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Abdelhadi AA, Elarabi NI, Ibrahim SM, Abdel-Maksoud MA, Abdelhaleem HAR, Almutairi S, Malik A, Kiani BH, Henawy AR, Halema AA. Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain. Funct Integr Genomics 2024; 24:174. [PMID: 39320439 DOI: 10.1007/s10142-024-01441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/26/2024]
Abstract
Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na2HAsO4·7H2O was identified using the 16S rRNA gene and whole genome analysis as Enterobacter cloacae FACU. The arsenic E. cloacae FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of E. cloacae FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the E. cloacae FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five arsRDABC genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of E. cloacae FACU at the genetic level.
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Affiliation(s)
- Abdelhadi A Abdelhadi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Nagwa I Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Saifeldeen M Ibrahim
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
- Bioinformatics Department, Agricultural Genetic Engineering Research Institute, ARC, Giza, Egypt
| | - Mostafa A Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Heba A R Abdelhaleem
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Saeedah Almutairi
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bushra Hafeez Kiani
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachuesetts, 01609, USA
| | - Ahmed R Henawy
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Asmaa A Halema
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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2
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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2024; 27:967-975. [PMID: 37968548 PMCID: PMC11300574 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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3
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Daddy Gaoh S, Alusta P, Lee YJ, LiPuma JJ, Hussong D, Marasa B, Ahn Y. A Comparative Metagenomic Analysis of Specified Microorganisms in Groundwater for Non-Sterilized Pharmaceutical Products. Curr Microbiol 2024; 81:273. [PMID: 39017960 PMCID: PMC11255085 DOI: 10.1007/s00284-024-03791-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
In pharmaceutical manufacturing, ensuring product safety involves the detection and identification of microorganisms with human pathogenic potential, including Burkholderia cepacia complex (BCC), Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma spp., some of which may be missed or not identified by traditional culture-dependent methods. In this study, we employed a metagenomic approach to detect these taxa, avoiding the limitations of conventional cultivation methods. We assessed the groundwater microbiome's taxonomic and functional features from samples collected at two locations in the spring and summer. All datasets comprised 436-557 genera with Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Cyanobacteria accounting for > 95% of microbial DNA sequences. The aforementioned species constituted less than 18.3% of relative abundance. Escherichia and Salmonella were mainly detected in Hot Springs, relative to Jefferson, while Clostridium and Pseudomonas were mainly found in Jefferson relative to Hot Springs. Multidrug resistance efflux pumps and BlaR1 family regulatory sensor-transducer disambiguation dominated in Hot Springs and in Jefferson. These initial results provide insight into the detection of specified microorganisms and could constitute a framework for the establishment of comprehensive metagenomic analysis for the microbiological evaluation of pharmaceutical-grade water and other non-sterile pharmaceutical products, ensuring public safety.
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Affiliation(s)
- Soumana Daddy Gaoh
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079-9502, USA
| | - Pierre Alusta
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yong-Jin Lee
- Department of Natural Sciences, Albany State University, Albany, GA, 31707, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Bernard Marasa
- Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079-9502, USA.
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4
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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5
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O'Malley K, McNamara P, Marshall C, LaMartina EL, Lam TD, Ali N, McDonald W. Environmental drivers impact the accumulation and diversity of antibiotic resistance in green stormwater infrastructure. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133923. [PMID: 38457973 DOI: 10.1016/j.jhazmat.2024.133923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Antibiotic resistance poses an urgent public health concern, with the environment playing a crucial role in the development and dissemination of resistant bacteria. There is a growing body of research indicating that stormwater is a significant source and transport vector of resistance elements. This research sought to characterize the role of green stormwater infrastructure (GSI), designed for stormwater infiltration, in accumulating and propagating antibiotic resistance in the urban water cycle. Sampling included 24 full-scale GSI systems representing three distinct types of GSI - bioswales, bioretention cells, and constructed wetlands. The results indicated that GSI soils accumulate antibiotic resistance genes (ARGs) at elevated concentrations compared to nonengineered soils. Bioretention cells specifically harbored higher abundances of ARGs, suggesting that the type of GSI influences ARG accumulation. Interestingly, ARG diversity in GSI soils was not impacted by the type of GSI design or the diversity of the microbial community and mobile genetic elements. Instead, environmental factors (catchment imperviousness, metals, nutrients, and salts) were identified as significant drivers of ARG diversity. These findings highlight how environmental selective pressures in GSI promote ARG persistence and proliferation independently of the microbial community. Therefore, GSI systems have the potential to be a substantial contributor of abundant and diverse ARGs to the urban water cycle.
