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Wang HM, Hu GR, Luo WY, Li FL. The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche. Appl Microbiol Biotechnol 2024; 108:22. [PMID: 38159121 DOI: 10.1007/s00253-023-12827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 01/03/2024]
Abstract
Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 μm long and 0.5-0.6 μm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.
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Affiliation(s)
- Hao-Ming Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Guang-Rong Hu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Wen-Yong Luo
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- School of Environmental and Municipal Engineering, Qingdao University of Technology, Qingdao, 266400, China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research CenterQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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2
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Song H, Yoo JS, Unno T. Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea. Sci Total Environ 2024; 926:172068. [PMID: 38554973 DOI: 10.1016/j.scitotenv.2024.172068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.
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Affiliation(s)
- Hokyung Song
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Jung Sik Yoo
- Division of Antimicrobial Resistance Research, National Institute of Health, Korea Disease Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea
| | - Tatsuya Unno
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea.
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Sun H, Chang H, Zhu Y, Li X, Yang X, Zhou X, Wu D, Ding J, Liu Y. Strong suppression of silver nanoparticles on antibiotic resistome in anammox process. J Hazard Mater 2024; 470:134128. [PMID: 38555673 DOI: 10.1016/j.jhazmat.2024.134128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
This study comprehensively deciphered the effect of silver nanoparticles (AgNPs) on anammox flocculent sludge, including nitrogen removal performance, microbial community structure, functional enzyme abundance, antibiotic resistance gene (ARGs) dissemination, and horizontal gene transfer (HGT) mechanisms. After long-term exposure to 0-2.5 mg/L AgNPs for 200 cycles, anammox performance significantly decreased (P < 0.05), while the relative abundances of dominant Ca. Kuenenia and anammox-related enzymes (hzsA, nirK) increased compared to the control (P < 0.05). For antibiotic resistome, ARG abundance hardly changed with 0-0.5 mg/L AgNPs but decreased by approximately 90% with 1.5-2.5 mg/L AgNPs. More importantly, AgNPs effectively inhibited MGE-mediated HGT of ARGs. Additionally, structural equation model (SEM) disclosed the underlying relationship between AgNPs, the antibiotic resistome, and the microbial community. Overall, AgNPs suppressed the anammox-driven nitrogen cycle, regulated the microbial community, and prevented the spread of ARGs in anammox flocs. This study provides a theoretical baseline for an advanced understanding of the ecological roles of nanoparticles and resistance elements in engineered ecosystems.
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Affiliation(s)
- Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China.
| | - Huanhuan Chang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Yuliang Zhu
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China; School of Civil Engineering, Yantai University, Yantai, Shandong 264005, China
| | - Xiaoli Li
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China
| | - Xiaoyong Yang
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China
| | - Xin Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Daishun Wu
- Fujian Provincial Key Laboratory of Coastal Basin Environment, School of Marine and Biochemical Engineering, Fujian Polytechnic Normal University, Fuqing, Fujiang 350300, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China
| | - Yucan Liu
- School of Environmental and Material Engineering, Yantai University, Yantai, Shandong 264005, China; School of Civil Engineering, Yantai University, Yantai, Shandong 264005, China.
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Qin J, Qi X, Li Y, Tang Z, Zhang X, Ru S, Xiong JQ. Bisphenols can promote antibiotic resistance by inducing metabolic adaptations and natural transformation. J Hazard Mater 2024; 470:134149. [PMID: 38554512 DOI: 10.1016/j.jhazmat.2024.134149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Whether bisphenols, as plasticizers, can influence bacterial uptake of antibiotic resistance genes (ARGs) in natural environment, as well as the underlying mechanism remains largely unknown. Our results showed that four commonly used bisphenols (bisphenol A, S, F, and AF) at their environmental relative concentrations can significantly promote transmission of ARGs by 2.97-3.56 times in Acinetobacter baylyi ADP1. Intriguingly, we observed ADP1 acquired resistance by integrating plasmids uptake and cellular metabolic adaptations other than through reactive oxygen species mediated pathway. Metabolic adaptations including upregulation of capsules polysaccharide biosynthesis and intracellularly metabolic enzymes, which enabled formation of thicker capsules for capturing free plasmids, and degradation of accumulated compounds. Simultaneously, genes encoding DNA uptake and translocation machinery were incorporated to enhance natural transformation of antibiotic resistance carrying plasmids. We further exposed aquatic fish to bisphenols for 120 days to monitor their long-term effects in aquatic environment, which showed that intestinal bacteria communities were dominated by a drug resistant microbiome. Our study provides new insight into the mechanism of enhanced natural transformation of ARGs by bisphenols, and highlights the investigations for unexpectedly-elevated antibiotic-resistant risks by structurally related environmental chemicals.
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Affiliation(s)
- Jingyu Qin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xin Qi
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yuejiao Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhuyun Tang
- School of Life Sciences, Department of Immunology and Microbiology, Department of Chemical Biology, Southern University of Science and Technology, No. 1088, Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong, China
| | - Xiaona Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shaoguo Ru
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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Wang YC, Mao Y, Fu HM, Wang J, Weng X, Liu ZH, Xu XW, Yan P, Fang F, Guo JS, Shen Y, Chen YP. New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis. Sci Total Environ 2024; 924:171530. [PMID: 38453092 DOI: 10.1016/j.scitotenv.2024.171530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, Guangdong, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xun Weng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Zi-Hao Liu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xiao-Wei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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6
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Zheng W, Teng X, Jiang T, Tang W, Jiang L, Zhu H, Yu X, Chen G, Wang J, Zhang J, Qu M, Zhang X. Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer. Virology 2024; 593:109999. [PMID: 38368638 DOI: 10.1016/j.virol.2024.109999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.
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Affiliation(s)
- Weibo Zheng
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Xiaopeng Teng
- Department of Pharmacy, Yantai Yuhuangding Hospital, Yantai 264000, Shandong China
| | - Tingshu Jiang
- Department of Pulmonary and Critical Care Medicine, Yantai Yuhuangding Hospital, Yantai 264000, Shandong China
| | - Wenli Tang
- Shandong Provincial Key Laboratory of Quality Safety Monitoring and Risk Assessment for Animal Products, Jinan 250022, Shandong, China
| | - Linlin Jiang
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Hongwei Zhu
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Xin Yu
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Guozhong Chen
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Jiao Wang
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Jianlong Zhang
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China
| | - Mingjuan Qu
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China.
| | - Xingxiao Zhang
- School of Life Sciences, Ludong University, Yantai 264000, Shandong, China; Yantai Key Laboratory of Animal Pathogenetic Microbiology and Immunology, Yantai 264000, Shandong, China; Shandong Breeding Environmental Control Engineering Laboratory, Yantai 264000, Shandong, China.
