nowak KP, Sobolewska-Ruta A, Jagiełło A, Bierczyńska-Krzysik A, Kierył P, Wawrzyniak P. Molecular and Functional Characterization of MobK Protein-A Novel-Type Relaxase Involved in Mobilization for Conjugational Transfer of Klebsiella pneumoniae Plasmid pIGRK. Int J Mol Sci 2021; 22:5152. [PMID: 34068033 PMCID: PMC8152469 DOI: 10.3390/ijms22105152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/01/2023] Open
Abstract
Conjugation, besides transformation and transduction, is one of the main mechanisms of horizontal transmission of genetic information among bacteria. Conjugational transfer, due to its essential role in shaping bacterial genomes and spreading of antibiotics resistance genes, has been widely studied for more than 70 years. However, new and intriguing facts concerning the molecular basis of this process are still being revealed. Most recently, a novel family of conjugative relaxases (Mob proteins) was distinguished. The characteristic feature of these proteins is that they are not related to any of Mobs described so far. Instead of this, they share significant similarity to tyrosine recombinases. In this study MobK-a tyrosine recombinase-like Mob protein, encoded by pIGRK cryptic plasmid from the Klebsiella pneumoniae clinical strain, was characterized. This study revealed that MobK is a site-specific nuclease and its relaxase activity is dependent on both a conserved catalytic tyrosine residue (Y179) that is characteristic of tyrosine recombinases and the presence of Mg2+ divalent cations. The pIGRK minimal origin of transfer sequence (oriT) was also characterized. This is one of the first reports presenting tyrosine recombinase-like conjugative relaxase protein. It also demonstrates that MobK is a convenient model for studying this new protein family.
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Affiliation(s)
- Katarzyna Paulina Nowak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agnieszka Sobolewska-Ruta
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Agata Jagiełło
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Central Forensic Laboratory of the Police, Biology Department, Iwicka 14, 00-735 Warsaw, Poland
| | - Anna Bierczyńska-Krzysik
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
- Curiosity Diagnostics Sp. z o.o., Duchnicka 3, Building 16, Entrance A, 01-796 Warsaw, Poland
| | - Piotr Kierył
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
| | - Paweł Wawrzyniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland;
- Department of Biomedical Technology, Cosmetics Chemicals and Electrochemistry, Łukasiewicz Research Network—Industrial Chemistry Institute, Rydygiera 8, 01-793 Warsaw, Poland; (A.S.-R.); (A.J.); (A.B.-K.); (P.K.)
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Arana L, Gallego L, Alkorta I. Incorporation of Antibiotics into Solid Lipid Nanoparticles: A Promising Approach to Reduce Antibiotic Resistance Emergence. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:nano11051251. [PMID: 34068834 PMCID: PMC8151913 DOI: 10.3390/nano11051251] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
Antimicrobial resistance is one of the biggest threats to global health as current antibiotics are becoming useless against resistant infectious pathogens. Consequently, new antimicrobial strategies are urgently required. Drug delivery systems represent a potential solution to improve current antibiotic properties and reverse resistance mechanisms. Among different drug delivery systems, solid lipid nanoparticles represent a highly interesting option as they offer many advantages for nontoxic targeted drug delivery. Several publications have demonstrated the capacity of SLNs to significantly improve antibiotic characteristics increasing treatment efficiency. In this review article, antibiotic-loaded solid lipid nanoparticle-related works are analyzed to summarize all information associated with applying these new formulations to tackle the antibiotic resistance problem. The main antimicrobial resistance mechanisms and relevant solid lipid nanoparticle characteristics are presented to later discuss the potential of these nanoparticles to improve current antibiotic treatment characteristics and overcome antimicrobial resistance mechanisms. Moreover, solid lipid nanoparticles also offer new possibilities for other antimicrobial agents that cannot be administrated as free drugs. The advantages and disadvantages of these new formulations are also discussed in this review. Finally, given the progress of the studies carried out to date, future directions are discussed.
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Affiliation(s)
- Lide Arana
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Unibertsitateko Ibilbidea, 7, 01006 Vitoria-Gasteiz, Spain
- Correspondence:
| | - Lucia Gallego
- Department of Immunology, Microbiology and Parasitology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Sarriena Auzoa z/g, 48940 Leioa, Bizkaia, Spain;
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Sarriena Auzoa z/g, 48940 Leioa, Bizkaia, Spain;
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Costa TRD, Harb L, Khara P, Zeng L, Hu B, Christie PJ. Type IV secretion systems: Advances in structure, function, and activation. Mol Microbiol 2021; 115:436-452. [PMID: 33326642 DOI: 10.1111/mmi.14670] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022]
Abstract
Bacterial type IV secretion systems (T4SSs) are a functionally diverse translocation superfamily. They consist mainly of two large subfamilies: (i) conjugation systems that mediate interbacterial DNA transfer and (ii) effector translocators that deliver effector macromolecules into prokaryotic or eukaryotic cells. A few other T4SSs export DNA or proteins to the milieu, or import exogenous DNA. The T4SSs are defined by 6 or 12 conserved "core" subunits that respectively elaborate "minimized" systems in Gram-positive or -negative bacteria. However, many "expanded" T4SSs are built from "core" subunits plus numerous others that are system-specific, which presumptively broadens functional capabilities. Recently, there has been exciting progress in defining T4SS assembly pathways and architectures using a combination of fluorescence and cryoelectron microscopy. This review will highlight advances in our knowledge of structure-function relationships for model Gram-negative bacterial T4SSs, including "minimized" systems resembling the Agrobacterium tumefaciens VirB/VirD4 T4SS and "expanded" systems represented by the Helicobacter pylori Cag, Legionella pneumophila Dot/Icm, and F plasmid-encoded Tra T4SSs. Detailed studies of these model systems are generating new insights, some at atomic resolution, to long-standing questions concerning mechanisms of substrate recruitment, T4SS channel architecture, conjugative pilus assembly, and machine adaptations contributing to T4SS functional versatility.
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Affiliation(s)
- Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Laith Harb
- Department of Biochemistry and Biophysics and Center for Phage Technology, Texas A&M University, College Station, TX, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics and Center for Phage Technology, Texas A&M University, College Station, TX, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
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Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. BIOLOGY 2020; 9:biology9110365. [PMID: 33126516 PMCID: PMC7694136 DOI: 10.3390/biology9110365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022]
Abstract
Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a trained machine learning algorithm can be exploited for validating the model and obtaining new information about resistance mechanisms. Different feature extraction methods, such as SNP calling and counting nucleotide k-mers have been proposed for presenting DNA sequences to the model. However, there are trade-offs between interpretability, computational complexity and accuracy for different feature extraction methods. In this study, we have proposed a new feature extraction method, counting amino acid k-mers or oligopeptides, which provides easier model interpretation compared to counting nucleotide k-mers and reaches the same or even better accuracy in comparison with different methods. Additionally, we have trained machine learning algorithms using different feature extraction methods and compared the results in terms of accuracy, model interpretability and computational complexity. We have built a new feature selection pipeline for extraction of important features so that new AMR determinants can be discovered by analyzing these features. This pipeline allows the construction of models that only use a small number of features and can predict resistance accurately.
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