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Affiliation(s)
- Kassidy O'Malley
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Patrick McNamara
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Christopher Marshall
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Emily Lou LaMartina
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA; Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Thuy Duyen Lam
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Numair Ali
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Walter McDonald
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA.
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6
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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. ENVIRONMENTAL RESEARCH 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] [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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7
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Ferreira PFA, Rocha FI, Howe A, Barbosa DR, da Conceição Jesus E, do Amaral Sobrinho NMB, da Silva Coelho I. Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:123. [PMID: 38483669 DOI: 10.1007/s10653-024-01894-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.
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Affiliation(s)
- Paula Fernanda Alves Ferreira
- Departament of Soil, Institute of Agronomy, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil
| | - Fernando Igne Rocha
- Mokichi Okada Research Center, Korin Agriculture and Environment, Ipeúna, São Paulo, Brazil
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Daniele Rodrigues Barbosa
- Departament of Soil, Institute of Agronomy, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil
| | - Ederson da Conceição Jesus
- Embrapa Agrobiology, Brazilian Agricultural Research Corporation, Seropédica, Rio de Janeiro, 23891-000, Brazil
| | | | - Irene da Silva Coelho
- Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil.
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Tan Y, Zhao K, Yang S, Chen S, Li C, Han X, Li J, Hu K, Liu S, Ma M, Yu X, Zou L. Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119935. [PMID: 38154221 DOI: 10.1016/j.jenvman.2023.119935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/12/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.
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Affiliation(s)
- Yulan Tan
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Ke Zhao
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
| | - Chun Li
- Sichuan Province Center for Animal Disease Prevention and Control, Chengdu, Sichuan, China.
| | - Xinfeng Han
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
| | - Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
| | - Menggen Ma
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Xiumei Yu
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Likou Zou
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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Bodus B, O'Malley K, Dieter G, Gunawardana C, McDonald W. Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167195. [PMID: 37777137 DOI: 10.1016/j.scitotenv.2023.167195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.
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Affiliation(s)
- Benjamin Bodus
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Kassidy O'Malley
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Greg Dieter
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Charitha Gunawardana
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
| | - Walter McDonald
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA.
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10
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Seethalakshmi PS, Prabhakaran A, Kiran GS, Selvin J. Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04. Arch Microbiol 2023; 206:33. [PMID: 38133813 DOI: 10.1007/s00203-023-03746-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
The dissemination of antimicrobial-resistant bacteria through environment is a major health concern for public health. Pathogenic bacteria in natural environment can mediate the transfer of antimicrobial-resistant genes via horizontal gene transfer to naturally occurring bacteria in the soil. Bhargavaea beijingensis is a Gram-negative bacterium that is commonly found in soil and water. In recent years, there has been an emergence of antibiotic-resistant strains of environmental bacteria, which pose a significant threat to human health. One mechanism of antibiotic resistance in bacteria is through the acquisition of plasmids, which can carry genes that confer resistance to various antibiotics. In this study, a novel plasmid of repUS12 replicon type was identified in the strain PS04 of B. beijingensis, which carried the ermT and tet(L) genes, encoding resistance to macrolides, lincosamides, and tetracycline. The plasmid was found to be the first of its kind in B. beijingensis and was thought to have been acquired through horizontal gene transfer. The emergence of plasmid-mediated resistance in B. beijingensis highlights the need for continued surveillance and monitoring of antibiotic resistance in environmental bacteria.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India.