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De R, Jani M, Azad RK. DICEP: An integrative approach to augmenting genomic island detection. J Biotechnol 2024; 388:S0168-1656(24)00110-X. [PMID: 38641137 DOI: 10.1016/j.jbiotec.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/17/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Mobilization of clusters of genes called genomic islands (GIs) across bacterial lineages facilitates dissemination of traits, such as, resistance against antibiotics, virulence or hypervirulence, and versatile metabolic capabilities. Robust delineation of GIs is critical to understanding bacterial evolution that has a vast impact on different life forms. Methods for identification of GIs exploit different evolutionary features or signals encoded within the genomes of bacteria, however, the current state-of-the-art in GI detection still leaves much to be desired. Here, we have taken a combinatorial approach that accounted for GI specific features such as compositional bias, aberrant phyletic pattern, and marker gene enrichment within an integrative framework to delineate GIs in bacterial genomes. Our GI prediction tool, DICEP, was assessed on simulated genomes and well-characterized bacterial genomes. DICEP compared favorably with current GI detection tools on real and synthetic datasets.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, United States of America
| | - Mehul Jani
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, United States of America
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, Texas, 76203, United States of America; Department of Mathematics, University of North Texas, Denton, Texas, 76203, United States of America.
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Ouzounis CA. The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA. Biosystems 2024; 239:105199. [PMID: 38641198 DOI: 10.1016/j.biosystems.2024.105199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.
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Affiliation(s)
- Christos A Ouzounis
- Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Faculty of Sciences, Aristotle University of Thessalonica, Thessalonica, Greece; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece.
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Liu H, Al-Dhabi NA, Jiang H, Liu B, Qing T, Feng B, Ma T, Tang W, Zhang P. Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin. Water Res 2024; 256:121624. [PMID: 38669903 DOI: 10.1016/j.watres.2024.121624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.
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Affiliation(s)
- Hongyuan Liu
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Huiling Jiang
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Bingzhi Liu
- Faculty of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, Guangdong, China
| | - Taiping Qing
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Bo Feng
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Tengfei Ma
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Wangwang Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Peng Zhang
- Department of Environment, College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
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Sajjad W, Ilahi N, Haq A, Shang Z, Nabi G, Rafiq M, Bahadur A, Banerjee A, Kang S. Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes. Environ Res 2024; 247:118288. [PMID: 38262510 DOI: 10.1016/j.envres.2024.118288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Abdul Haq
- Peshawar Laboratories Complex, Pakistan Council of Scientific and Industrial Research, Peshawar, 25120, Pakistan
| | - Zhanhuan Shang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ghulam Nabi
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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11
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Zheng B, Wang G, Qu Z, Hu J, Bao Z, Wang M. Glycosaminoglycan lyase: A new competition between bacteria and the pacific white shrimp Litopenaeus vannamei. Dev Comp Immunol 2024; 156:105177. [PMID: 38593892 DOI: 10.1016/j.dci.2024.105177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Horizontal gene transfer (HGT) is an important evolutionary force in the formation of prokaryotic and eukaryotic genomes. In recent years, many HGT genes horizontally transferred from prokaryotes to eukaryotes have been reported, and most of them are present in arthropods. The Pacific white shrimp Litopenaeus vannamei, an important economic species of arthropod, has close relationships with bacteria, providing a platform for horizontal gene transfer (HGT). In this study, we analyzed bacteria-derived HGT based on a high-quality genome of L. vannamei via a homology search and phylogenetic analysis, and six HGT genes were identified. Among these six horizontally transferred genes, we found one gene (LOC113799989) that contains a bacterial chondroitinase AC structural domain and encodes an unknown glycosaminoglycan (GAG) lyase in L. vannamei. The real-time quantitative PCR results showed that the mRNA expression level of LOC113799989 was highest in the hepatopancreas and heart, and after stimulation by Vibrio parahaemolyticus, its mRNA expression level was rapidly up-regulated within 12 h. Furthermore, after injecting si-RNA and stimulation by V. parahaemolyticus, we found that the experimental group had a higher cumulative mortality rate in 48 h than the control group, indicating that the bacteria-derived GAG lyase can reduce the mortality of shrimp with respect to infection by V. parahaemolyticus and might be related to the resistance of shrimp to bacterial diseases. Our findings contribute to the study of the function of GAGs and provide new insights into GAG-related microbial pathogenesis and host defense mechanisms in arthropods.
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Affiliation(s)
- Bo Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China
| | - Gengzhuo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China
| | - Zhe Qu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572024, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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12
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Ormsby MJ, Woodford L, Quilliam RS. Can plastic pollution drive the emergence and dissemination of novel zoonotic diseases? Environ Res 2024; 246:118172. [PMID: 38220083 DOI: 10.1016/j.envres.2024.118172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
As the volume of plastic in the environment increases, so too does human interactions with plastic pollution. Similarly, domestic, feral, and wild animals are increasingly interacting with plastic pollution, highlighting the potential for contamination of plastic wastes with animal faeces, urine, saliva, and blood. Substantial evidence indicates that once in the environment, plastics rapidly become colonised by microbial biofilm (the so-called 'plastisphere), which often includes potentially harmful microbial pathogens (including pathogens that are zoonotic in nature). Climate change, increased urbanisation, and the intensification of agriculture, mean that the three-way interactions between humans, animals, and plastic pollution are becoming more frequent, which is significant as almost 60% of emerging human infectious diseases during the last century have been zoonotic. Here, we critically review the potential for contaminated environmental plastics to facilitate the evolution of novel pathogenic strains of microorganisms, and the subsequent role of plastic pollution in the cyclical dissemination of zoonotic pathogens. As the interactions between humans, animals, and plastic pollution continues to grow, and the volume of plastics entering the environment increases, there is clearly an urgent need to better understand the role of plastic waste in facilitating zoonotic pathogen evolution and dissemination, and the effect this can have on environmental and human health.
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Affiliation(s)
- Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - Luke Woodford
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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13
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Veloo ACM, Boiten KE, Hendrickx APA, van Prehn J, Rossen JWA. Horizontal gene transfer of a cfiA element between two different Bacteroides species within a clinical specimen. Clin Microbiol Infect 2024; 30:554-555. [PMID: 38141819 DOI: 10.1016/j.cmi.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Affiliation(s)
- Alida C M Veloo
- University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, the Netherlands.
| | - Kathleen E Boiten
- University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, the Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - John W A Rossen
- University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, University of Groningen, Groningen, the Netherlands; Laboratory of Medical Microbiology and Infectious Diseases & Isala Academie, Isala Hospital, Zwolle, the Netherlands; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
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14
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Liu X, Zhao H, Wong A. Accounting for the health risk of probiotics. Heliyon 2024; 10:e27908. [PMID: 38510031 PMCID: PMC10950733 DOI: 10.1016/j.heliyon.2024.e27908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Probiotics have long been associated with a myriad of health benefits, so much so that their adverse effects whether mild or severe, are often neglected or overshadowed by the enormous volume of articles describing their beneficial effects in the current literature. Recent evidence has demonstrated several health risks of probiotics that warrant serious reconsideration of their applications and further investigations. This review aims to highlight studies that report on how probiotics might cause opportunistic systemic and local infections, detrimental immunological effects, metabolic disturbance, allergic reactions, and facilitating the spread of antimicrobial resistance. To offer a recent account of the literature, articles within the last five years were prioritized. The narration of these evidence was based on the nature of the studies in the following order of preference: clinical studies or human samples, in vivo or animal models, in situ, in vitro and/or in silico. We hope that this review will inform consumers, food scientists, and medical practitioners, on the health risks, while also encouraging research that will focus on and clarify the adverse effects of probiotics.
