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Olatunji I, Bardaji DKR, Miranda RR, Savka MA, Hudson AO. Artificial intelligence tools for the identification of antibiotic resistance genes. Front Microbiol 2024; 15:1437602. [PMID: 39070267 PMCID: PMC11272472 DOI: 10.3389/fmicb.2024.1437602] [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: 05/24/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
The fight against bacterial antibiotic resistance must be given critical attention to avert the current and emerging crisis of treating bacterial infections due to the inefficacy of clinically relevant antibiotics. Intrinsic genetic mutations and transferrable antibiotic resistance genes (ARGs) are at the core of the development of antibiotic resistance. However, traditional alignment methods for detecting ARGs have limitations. Artificial intelligence (AI) methods and approaches can potentially augment the detection of ARGs and identify antibiotic targets and antagonistic bactericidal and bacteriostatic molecules that are or can be developed as antibiotics. This review delves into the literature regarding the various AI methods and approaches for identifying and annotating ARGs, highlighting their potential and limitations. Specifically, we discuss methods for (1) direct identification and classification of ARGs from genome DNA sequences, (2) direct identification and classification from plasmid sequences, and (3) identification of putative ARGs from feature selection.
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Affiliation(s)
- Isaac Olatunji
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Danae Kala Rodriguez Bardaji
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Renata Rezende Miranda
- School of Chemistry and Materials Science, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, United States
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Li W, Guo H, Gao Y, Yang X, Li R, Li S, Sun C, Du W, Chen S, Xu P, Huang W, Shi J, Yi X, Li X. Comparative genomic analysis of plasmids harboring bla OXA-48-like genes in Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:1082813. [PMID: 36605127 PMCID: PMC9807924 DOI: 10.3389/fcimb.2022.1082813] [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: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence and spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious medical problem worldwide. Acquired OXA-48-like carbapenemases encoded by plasmids are important causes of carbapenem resistance in K. pneumoniae. To explore the links between plasmids and bla OXA-48-like genes in K. pneumoniae, we systematically analyzed the variants of bla OXA-48-like plasmid replicon types, phylogenetic patterns, geographic distribution, conjugative transfer regions, and the genetic environments surrounding bla OXA-48-like of 191 bla OXA-48-like-harboring plasmids, which were identified from 4451 plasmids of K. pneumoniae downloaded from GenBank. Our results showed that seven different variants of bla OXA-48-like genes were identified from the 191 bla OXA-48-like-harboring plasmids in K. pneumoniae, with bla OXA-48, bla OXA-232, and bla OXA-181 being highly prevalent. In K. pneumoniae, bla OXA-48 was mainly carried by the composite transposon Tn1999.2 located on IncL/M-type conjugative plasmids, which were mainly geographically distributed in Switzerland, Germany, and China. In K. pneumoniae, the blaOXA-232 gene was mainly carried by 6.1-kb ColKP3-type mobilizable plasmids, which were mainly isolated in India. In K. pneumoniae, bla OXA-181 was mainly carried by a group of 50-kb ColKP3-IncX3 hybrid conjugative plasmids and a group of small ColKP3-type mobilizable plasmids with lengths of 5.9-9.3 kb, the former was sporadically discovered in China, South Korea, India, and Czech Republic, while the latter was almost all isolated in India. In addition, five bla OXA-245-harboring 65.9-kb IncL plasmids of K. pneumoniae isolated in Spain were found to have the genetic context of bla OXA-245 more complicated than that of bla OXA-48-harboring IncL/M-type plasmids, with two copies of IS1R inserted both upstream and downstream of bla OXA-245-lysR. These findings enhance our understanding of the genetic diversity of bla OXA-48-like-harboring plasmids in K. pneumoniae.
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Affiliation(s)
- Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Hengzhao Guo
- Department of Radiation Oncology, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China
| | - Yi Gao
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xiaofan Yang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Ruirui Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuangyu Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Chunlong Sun
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Wen Du
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Shaopeng Chen
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Pengpeng Xu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Wenwen Huang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Jia Shi
- Department of Stomatology, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
| | - Xinfeng Yi
- Department of Neurosurgery, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
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Dell’Annunziata F, Folliero V, Giugliano R, De Filippis A, Santarcangelo C, Izzo V, Daglia M, Galdiero M, Arciola CR, Franci G. Gene Transfer Potential of Outer Membrane Vesicles of Gram-Negative Bacteria. Int J Mol Sci 2021; 22:ijms22115985. [PMID: 34205995 PMCID: PMC8198371 DOI: 10.3390/ijms22115985] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The increasing spread of multidrug-resistant pathogenic bacteria is one of the major threats to public health worldwide. Bacteria can acquire antibiotic resistance and virulence genes through horizontal gene transfer (HGT). A novel horizontal gene transfer mechanism mediated by outer membrane vesicles (OMVs) has been recently identified. OMVs are rounded nanostructures released during their growth by Gram-negative bacteria. Biologically active toxins and virulence factors are often entrapped within these vesicles that behave as molecular carriers. Recently, OMVs have been reported to contain DNA molecules, but little is known about the vesicle packaging, release, and transfer mechanisms. The present review highlights the role of OMVs in HGT processes in Gram-negative bacteria.
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Affiliation(s)
- Federica Dell’Annunziata
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Rosa Giugliano
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Cristina Santarcangelo
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy; (C.S.); (M.D.)
| | - Viviana Izzo
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, 84081 Salerno, Italy;
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy; (C.S.); (M.D.)
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Carla Renata Arciola
- Research Unit on Implant Infections, Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Correspondence: (C.R.A.); (G.F.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, 84081 Salerno, Italy;
- Correspondence: (C.R.A.); (G.F.)
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Duedu KO, Mends JQ, Ayivor-Djanie R, Essandoh PE, Nattah EM, Gyamfi J, Kpeli GS. Plasmidome AMR screening (PAMRS) workflow: a rapid screening workflow for phenotypic characterization of antibiotic resistance in plasmidomes. AAS Open Res 2021. [DOI: 10.12688/aasopenres.13111.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Phenotypic characterization of antimicrobial resistance (AMR) in bacteria has remained the gold standard for investigation and monitoring of what resistance is present in an organism. However, the process is laborious and not attractive for screening multiple plasmids from a microbial community (plasmidomes). Instead, genomic tools are used, but a major bottle neck that presence of genes does not always translate into phenotypes. Methods: We designed the plasmidome AMR screening (PAMRS) workflow to investigate the presence of antibiotic resistant phenotypes in a plasmidome using Escherichia coli as a host organism. Plasmidomes were extracted from the faecal matter of chicken, cattle and humans using commercial plasmid extraction kits. Competent E. coli cells were transformed and evaluated using disk diffusion. Thirteen antibiotic resistant phenotypes were screened. Results: Here, we show that multiple antibiotic resistant phenotypes encoded by plasmids can be rapidly screened simultaneously using the PAMRS workflow. E. coli was able to pick up to 7, 5 or 8 resistant phenotypes from a single plasmidome from chicken, cattle or humans, respectively. Resistance to ceftazidime was the most frequently picked up phenotype in humans (52.6%) and cattle (90.5%), whereas in chickens, the most picked up resistant phenotype was resistance to co-trimoxazole, ceftriaxone and ampicillin (18.4% each). Conclusions: This workflow is a novel tool that could facilitate studies to evaluate the occurrence and expression of plasmid-encoded antibiotic resistance in microbial communities and their associated plasmid-host ranges. It could find application in the screening of plasmid-encoded virulence genes.
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