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11
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Sajjad W, Ali B, Niu H, Ilahi N, Rafiq M, Bahadur A, Banerjee A, Kang S. High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment. ENVIRONMENTAL RESEARCH 2023; 239:117444. [PMID: 37858689 DOI: 10.1016/j.envres.2023.117444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.
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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
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Hewen Niu
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China; National Field Science Observation and Research Station of Yulong Snow Mountain Cryosphere and Sustainable Development, 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
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Engineering and Management Sciences, Balochistan University of Information Technology, 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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Balcha ES, Gómez F, Gemeda MT, Bekele FB, Abera S, Cavalazzi B, Woldesemayat AA. Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region. Antibiotics (Basel) 2023; 12:1697. [PMID: 38136731 PMCID: PMC10740858 DOI: 10.3390/antibiotics12121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.
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Affiliation(s)
- Ermias Sissay Balcha
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Felipe Gómez
- Centro de Astrobiología (INTA-CSIC) Crtera, Ajalvir km 4 Torrejón de Ardoz, P.O. Box 28850 Madrid, Spain;
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
| | - Fanuel Belayneh Bekele
- School of Public Health, College of Medicine and Health Sciences, Hawassa University, Hawassa P.O. Box 1560, Ethiopia;
| | - Sewunet Abera
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands;
- Institute of Biology, Leiden University, P.O. Box 9500, 2300 RA Leiden, The Netherlands
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa P.O. Box 2003, Ethiopia
| | - Barbara Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, 40100 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg P.O. Box 524, South Africa
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa P.O. Box 16417, Ethiopia;
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Qaria MA, Xu C, Hussain A, Nawaz MZ, Zhu D. Metagenomic investigations on antibiotic resistance and microbial virulence in oil-polluted soils from China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:110590-110599. [PMID: 37792198 DOI: 10.1007/s11356-023-30137-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil microbial communities. In this study, three samples were collected from oil-polluted soils (OPS), and one control soil (CS) from Taolin town, China, near the old engine's scrapes was used. The aims of this study were to conduct metagenomic sequencing and subsequently perform resistome and virulome analysis. We also aimed to validate anti-microbial resistance and virulence genes and anti-bacterial sensitivity profiles among the isolates from oil-polluted soils. The OPS microbial community was dominated by bacterial species compared to the control samples which were dominated by metazoans and other organisms. Secondly, the resistosome and virulome analysis showed that ARGs and virulence factors were higher among OPS microbial communities. Antibiotic susceptibility assay and qPCR analysis for ARGs and virulence factors showed that the oil-polluted soil samples had remarkably enhanced expression of these ARGs and some virulence genes. Our study suggests that oil pollution contributes to shifting microbial communities to more resilient types that could survive the toxicity of oil pollution and subsequently become more resilient in terms of higher resistance and virulence potential.
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Affiliation(s)
- Majjid A Qaria
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Chunyan Xu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | | | - Muhammad Zohaib Nawaz
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Yang L, Lyu J, Zhang L, Wang L, Yu J, Cao Z, Tudi M, Meng M. Spatial distribution of antibiotics and antibiotic resistance genes in tidal flat reclamation areas in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:112863-112876. [PMID: 37843708 DOI: 10.1007/s11356-023-30087-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023]
Abstract
Tidal flat areas are important resources for land development and are becoming antibiotic resistance receivers that trigger major health concerns. The spatial distributions of forty-nine antibiotics, nine antibiotic resistance genes (ARGs), one mobile gene element (MGE) gene, and nine available metals in the soils and sediments along the coastlines of the Yellow Sea in China were quantified. Hierarchical linear model analysis was used to explore relationships between the antibiotics and ARGs across multiple effects resulting from human activities and environmental factors. Fish farm sediments and farmland soils showed high levels of quinolones (QNs) (maximum 637 ng·g-1), sulfonamides (SAs) (maximum 221 ng·g-1), and corresponding ARGs. Significant positive correlations (P from 5.47 × 10-14 to 0.0487) were observed between the antibiotics (QNs, SAs, and chlortetracycline) and their corresponding ARGs (qnrA, qnrD, aac(6')-Ib-cr, dfrA, sul2, and tetA), indicating the selective pressure from antibiotics in soils and sediments. Nine available metals had positive correlations with at least one ARG, indicating heavy metal pollution could enhance the ARGs. Sheep and poultry husbandry and marine aquaculture contribute the most to the antibiotic resistance in the coastlines. In conclusion, antibiotic pollutions have promoting effects at sub-inhibitory concentrations and more attention should be given to inhibit the enrichment of ARGs during tidal flat reclamation processes. The study also suggests the induction effects from metal pollutions, MGE spread, and the antibiotic pollutions from the usage in livestock and aquaculture.