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Affiliation(s)
- Xiangyi Liu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Haiyi Zhao
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Department of Biology, Dorothy and George Hennings College of Science, Mathematics and Technology, Kean, University, 1000 Morris Ave, Union, NJ, 07083, USA
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province, 325060, China
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15
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You Z, Wang C, Yang X, Liu Z, Guan Y, Mu J, Shi H, Zhao Z. Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems. Environ Res 2024; 251:118692. [PMID: 38493856 DOI: 10.1016/j.envres.2024.118692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.
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Affiliation(s)
- Ziqi You
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China.
| | - Ce Wang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Xiaobin Yang
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Zikuo Liu
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Yueqiang Guan
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Jiandong Mu
- Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, 066200, China
| | - Huijuan Shi
- Museum of Hebei University, Hebei University, Baoding, Hebei, China.
| | - Zhao Zhao
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China.
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16
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Xu H, Tan C, Li C, Li J, Han Y, Tang Y, Lei C, Wang H. ESBL- Escherichia coli extracellular vesicles mediate bacterial resistance to β-lactam and mediate horizontal transfer of bla CTX-M-55. Int J Antimicrob Agents 2024; 63:107145. [PMID: 38494146 DOI: 10.1016/j.ijantimicag.2024.107145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/08/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
OBJECTIVES Extracellular vesicles (EVs) have become the focus of research as an emerging method of horizontal gene transfer. In recent years, studies on the association between EVs and the spread of bacterial resistance have emerged, but there is a lack of research on the role of EVs secreted by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in the spread of β-lactam resistance. Therefore, the aim of this study was to investigate the role of EVs in the transmission of β-lactam resistance. METHODS In this study, the role of EVs in the transmission of β-lactam resistance in E. coli was evaluated by the EVs-mediated bacterial resistance to β-lactam antibiotics test and the EVs-mediated blaCTX-M-55 transfer experiments using EVs secreted by ESBL-E. coli. RESULTS The results showed that ESBL-EVs were protective against β-lactam antibiotic-susceptible bacteria, and this protective effect was dependent on the integrity of the EVs and showed dose- and time-dependent effects. At the same time, ESBL-EVs can also mediate the horizontal transmission of blaCTX-M-55, and EVs-mediated gene transfer is selective, preferring to transfer in more closely related species. CONCLUSIONS In this study, we demonstrated the important role of EVs in the transmission of β-lactam resistance in chicken ESBL-E. coli, and evaluated the risk of EVs-mediated horizontal gene transfer, which provided a theoretical basis for elucidating the mechanism of EVs-mediated resistance transmission.
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Affiliation(s)
- Heting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Chang Tan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China; Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China.
| | - Jinpeng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610022, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610022, China.
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17
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Kang Y, Wang J, Li Z. Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater. J Hazard Mater 2024; 466:133577. [PMID: 38281357 DOI: 10.1016/j.jhazmat.2024.133577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.
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Affiliation(s)
- Yutong Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenjun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China.
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18
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Zhuang X, Fan H, Li X, Dong Y, Wang S, Zhao B, Wu S. Transfer and accumulation of antibiotic resistance genes and bacterial pathogens in the mice gut due to consumption of organic foods. Sci Total Environ 2024; 915:169842. [PMID: 38215844 DOI: 10.1016/j.scitotenv.2023.169842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/27/2023] [Accepted: 12/30/2023] [Indexed: 01/14/2024]
Abstract
Over the last few decades, organic food demand has grown largely because of increasing personal health concerns. Organic farming introduces antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) into foods. However, potential effects of organic foods on the gut microbiome and ARGs have been overlooked. Using high-throughput quantitative PCR and 16S rRNA high-throughput sequencing technology, we examined 132 ARGs from major classes, eight transposase genes, universal class I integron-integrase gene (intI), clinical class I integron-integrase gene (cintI), and the bacterial community in mouse gut after 8 weeks with an either organic or inorganic lettuce and wheat diet. A total of 8 types of major ARGs and 10 mobile genetic elements (MGEs) were detected in mice gut, including tetracycline, multidrug, sulfonamide, aminoglycoside, beta-lactamase, chloramphenicol, MLSB and vancomycin resistance genes. We found that abundance and diversity of ARGs, mobile gene elements, and potential ARB in the gut increased with time after consumption of organic foods, whereas no significant changes were observed in inorganic treated groups. Moreover, MGEs, including IS613, Tp614 and tnpA_03 were found to play an important role in regulating ARG profiles in the gut microbiome following consumption of organic foods. Importantly, feeding organic food increased the relative abundance of the potentially antibiotic-resistant pathogens, Bacteroides and Streptococcus. Our results confirm that there is an increasing risk of ARGs and ARB in the gut microbiome, which highlights the importance of organic food industries taking into account the potential accumulation and transmission of ARGs as a risk factor.
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Affiliation(s)
- Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Zhao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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19
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Xu JY, Ding J, Du S, Zhu D. Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments. J Hazard Mater 2024; 465:133333. [PMID: 38147751 DOI: 10.1016/j.jhazmat.2023.133333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023]
Abstract
Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.
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Affiliation(s)
- Jia-Yang Xu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People' s Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People' s Republic of China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, People' s Republic of China
| | - Shuai Du
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People' s Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People' s Republic of China.
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People' s Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People' s Republic of China.
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Fang Y, Chen C, Cui B, Zhou D. Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network. J Hazard Mater 2024; 465:133238. [PMID: 38134694 DOI: 10.1016/j.jhazmat.2023.133238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.
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Affiliation(s)
- Yuanping Fang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Congli Chen
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China
| | - Bin Cui
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun 130117, China; Jilin Engineering Lab for Water Pollution Control and Resources Recovery, Northeast Normal University, Changchun 130117, China.
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Zhang J, Lu K, Zhu L, Li N, Lin D, Cheng Y, Wang M. Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil. J Hazard Mater 2024; 465:133272. [PMID: 38134686 DOI: 10.1016/j.jhazmat.2023.133272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.
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Affiliation(s)
- Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Kun Lu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Na Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yangjuan Cheng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China.
