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Dai R, Jin C, Xiao M. The influence of urban environmental effects on the orchard soil microbial community structure and function: a case study in Zhejiang, China. Front Microbiol 2024; 15:1403443. [PMID: 39314879 PMCID: PMC11417026 DOI: 10.3389/fmicb.2024.1403443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/08/2024] [Indexed: 09/25/2024] Open
Abstract
The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture.
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Affiliation(s)
- Rongchen Dai
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Cuixiang Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Emergence of carbapenem-resistant Klebsiella pneumoniae species complex from agrifood systems: detection of ST6326 co-producing KPC-2 and NDM-1. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7347-7354. [PMID: 38651793 DOI: 10.1002/jsfa.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Klebsiella pneumoniae species complex (KpSC) is an important disseminator of carbapenemase-encoding genes, mainly blaKPC-2 and blaNDM-1, from hospitals to the environment. Consequently, carbapenem-resistant strains can be spread through the agrifood system, raising concerns about food safety. This study therefore aimed to isolate carbapenem-resistant KpSC strains from the agricultural and environmental sectors and characterize them using phenotypic, molecular, and genomic analyses. RESULTS Klebsiella pneumoniae and Klebsiella quasipneumoniae strains isolated from soils used for lemon, guava, and fig cultivation, and from surface waters, displayed an extensive drug-resistance profile and carried blaKPC-2, blaNDM-1, or both. In addition to carbapenemase-encoding genes, KpSC strains harbor a broad resistome (antimicrobial resistance and metal tolerance) and present putative hypervirulence. Soil-derived K. pneumoniae strains were assigned as high-risk clones (ST11 and ST307) and harbored the blaKPC-2 gene associated with Tn4401b and Tn3-like elements on IncN-pST15 and IncX5 plasmids. In surface waters, the coexistence of blaKPC-2 and blaNDM-1 genes was identified in K. pneumoniae ST6326, a new carbapenem-resistant regional Brazilian clone. In this case, blaKPC-2 with Tn4401a isoform and blaNDM-1 associated with a Tn125-like transposon were located on different plasmids. Klebsiella quasipneumoniae ST526 also presented the blaNDM-1 gene associated with a Tn3000 transposon on an IncX3 plasmid. CONCLUSION These findings provide a warning regarding the transmission of carbapenemase-positive KpSC across the agricultural and environmental sectors, raising critical food safety and environmental issues. © 2024 Society of Chemical Industry.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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Furlan JPR, Ramos MS, Sellera FP, Gonzalez IHL, Ramos PL, Stehling EG. Gram-negative bacterial diversity and evidence of international clones of multidrug-resistant strains in zoo animals. Integr Zool 2024; 19:417-423. [PMID: 37984552 DOI: 10.1111/1749-4877.12790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Enterobacterales and Pseudomonas aeruginosa have been colonizing or infecting wild hosts and antimicrobial-resistant strains are present in mammals and birds. Furthermore, international high-risk clones of multidrug-resistant Escherichia coli are identified and the implications of multidrug-resistant Gram-negative bacteria in zoo animals are discussed.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Irys Hany Lima Gonzalez
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Stehling EG, Sellera FP, de Almeida OGG, Gonzalez IHL, Ramos PL, da Rosa-Garzon NG, von Zeska Kress MR, Cabral H, Furlan JPR. Genomic features and comparative analysis of a multidrug-resistant Acinetobacter bereziniae strain infecting an animal: a novel emerging one health pathogen? World J Microbiol Biotechnol 2024; 40:63. [PMID: 38190002 DOI: 10.1007/s11274-023-03867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
Acinetobacter bereziniae has recently gained medical notoriety due to its emergence as a multidrug resistance and healthcare-associated pathogen. In this study, we report the whole-genome characterization of an A. bereziniae strain (A321) recovered from an infected semiaquatic turtle, as well as a comparative analysis of A. bereziniae strains circulating at the human-animal-environment interface. Strain A321 displayed a multidrug resistance profile to medically important antimicrobials, which was supported by a wide resistome. The novel Tn5393m transposon and a qnrB19-bearing ColE1-like plasmid were identified in A321 strain. Novel OXA-229-like β-lactamases were detected and expression of OXA-931 demonstrated a 2-64-fold increase in the minimum inhibitory concentration for β-lactam agents. Comparative genomic analysis revealed that most A. bereziniae strains did not carry any antimicrobial resistance genes (ARGs); however, some strains from China, Brazil, and India harbored six or more ARGs. Furthermore, A. bereziniae strains harbored conserved virulence genes. These results add valuable information regarding the spread of ARGs and mobile genetic elements that could be shared not only between A. bereziniae but also by other bacteria of clinical interest. This study also demonstrates that A. bereziniae can spill over from anthropogenic sources into natural environments and subsequently be transmitted to non-human hosts, making this a potential One Health bacteria that require close surveillance.
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Affiliation(s)
- Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Otávio Guilherme Gonçalves de Almeida
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Irys Hany Lima Gonzalez
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Nathália Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Marcia Regina von Zeska Kress
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.
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Sellera FP, Fuentes-Castillo D, Fuga B, Goldberg DW, Kolesnikovas CK, Lincopan N. New Delhi metallo-β-lactamase-1-producing Citrobacter portucalensis belonging to the novel ST264 causing fatal sepsis in a vulnerable migratory sea turtle. One Health 2023; 17:100590. [PMID: 37388191 PMCID: PMC10302118 DOI: 10.1016/j.onehlt.2023.100590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
Olive ridley (Lepidochelys olivacea) turtles migrate across tropical regions of the Atlantic, Pacific, and Indian Oceans. Worryingly, olive ridley populations have been declining substantially and is now considered a threatened species. In this regard, habitat degradation, anthropogenic pollution, and infectious diseases have been the most notorious threats for this species. We isolated a metallo-β-lactamase (NDM-1)-producing Citrobacter portucalensis from the blood sample of an infected migratory olive ridley turtle found stranded sick in the coast of Brazil. Genomic analysis of C. portucalensis confirmed a novel sequence type (ST), named ST264, and a wide resistome to broad-spectrum antibiotics. The production of NDM-1 by the strain contributed to treatment failure and death of the animal. Phylogenomic relationship with environmental and human strains from African, European and Asian countries confirmed that critical priority clones of C. portucalensis are spreading beyond hospital settings, representing an emerging ecological threat to marine ecosystems.
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Affiliation(s)
- Fábio P. Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Bruna Fuga
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, University of São Paulo, São Paulo, Brazil
| | | | | | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, University of São Paulo, São Paulo, Brazil
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