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Affiliation(s)
- Linsheng Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Road, Beijing, 101408, China
| | - Jia Lyu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.1 Yanqihu East Road, Beijing, 101408, China
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, No. 29 Nanwei Road, Beijing, 100050, China
| | - Lan Zhang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, No. 29 Nanwei Road, Beijing, 100050, China
| | - Li Wang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China.
| | - Jiangping Yu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China
| | - Zhiqiang Cao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China
| | - Muyesaier Tudi
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, No.11 Datun Road, Beijing, 100101, China
- School of Engineering and Built Environment, Griffith University, Brisbane, QLD, 4111, Australia
| | - Min Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, No.27 Shanda Nanlu, Jinan, 250100, China
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15
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K S, Vasanthrao R, Chattopadhyay I. Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance. Folia Microbiol (Praha) 2023; 68:657-675. [PMID: 37589876 DOI: 10.1007/s12223-023-01083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.
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Affiliation(s)
- Suganya K
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ramavath Vasanthrao
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Indranil Chattopadhyay
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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16
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Kim HW, Kim NK, Phillips APR, Parker DA, Liu P, Whitaker RJ, Rao CV, Mackie RI. Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Front Microbiol 2023; 14:1232587. [PMID: 37822751 PMCID: PMC10562698 DOI: 10.3389/fmicb.2023.1232587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Alicyclobacillus has been isolated from extreme environments such as hot springs, volcanoes, as well as pasteurized acidic beverages, because it can tolerate extreme temperatures and acidity. In our previous study, Alicyclobacillus was isolated during the enrichment of methane oxidizing bacteria from Yellowstone Hot Spring samples. Methods Physiological characterization and genomic exploration of two new Alicyclobacillus isolates, AL01A and AL05G, are the main focus of this study to identify their potential relationships with a thermoacidophilic methanotroph (Methylacidiphilum) isolated from the same hot spring sediments. Results and discussion In the present study, both Alicyclobacillus isolates showed optimal growth at pH 3.5 and 55°C, and contain ω-alicyclic fatty acids as a major lipid (ca. 60%) in the bacterial membrane. Genomic analysis of these strains revealed specific genes and pathways that the methanotroph genome does not have in the intermediary carbon metabolism pathway such as serC (phosphoserine aminotransferase), comA (phosphosulfolactate synthase), and DAK (glycerone kinase). Both Alicyclobacillus strains were also found to contain transporter systems for extracellular sulfate (ABC transporter), suggesting that they could play an important role in sulfur metabolism in this extreme environment. Genomic analysis of vitamin metabolism revealed Alicyclobacillus and Methylacidiphilum are able to complement each other's nutritional deficiencies, resulting in a mutually beneficial relationship, especially in vitamin B1(thiamin), B3 (niacin), and B7 (biotin) metabolism. These findings provide insights into the role of Alicyclobacillus isolates in geothermal environments and their unique metabolic adaptations to these environments.