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Kim H, Yoo K. Marine plastisphere selectively enriches microbial assemblages and antibiotic resistance genes during long-term cultivation periods. Environ Pollut 2024; 344:123450. [PMID: 38280464 DOI: 10.1016/j.envpol.2024.123450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
Several studies have focused on identifying and quantifying suspended plastics in surface and subsurface seawater. Microplastics (MPs) have attracted attention as carriers of antibiotic resistance genes (ARGs) in the marine environment. Plastispheres, specific biofilms on MP, can provide an ideal niche to spread more widely through horizontal gene transfer (HGT), thereby increasing risks to ecosystems and human health. However, the microbial communities formed on different plastic types and ARG abundances during exposure time in natural marine environments remain unclear. Four types of commonly used MPs (polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)) were periodically cultured (46, 63, and 102 d) in a field-based marine environment to study the co-selection of ARGs and microbial communities in marine plastispheres. After the first 63 d of incubation (p < 0.05), the initial 16S rRNA gene abundance of microorganisms in the plastisphere increased significantly, and the biomass subsequently decreased. These results suggest that MPs can serve as vehicles for various microorganisms to travel to different environments and eventually provide a niche for a variety of microorganisms. Additionally, the qPCR results showed that MPs selectively enriched ARGs. In particular, tetA, tetQ, sul1, and qnrS were selectively enriched in the PVC-MPs. The abundances of intl1, a mobile genetic element, was measured in all MP types for 46 d (5.22 × 10-5 ± 8.21 × 10-6 copies/16s rRNA gene copies), 63 d (5.90 × 10-5 ± 2.49 × 10-6 copies/16s rRNA gene copies), and 102 d (4.00 × 10-5 ± 5.11 × 10-6 copies/16s rRNA gene copies). Network analysis indicated that ARG profiles co-occurred with key biofilm-forming bacteria. This study suggests that the selection of ARGs and their co-occurring bacteria in MPs could potentially accelerate their transmission through HGT in natural marine plastics.
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Affiliation(s)
- Hyunsu Kim
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea.
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Zhu X, Wang X, Wang F, Tian X, Pang J. The integrative and conjugative element ICECiPOL15 mediates horizontal transfer of β-lactam resistance gene in Chryseobacterium indoltheticum POL15. J Glob Antimicrob Resist 2024; 36:223-229. [PMID: 38185239 DOI: 10.1016/j.jgar.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
OBJECTIVES The dissemination of antibiotic resistance genes (ARGs) from the environment, including agricultural sources, is of increasing concern. In this study, we examined the antibiotic resistance profile and genomic sequence of a strain of Chryseobacterium indoltheticum obtained from an agricultural location. METHODS The multidrug-resistant bacterial strain POL15 was isolated from the wastewater of a livestock farm in China. Whole-genome sequencing was performed followed by bioinformatics analyses to identify integrative and conjugative elements (ICEs) and ARGs. Mating assays were performed to analyse ICE transferability. RESULTS Whole-genome sequencing and annotation showed that the genome of POL15 encodes ARGs. Additionally, an ICE named ICECiPOL15, which carries a class C β-lactamase-encoding gene blaAQU, was identified in the POL15 genome. Genes encoding an integrase, an excisionase, a relaxase, a type IV coupling protein and conjugative transposon proteins involved in a type IV secretion system were also identified in ICECiPOL15. Sequence alignment revealed that ICECiPOL15 might have evolved from other Chryseobacterium species. The horizontal transferability of ICECiPOL15 was demonstrated by mating experiments between C. indoltheticum POL15 and Escherichia coli DL21. CONCLUSIONS This study represents the first characterization of a mobilizable antibiotic resistance ICE in a species of C. indoltheticum and provides evidence that C. indoltheticum strains could be important reservoirs and vehicles for ARGs on livestock farms.
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Affiliation(s)
- Xiaoyan Zhu
- Shandong Center for Disease Control and Prevention, Ji'nan, 250014, China
| | - Xiangpeng Wang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Fengtian Wang
- Jinan Municipal Minzu Hospital, Ji'nan, 250001, China
| | - Xinyi Tian
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Jingxiang Pang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
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Souguir M, Châtre P, Drapeau A, Azaiez S, Hmidi I, Ncir S, Lupo A, Madec JY, Haenni M, Mansour W. CTX-M-15/27-positive Escherichia coli and VIM-2-producing Pseudomonas putida in free-living pigeons (Columba livia) in Tunisia. J Glob Antimicrob Resist 2024; 36:70-75. [PMID: 38145799 DOI: 10.1016/j.jgar.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023] Open
Abstract
OBJECTIVES Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially prone to acquire resistance genes such as those encoding extended-spectrum beta-lactamases (ESBLs) and carbapenemases. METHODS Cloacal samples (n = 206) of free-living feral pigeons (C. livia) were collected in Sousse and Monastir, Tunisia. Antimicrobial susceptibility profiles were determined by disc-diffusion, and resistant isolates were short- and long-read whole-genome sequenced. Sequence analysis was performed using tools of the Centre for Genomic Epidemiology, and Phylogenetic analysis was performed based on the core-genome MLST. RESULTS Fourteen (14/206, 6.8%) pigeons harboured Enterobacterales resistant to last-generations cephalosporins, of which 10 were CTX-M-15- or CTX-M-27-producers, while two (1.0%) carried a VIM-2-producing Pseudomonas putida. Positive pigeons lived on four different livestock farms. Three STs (ST206, ST5584, ST8149) were identified among E. coli, of which ST5584 and ST8149 were found in two different farms. Genetic diversity was also observed in Enterobacter cloacae and P. putida isolates. The blaCTX-M-27 genes were chromosomally encoded, while the blaCTX-M-15 genes were carried on highly similar IncF/F-:A-:B53 plasmids. The blaVIM-2 gene was located on a class 1 integron co-harbouring several resistance genes. CONCLUSION Pigeons living on livestock farms carried clinically important resistance genes encoding ESBLs and carbapenemases. Our results evidenced that both clonal (ST8149 and ST5584) and plasmidic (IncF/F-:A-:B53) transfers played a role in the spread of resistance genes among pigeons. Further studies are needed to identify factors favouring the transfer and persistence of resistance genes within the pigeon communities.
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Affiliation(s)
- Meriem Souguir
- Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Université de Sousse, Sousse, Tunisia; Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Pierre Châtre
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Sana Azaiez
- Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Université de Sousse, Sousse, Tunisia
| | - Imen Hmidi
- Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Université de Sousse, Sousse, Tunisia
| | - Sana Ncir
- Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Université de Sousse, Sousse, Tunisia; Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Agnese Lupo
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES - Université de Lyon, Lyon, France.
| | - Wejdene Mansour
- Faculté de Médecine Ibn Al Jazzar Sousse, Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée, Université de Sousse, Sousse, Tunisia
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25
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Fang GY, Liu XQ, Jiang YJ, Mu XJ, Huang BW. Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence. Sci Total Environ 2024; 912:168908. [PMID: 38013098 DOI: 10.1016/j.scitotenv.2023.168908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
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Arbulu S, Kjos M. Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins. Microb Ecol 2024; 87:41. [PMID: 38351266 PMCID: PMC10864542 DOI: 10.1007/s00248-024-02357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.
