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Ordine JVW, de Souza GM, Tamasco G, Virgilio S, Fernandes AFT, Silva-Rocha R, Guazzaroni ME. Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil. Antibiotics (Basel) 2023; 12:antibiotics12020334. [PMID: 36830245 PMCID: PMC9952835 DOI: 10.3390/antibiotics12020334] [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: 12/06/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.
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Affiliation(s)
- João Vitor Wagner Ordine
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
| | - Gabrielle Messias de Souza
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
| | - Gustavo Tamasco
- ByMyCell Inova Simples. Avenue Dra. Nadir Águiar, 1805-Supera Parque, Ribeirão Preto 14056-680, SP, Brazil
| | - Stela Virgilio
- ByMyCell Inova Simples. Avenue Dra. Nadir Águiar, 1805-Supera Parque, Ribeirão Preto 14056-680, SP, Brazil
| | - Ana Flávia Tonelli Fernandes
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
| | - Rafael Silva-Rocha
- ByMyCell Inova Simples. Avenue Dra. Nadir Águiar, 1805-Supera Parque, Ribeirão Preto 14056-680, SP, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
- Correspondence: ; Tel.: +55-(16)-33153680
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Yun Y, Han S, Park YS, Park H, Kim D, Kim Y, Kwon Y, Kim S, Lee JH, Jeon JH, Lee SH, Kang LW. Structural Insights for Core Scaffold and Substrate Specificity of B1, B2, and B3 Metallo-β-Lactamases. Front Microbiol 2022; 12:752535. [PMID: 35095785 PMCID: PMC8792953 DOI: 10.3389/fmicb.2021.752535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics, including penicillins, cephalosporins, and carbapenems; however, no effective inhibitors are currently clinically available. MBLs are classified into three subclasses: B1, B2, and B3. Although the amino acid sequences of MBLs are varied, their overall scaffold is well conserved. In this study, we systematically studied the primary sequences and crystal structures of all subclasses of MBLs, especially the core scaffold, the zinc-coordinating residues in the active site, and the substrate-binding pocket. We presented the conserved structural features of MBLs in the same subclass and the characteristics of MBLs of each subclass. The catalytic zinc ions are bound with four loops from the two central β-sheets in the conserved αβ/βα sandwich fold of MBLs. The three external loops cover the zinc site(s) from the outside and simultaneously form a substrate-binding pocket. In the overall structure, B1 and B2 MBLs are more closely related to each other than they are to B3 MBLs. However, B1 and B3 MBLs have two zinc ions in the active site, while B2 MBLs have one. The substrate-binding pocket is different among all three subclasses, which is especially important for substrate specificity and drug resistance. Thus far, various classes of β-lactam antibiotics have been developed to have modified ring structures and substituted R groups. Currently available structures of β-lactam-bound MBLs show that the binding of β-lactams is well conserved according to the overall chemical structure in the substrate-binding pocket. Besides β-lactam substrates, B1 and cross-class MBL inhibitors also have distinguished differences in the chemical structure, which fit well to the substrate-binding pocket of MBLs within their inhibitory spectrum. The systematic structural comparison among B1, B2, and B3 MBLs provides in-depth insight into their substrate specificity, which will be useful for developing a clinical inhibitor targeting MBLs.
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Affiliation(s)
- Yeongjin Yun
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Sangjun Han
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Dogyeong Kim
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Yeseul Kim
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Yongdae Kwon
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Sumin Kim
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
- *Correspondence: Sang Hee Lee,
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, South Korea
- Lin-Woo Kang,
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