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Affiliation(s)
- Sara Arbulu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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Neil B, Cheney GL, Rosenzweig JA, Sha J, Chopra AK. Antimicrobial resistance in aeromonads and new therapies targeting quorum sensing. Appl Microbiol Biotechnol 2024; 108:205. [PMID: 38349402 PMCID: PMC10864486 DOI: 10.1007/s00253-024-13055-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/15/2024]
Abstract
Aeromonas species (spp.) are well-known fish pathogens, several of which have been recognized as emerging human pathogens. The organism is capable of causing a wide spectrum of diseases in humans, ranging from gastroenteritis, wound infections, and septicemia to devastating necrotizing fasciitis. The systemic form of infection is often fatal, particularly in patients with underlying chronic diseases. Indeed, recent trends demonstrate rising numbers of hospital-acquired Aeromonas infections, especially in immuno-compromised individuals. Additionally, Aeromonas-associated antibiotic resistance is an increasing challenge in combating both fish and human infections. The acquisition of antibiotic resistance is related to Aeromonas' innate transformative properties including its ability to share plasmids and integron-related gene cassettes between species and with the environment. As a result, alternatives to antibiotic treatments are desperately needed. In that vein, many treatments have been proposed and studied extensively in the fish-farming industry, including treatments that target Aeromonas quorum sensing. In this review, we discuss current strategies targeting quorum sensing inhibition and propose that such studies empower the development of novel chemotherapeutic approaches to combat drug-resistant Aeromonas spp. infections in humans. KEY POINTS: • Aeromonas notoriously acquires and maintains antimicrobial resistance, making treatment options limited. • Quorum sensing is an essential virulence mechanism in Aeromonas infections. • Inhibiting quorum sensing can be an effective strategy in combating Aeromonas infections in animals and humans.
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Affiliation(s)
- Blake Neil
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Gabrielle L Cheney
- John Sealy School of Medicine, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Jason A Rosenzweig
- Department of Biology, Texas Southern University, Houston, TX, 77004, USA
| | - Jian Sha
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA
| | - Ashok K Chopra
- Department of Microbiology and Immunology, Medical Branch, University of Texas, Galveston, TX, 77555, USA.
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Behling AH, Wilson BC, Ho D, Cutfield WS, Vatanen T, O'Sullivan JM. Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity. Microbiome 2024; 12:26. [PMID: 38347627 PMCID: PMC10860221 DOI: 10.1186/s40168-024-01748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors. RESULTS Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention. CONCLUSION Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.
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Affiliation(s)
- Anna H Behling
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Daniel Ho
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wayne S Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
- Australian Parkinsons Mission, Garvan Institute of Medical Research, 384 Victoria Street, SydneyDarlinghurst, NSWNSW, 2010, Australia.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, SO16 6YD, UK.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore.
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29
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López Sánchez A, Lafond M. Predicting horizontal gene transfers with perfect transfer networks. Algorithms Mol Biol 2024; 19:6. [PMID: 38321476 PMCID: PMC10848447 DOI: 10.1186/s13015-023-00242-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/25/2023] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and species trees. However, it is well-known that sequences have difficulty identifying ancient transfers since mutations have enough time to erase all evidence of such events. In this work, we ask whether character-based methods can predict gene transfers. Their advantage over sequences is that homologous genes can have low DNA similarity, but still have retained enough important common motifs that allow them to have common character traits, for instance the same functional or expression profile. A phylogeny that has two separate clades that acquired the same character independently might indicate the presence of a transfer even in the absence of sequence similarity. OUR CONTRIBUTIONS We introduce perfect transfer networks, which are phylogenetic networks that can explain the character diversity of a set of taxa under the assumption that characters have unique births, and that once a character is gained it is rarely lost. Examples of such traits include transposable elements, biochemical markers and emergence of organelles, just to name a few. We study the differences between our model and two similar models: perfect phylogenetic networks and ancestral recombination networks. Our goals are to initiate a study on the structural and algorithmic properties of perfect transfer networks. We then show that in polynomial time, one can decide whether a given network is a valid explanation for a set of taxa, and show how, for a given tree, one can add transfer edges to it so that it explains a set of taxa. We finally provide lower and upper bounds on the number of transfers required to explain a set of taxa, in the worst case.
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Affiliation(s)
| | - Manuel Lafond
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Canada
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Wang M, Wang C, Yang J, Liu X, Xie B, Ren P, Kong X, Fu Y. Biochar induces different responses of intracellular and extracellular antibiotic resistance genes and suppresses horizontal transfer during lincomycin fermentation dregs composting. Bioresour Technol 2024; 394:130227. [PMID: 38135225 DOI: 10.1016/j.biortech.2023.130227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
This study aims to indicate the influence of biochar on extracellular and intracellular ARGs (e/iARGs) variation and proliferation during lincomycin fermentation dregs (LFDs) compost. Biochar addition made iARGs keep reducing but eARGs increase to the maximum at the middle thermophilic phase and reduce at the end of the compost. Compared to control 3.15-log and 5.42-log reduction of iARGs and eARGs were observed, respectively. Biochar addition, bacterial community, and MGEs were the major contributors to iARGs and eARGs removal, with the contribution percentages of 38.4%, 31.0%, 23.7%, and 27.2%, 29.1%, and 34.9%, respectively. Moreover, biochar significantly inhibited eARGs transformation and RP4 plasmid conjugative transfer among E. coli DH5α and Pseudomonas aeruginosa HLS-6. The underlying mechanism involved in broken cell membranes of bacteria, and altered expression of oxidative stress genes and save our souls (SOS) response-related genes. The results indicated that biochar addition in composting could limit the dissemination of ARGs.
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Affiliation(s)
- Mengmeng Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chenhao Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jie Yang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiangyu Liu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Binghan Xie
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, China
| | - Peng Ren
- Laoshan Laboratory, Qingdao 266061, China
| | - Xiaowei Kong
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yunxia Fu
- Key Laboratory of Geological Safety of Coastal Urban Underground Space, Ministry of Natural Resources, Qingdao 266100, China; Qingdao Geo-Engineering Surveying Institute (Qingdao Geological Exploration Development Bureau), Qingdao 266100, China
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La Manna P, De Carluccio M, Oliva G, Vigliotta G, Rizzo L. Urban wastewater disinfection by iron chelates mediated solar photo-Fenton: Effects on seven pathogens and antibiotic resistance transfer potential. Water Res 2024; 249:120966. [PMID: 38070340 DOI: 10.1016/j.watres.2023.120966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/25/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
The effects of solar photo-Fenton (SPF) process mediated by the iron chelate Fe3+ imminodisuccinic acid (Fe:IDS) on both the inactivation of seven relevant pathogens and the potential for antibiotic resistance transfer (degradation of antibiotic resistance genes (ARGs) and after treatment regrowth), in real secondary treated urban wastewater, were investigated for the first time. A comparison with results obtained by sunlight/H2O2 process and Fe3+ ethylenediaminedisuccinic acid (Fe:EDDS) SPF was also carried out. ARGs were quantified by polymerase chain reaction (PCR) in samples before and after (3 h) the treatment. The persistence of the selected pathogens and ARGs was also evaluated in regrowth tests (72 h) under environmentally mimicking conditions. Fe:IDS SPF resulted to be more effective (from 1.4 log removal for Staphylococcus spp. to 4.3 log removal for Escherichia coli) than Fe:EDDS SPF (from 0.8 log removal for Pseudomonas aeruginosa to 2.0 log removal for Total coliphages) and sunlight/H2O2 (from 1.2 log removal for Clostridium perfringens to 3.3 log removal for E. coli) processes for the seven pathogens investigated. Potential pathogens regrowth was also severely affected, as no substantial regrowth was observed, both in presence and absence of catalase. A similar trend was observed for ARGs removal too (until 0.001 fold change expression for qnrS after 3 h). However, a poor effect and a slight increase in fold change was observed after treatment especially for gyrA, mefA and intl1. Overall, the effect of the investigated processes on ARGs was found to be ARG dependent. Noteworthy, coliphages can regrow after sunlight/H2O2 treatment unlike SPF processes, increasing the risk of antibiotic resistance transfer by transduction mechanism. In conclusion, Fe:IDS SPF is an attractive solution for tertiary treatment of urban wastewater in small wastewater treatment plants as it can provide effective disinfection and a higher protection against antibiotic resistance transfer than the other investigated processes.
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Affiliation(s)
- Pellegrino La Manna
- Water Science and Technology group (WaSTe), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Marco De Carluccio
- Water Science and Technology group (WaSTe), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Gianmaria Oliva
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Giovanni Vigliotta
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Luigi Rizzo
- Water Science and Technology group (WaSTe), Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy.
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Chen Y, Yan Z, Zhou Y, Zhang Y, Jiang R, Wang M, Yuan S, Lu G. Dynamic evolution of antibiotic resistance genes in plastisphere in the vertical profile of urban rivers. Water Res 2024; 249:120946. [PMID: 38043355 DOI: 10.1016/j.watres.2023.120946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Microplastics (MPs) can vertically transport in the aquatic environment due to their aging and biofouling, forming distinct plastisphere in different water layers. However, even though MPs have been regarded as hotspots for antibiotic resistance genes (ARGs), little is known about the propagation and transfer of ARGs in plastisphere in waters, especially in the vertical profile. Therefore, this study investigated the dynamic responses and evolution of ARGs in different plastisphere distributed vertically in an urbanized river. The biofilm biomass in the polylactic acid (PLA) plastisphere was relatively higher than that in the polyethylene terephthalate (PET), showing depth-decay variations. The ARGs abundance in plastisphere were much higher than that in the surrounding waters, especially for the PLA. In the vertical profiles, the ARGs abundance in the PET plastisphere increased with water depths, while the highest abundance of ARGs in the PLA mostly appeared at intermediate waters. In the temporal dynamic, the ARGs abundance in plastisphere increased and then decreased, which may be dominated by the MP types at the initial periods. After long-term exposure, the influences of water depths seemed to be strengthened, especially in the PET plastisphere. Compared with surface waters, the microbiota attached in plastisphere in deep waters showed high species richness, strong diversity, and complex interactions, which was basically consistent with the changes of nutrient contents in different water layers. These vertical variations in microbiota and nutrients (e.g., nitrogen) may be responsible for the propagation of ARGs in plastisphere in deep waters. The host bacteria for ARGs in plastisphere was also developed as water depth increased, leading to an enrichment of ARGs in deep waters. In addition, the abundance of ARGs in plastisphere in bottom waters was positively correlated with the mobile genetic elements (MGEs) of intI1 and tnpA05, indicative of a frequent horizontal gene transfer of ARGs. Overall, water depth played a critical role in the propagation of ARGs in plastisphere, which should not be ignored in a long time series. This study provides new insights into the dynamic evolution of ARGs propagation in plastisphere under increasing global MPs pollution, especially in the vertical profile.
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Affiliation(s)
- Yufang Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Yan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
| | - Yixin Zhou
- College of Environment, Hohai University, Nanjing 210098, China
| | - Yan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Runren Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Min Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Saiyu Yuan
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China
| | - Guanghua Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
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Wan S, Zhou A, Chen R, Fang S, Lu J, Lv N, Wang C, Gao J, Li J, Wu W. Metagenomics next-generation sequencing (mNGS) reveals emerging infection induced by Klebsiella pneumoniaeniae. Int J Antimicrob Agents 2024; 63:107056. [PMID: 38081548 DOI: 10.1016/j.ijantimicag.2023.107056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
OBJECTIVES The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient. METHODS Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS). RESULTS A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence. CONCLUSIONS In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.
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Affiliation(s)
- Shuang Wan
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China; College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Aiping Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China; Shanghai East Hospital Ji'an Hospital, Ji'an, 343000, China
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shiqi Fang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jinfeng Lu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Na Lv
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chu Wang
- Genskey Medical Technology Co., Ltd., Beijing, 102206, China
| | - Jianpeng Gao
- Genskey Medical Technology Co., Ltd., Beijing, 102206, China
| | - Jun Li
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China.
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Jian J, Wu Z, Silva-Núñez A, Li X, Zheng X, Luo B, Liu Y, Fang X, Workman CT, Larsen TO, Hansen PJ, Sonnenschein EC. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum. Sci Total Environ 2024; 908:168042. [PMID: 37898203 DOI: 10.1016/j.scitotenv.2023.168042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Arisbe Silva-Núñez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Tecnologico de Monterrey, School of Engineering and Science, Monterrey, Nuevo León, Mexico
| | - Xiaohui Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Bei Luo
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yun Liu
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Per Juel Hansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Department of Biosciences, Swansea University, Swansea, United Kingdom.
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Tartik M. The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination. Mol Biol Rep 2024; 51:99. [PMID: 38206425 DOI: 10.1007/s11033-023-09058-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Horizontal gene transfer (HGT) is considered an important mechanism to contribute to the evolution of bacteria, plants, and animals by allowing the movement of genetic material between organisms, in difference to vertical inheritance. Thereby it can also play a significant role in spreading traits like antibiotic resistance among bacteria and virulence factors between pathogens. During the HGT, organisms take up free DNA from the environment and incorporate it into their genomes. Although HGT is known to be carried out by many organisms, there is limited information on how organisms select which genetic material for horizontal transfer. Here we have investigated the preference priority of Saccharomyces cerevisiae between different options of gene source presented under certain stress conditions to repair a double-strand break (DSB) in DNA via HR. RESULTS Each genetic module was designed with appropriate sequences being homologous for two sides of the DSB, which is important for yeast to repair the fracture with HR. S. cerevisiae made a random selection between two heterologous T1 (44%) and T2 (56%) modules to repair DSB. Interestingly, yeast corrected the DNA break only with the T3 module (almost 100%) when the homologous T3 module was an option for the selection. It seems that S. cerevisiae tends to prefer T3 over alternatives to fix DSBs when it exists among the options. CONCLUSIONS It seems that S. cerevisiae have a preference for priority to select a particular one under certain conditions when it has various DNA options to repair a DSB in its genome, further studies are required to support our findings.
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Affiliation(s)
- Musa Tartik
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bingol University, 12000, Bingol, Turkey.
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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Jiménez-Volkerink SN, Jordán M, Smidt H, Minguillón C, Vila J, Grifoll M. Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil. Sci Total Environ 2024; 907:167832. [PMID: 37863223 DOI: 10.1016/j.scitotenv.2023.167832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.
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Affiliation(s)
- Sara N Jiménez-Volkerink
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Maria Jordán
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, the Netherlands
| | - Cristina Minguillón
- Department of Nutrition, Food Science and Gastronomy, University of Barcelona, Avda. Prat de la Riba, 171, 08921 Sta. Coloma de Gramanet, Barcelona, Spain
| | - Joaquim Vila
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain.
| | - Magdalena Grifoll
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
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Wang YZ, An XL, Fan XT, Pu Q, Li H, Liu WZ, Chen Z, Su JQ. Visible light-activated photosensitizer inhibits the plasmid-mediated horizontal gene transfer of antibiotic resistance genes. J Hazard Mater 2024; 461:132564. [PMID: 37734313 DOI: 10.1016/j.jhazmat.2023.132564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Inhibition of plasmid transfer, including transformation and conjugation, is essential to prevent the spread of plasmid-encoded antimicrobial resistance. Photosensitizers have been successfully used in the treatment of serious infectious diseases, however, the effects of photosensitizers on the plasmid transfer are still elusive. In this study, we determined the transformation and conjugation efficiency of plasmid pUC19 and pRP4, respectively, when exposed to a photosensitizer (Visible Light-activated Rose Bengal, VLRB). The results showed that the activation of VLRB resulted in up to a 580-fold decrease in the transformation frequency of pUC19 and a 10-fold decrease in the conjugation frequency of pRP4 compared with the non-VLRB control. The inhibition of pUC19 transformation by VLRB exhibited a dose-dependent manner and was attributed to the changes in the plasmid conformation. The inhibition of pRP4 conjugation was associated with the generation of extracellular free radicals, induced oxidative stress, suppression of the mating pair formation gene (trbBp) and DNA transfer and replication gene (trfAp), and enhanced expression of the global regulatory genes (korA, korB, and trbA). These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes.
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Affiliation(s)
- Yan-Zi Wang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xiao-Ting Fan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Wen-Zhen Liu
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Structural Chemistry, CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Zhuo Chen
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Structural Chemistry, CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Choi DG, Baek JH, Han DM, Khan SA, Jeon CO. Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions. BMC Genomics 2024; 25:28. [PMID: 38172677 PMCID: PMC10765913 DOI: 10.1186/s12864-023-09945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. RESULTS E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. CONCLUSIONS Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
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Affiliation(s)
- Dae Gyu Choi
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Shehzad Abid Khan
- Atta‑ur‑Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000, Islamabad, Pakistan
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea.
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Takahashi T, Kim H, Kim HS, Kim HS, Song W, Kim JS. Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCC mec V Clinical Isolates in Korea. Ann Lab Med 2024; 44:47-55. [PMID: 37665285 PMCID: PMC10485862 DOI: 10.3343/alm.2024.44.1.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
Background Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains. Methods Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data. Results The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors. Conclusions Most Korean SCCmec V strains may have emerged during 2000-2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.
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Affiliation(s)
- Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Hyaekang Kim
- Bioresources Collection and Research Division, Bioresources Collection and Bioinformation Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
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Ye C, Chen C, Zhang K, Feng M, Yu X. Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane. Environ Pollut 2024; 340:122766. [PMID: 37865329 DOI: 10.1016/j.envpol.2023.122766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/09/2023] [Accepted: 10/15/2023] [Indexed: 10/23/2023]
Abstract
Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.
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Affiliation(s)
- Chengsong Ye
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Chenlan Chen
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Kaiting Zhang
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Mingbao Feng
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Xin Yu
- Fujian Key Laboratory of Coastal Pollution Prevention and Control, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China.
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Li N, Zheng N, Pan J, An Q, Li X, Sun S, Chen C, Zhu H, Li Z, Ji Y. Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. Sci Total Environ 2024; 906:167619. [PMID: 37806594 DOI: 10.1016/j.scitotenv.2023.167619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/05/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.
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Affiliation(s)
- Ning Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Na Zheng
- College of New Energy and Environment, Jilin University, Changchun 130012, China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China.
| | - Jiamin Pan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Qirui An
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Xiaoqian Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Siyu Sun
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Changcheng Chen
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Huicheng Zhu
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Zimeng Li
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Yining Ji
- College of New Energy and Environment, Jilin University, Changchun 130012, China
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Wu L, Wu Q, Xu J, Rong L, Yu X, Cai C, Huang X, Zou X. Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications. Sci Total Environ 2023; 905:167247. [PMID: 37739079 DOI: 10.1016/j.scitotenv.2023.167247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.
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Affiliation(s)
- Ligui Wu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Qiaofeng Wu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Fuzhou Urban and Rural Construction Group Co. Ltd, Fuzhou 350007, China
| | - Jingcheng Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lingling Rong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiaoli Yu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Chen Cai
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiangfeng Huang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China.
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Shen Z, Qin J, Xiang G, Chen T, Nurxat N, Gao Q, Wang C, Zhang H, Liu Y, Li M. Outer membrane vesicles mediating horizontal transfer of the epidemic blaOXA-232 carbapenemase gene among Enterobacterales. Emerg Microbes Infect 2023; 13:2290840. [PMID: 38044873 PMCID: PMC10810626 DOI: 10.1080/22221751.2023.2290840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
OXA-232 is one of the most common OXA-48-like carbapenemase derivatives and is widely disseminated in nosocomial settings across countries. The blaOXA-232 gene is located on a 6-kb non-conjugative ColKP3-type plasmid, while the dissemination of blaOXA-232 into different Enterobacterales species and the polyclonal dissemination of OXA-232-producing K. pneumoniae revealed the horizontal transfer of blaOXA-232. However, it's still unclear how this non-conjugative ColKP3 plasmid could facilitate the mobilization of blaOXA-232. Here, we observed the in vivo intraspecies transfer of blaOXA-232 during a nosocomial outbreak of OXA-232-producing K. pneumoniae. We demonstrated the presence of ColKP3 OXA-232 plasmid in the outer membrane vesicles (OMVs) derived from clinical isolates, and OMVs could facilitate the horizontal transfer of blaOXA-232 among Enterobacterales. In contrast, for the most prevalent carbapenemase genes, including blaKPC-2 and blaNDM-1, though the presence of carbapenemase genes and plasmid backbones in the vesicular lumen was observed, OMVs couldn't promote effective transformation, probably due to the low copy number of plasmids in clinical isolates and the low number of plasmids loaded into vesicles. Conjugation assay revealed that the epidemic IncX3 NDM-1 and IncFII(pHN7A8)/IncR KPC-2 plasmids were conjugative and could be horizontally transferred via independent conjugation or with the help of a co-existent conjugative plasmid. For the large-size and low-copy number conjugative plasmids carrying carbapenemase genes, OMVs-mediated gene exchange may only serve as an alternative pathway for horizontal transfer. In conclusion, diverse mobilization strategies were employed by plasmids harboring carbapenemase genes, and plasmids display a proper choice of mobility pathway due to their individual properties.
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Affiliation(s)
- Zhen Shen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Juanxiu Qin
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Tianchi Chen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Nadira Nurxat
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Qianqian Gao
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Chen Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Haomin Zhang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yao Liu
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD, USA
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Hull DM, Harrel E, Harden L, Thakur S. Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019. Food Microbiol 2023; 116:104348. [PMID: 37689422 DOI: 10.1016/j.fm.2023.104348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 09/11/2023]
Abstract
Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.
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Affiliation(s)
- Dawn M Hull
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Erin Harrel
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Lyndy Harden
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA.
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Cheatle Jarvela AM, Wexler JR. Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution. Dev Genes Evol 2023; 233:59-76. [PMID: 37982820 DOI: 10.1007/s00427-023-00712-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, MD, USA.
- HHMI Janelia Research Campus, Ashburn, VA, USA.
| | - Judith R Wexler
- Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, Jerusalem, Israel.
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Haghjooy Javanmard S, Rafiee L, Bahri Najafi M, Khorsandi D, Hasan A, Vaseghi G, Makvandi P. Microfluidic-based technologies in cancer liquid biopsy: Unveiling the role of horizontal gene transfer (HGT) materials. Environ Res 2023; 238:117083. [PMID: 37690629 DOI: 10.1016/j.envres.2023.117083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
Liquid biopsy includes the isolating and analysis of non-solid biological samples enables us to find new ways for molecular profiling, prognostic assessment, and better therapeutic decision-making in cancer patients. Despite the conventional theory of tumor development, a non-vertical transmission of DNA has been reported among cancer cells and between cancer and normal cells. The phenomenon referred to as horizontal gene transfer (HGT) has the ability to amplify the advancement of tumors by disseminating genes that encode molecules conferring benefits to the survival or metastasis of cancer cells. Currently, common liquid biopsy approaches include the analysis of extracellular vesicles (EVs) and tumor-free DNA (tfDNA) derived from primary tumors and their metastatic sites, which are well-known HGT mediators in cancer cells. Current technological and molecular advances expedited the high-throughput and high-sensitive HGT materials analyses by using new technologies, such as microfluidics in liquid biopsies. This review delves into the convergence of microfluidic-based technologies and the investigation of Horizontal Gene Transfer (HGT) materials in cancer liquid biopsy. The integration of microfluidics offers unprecedented advantages such as high sensitivity, rapid analysis, and the ability to analyze rare cell populations. These attributes are instrumental in detecting and characterizing CTCs, circulating nucleic acids, and EVs, which are carriers of genetic cargo that could potentially undergo HGT. The phenomenon of HGT in cancer has raised intriguing questions about its role in driving genomic diversity and acquired drug resistance. By leveraging microfluidic platforms, researchers have been able to capture and analyze individual cells or genetic material with enhanced precision, shedding light on the potential transfer of genetic material between cancer cells and surrounding stromal cells. Furthermore, the application of microfluidics in single-cell sequencing has enabled the elucidation of the genetic changes associated with HGT events, providing insights into the evolution of tumor genomes. This review also discusses the challenges and opportunities in studying HGT materials using microfluidic-based technologies. In conclusion, microfluidic-based technologies have significantly advanced the field of cancer liquid biopsy, enabling the sensitive and accurate detection of HGT materials. As the understanding of HGT's role in tumor evolution and therapy resistance continues to evolve, the synergistic integration of microfluidics and HGT research promises to provide valuable insights into cancer biology, with potential implications for precision oncology and therapeutic strategies.
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Affiliation(s)
- Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Laleh Rafiee
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majed Bahri Najafi
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Danial Khorsandi
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA, 90024, United States
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Golnaz Vaseghi
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
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Li S, Li X, Chang H, Zhong N, Ren N, Ho SH. Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives. Sci Total Environ 2023; 901:166029. [PMID: 37541493 DOI: 10.1016/j.scitotenv.2023.166029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.
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Affiliation(s)
- Shengnan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Xue Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Haixing Chang
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Nianbing Zhong
- Liangjiang International College, Chongqing University of Technology, Chongqing 401135, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
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Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M. Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. Microbiome 2023; 11:265. [PMID: 38007474 PMCID: PMC10675870 DOI: 10.1186/s40168-023-01644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster. RESULTS The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species. CONCLUSIONS Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.
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Affiliation(s)
- Yanting Liu
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl Von Ossietzky Str. 9-11, 26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, 26129, Oldenburg, Germany.
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Savin M, Hammerl JA, Hassa J, Hembach N, Kalinowski J, Schwartz T, Droop F, Mutters NT. Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes. Environ Pollut 2023; 337:122560. [PMID: 37716694 DOI: 10.1016/j.envpol.2023.122560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/28/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.
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Affiliation(s)
- Mykhailo Savin
- Institute of Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany.
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg, D-12277, Berlin, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, D-33615, Bielefeld, Germany
| | - Norman Hembach
- Department of Microbiology/Molecular Biology, Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Jörn Kalinowski
- Department for Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg, D-12277, Berlin, Germany
| | - Thomas Schwartz
- Department of Microbiology/Molecular Biology, Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Felix Droop
- Institute of Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Nico T Mutters
- Institute of Hygiene and Public Health, University Hospital Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
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Schaller D, Hartmann T, Lafond M, Stadler PF, Wieseke N, Hellmuth M. Relative timing information and orthology in evolutionary scenarios. Algorithms Mol Biol 2023; 18:16. [PMID: 37940998 PMCID: PMC10634191 DOI: 10.1186/s13015-023-00240-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/23/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. RESULTS Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.
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Affiliation(s)
- David Schaller
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
| | - Tom Hartmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
| | - Manuel Lafond
- Department of Computer Science, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, J1K 2R1, Canada
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Augustusplatz 12, Leipzig, 04107, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, 04109, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, 1090, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, 111321, DC, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA
| | - Nicolas Wieseke
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, Leipzig University, Augustusplatz 10, Leipzig, 04109, Germany
| | - Marc Hellmuth
- Department of Mathematics, Faculty of Science, Stockholm University, Stockholm, 10691, Sweden.
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