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Affiliation(s)
- Hye Won Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Na Kyung Kim
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Alex P. R. Phillips
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Ping Liu
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Westhollow Technology Center, Shell Exploration and Production Inc., Houston, TX, United States
| | - Rachel J. Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Roderick I. Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Materials Research Laboratory, Energy and Biosciences Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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17
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Andrade L, P Ryan M, P Burke L, Hynds P, Weatherill J, O'Dwyer J. Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121970. [PMID: 37343911 DOI: 10.1016/j.envpol.2023.121970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/08/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.
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Affiliation(s)
- Luisa Andrade
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon Midwest, Moylish, Ireland
| | - Liam P Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Paul Hynds
- Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Sustainability and Health Institute, Technological University Dublin, Dublin 7, Ireland
| | - John Weatherill
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jean O'Dwyer
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
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18
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Shen C, He M, Zhang J, Liu J, Su J, Dai J. Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115367. [PMID: 37586197 DOI: 10.1016/j.ecoenv.2023.115367] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/09/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.
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Affiliation(s)
- Cong Shen
- School of Life Sciences, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Mengyuan He
- School of Life Sciences, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Junhua Zhang
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwestern China, Yinchuan 750021, Ningxia, China; Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Yinchuan 750021, Ningxia, China.
| | - Jili Liu
- School of Ecology and Environment, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwestern China, Yinchuan 750021, Ningxia, China; Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education, Yinchuan 750021, Ningxia, China
| | - Jianyu Su
- School of Life Sciences, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Jinxia Dai
- School of Life Sciences, Ningxia University, Yinchuan, 750021, Ningxia, China
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Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? ENVIRONMENT INTERNATIONAL 2023; 178:108089. [PMID: 37441817 DOI: 10.1016/j.envint.2023.108089] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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Affiliation(s)
- Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden.
| | - Anna Abramova
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Food Authority, P.O.Box 100, 00027 Seinäjoki, Finland
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ayaz Ali Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biotechnology, University of Malakand, Chakdara, Dir (Lower), Khyber Pakhtunkhwa, Pakistan
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marmar Nekoro
- Swedish Knowledge Centre on Pharmaceuticals in the Environment, Swedish Medical Products Agency, P.O Box 26, 751 03 Uppsala, Sweden
| | - Adriana D Osińska
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tarja Pitkänen
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O.Box 95, FI-70701 Kuopio, Finland
| | | | - Etienne Ruppé
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | | | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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20
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de Souza ZN, de Moura DF, de Almeida Campos LA, Córdula CR, Cavalcanti IMF. Antibiotic resistance profiles on pathogenic bacteria in the Brazilian environments. Arch Microbiol 2023; 205:185. [PMID: 37043091 DOI: 10.1007/s00203-023-03524-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
The present study aimed to elaborate a review of multidrug-resistant (MDR) bacteria in soil, food, aquatic environments, cattle, poultry, and swine farms in Brazil. Initially, the literature database for published papers from 2012 to 2023 was Scientific Electronic Library Online (SciELO), U.S. National Library of Medicine (PubMed), and Google Scholar, through the descriptors: antimicrobial resistance, resistance profile, multidrug resistance, environmental bacteria, and pathogenic bacteria. The studies demonstrated the prevalence of pathogenic and resistant bacteria in environments that favor their rapid dissemination. Bacteria of medical importance, such as Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella spp., Shigella spp., Vibrio spp., were present in samples from animal farms and foods, including cheese and milk, urban aquatic environments, hospital effluents, and shrimp farms. Studies suggested that important bacteria have been disseminated through different niches with easy contact with humans, animals, and food, demonstrating the danger of the emergence of increasingly difficult conditions for treating and controlling these infections. Thus, better understanding and characterizing the resistance profiles of bacteria in these regions, mainly referring to MDR bacteria, can help develop solutions to prevent the progression of this public health problem.
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Affiliation(s)
- Zion Nascimento de Souza
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Danielle Feijó de Moura
- Laboratory of Microbiology and Immunology, Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Rua do Alto do Reservatório s/n, Bela Vista, Vitória de Santo Antão, Pernambuco, 55608-680, Brazil
| | - Luís André de Almeida Campos
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Carolina Ribeiro Córdula
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Isabella Macário Ferro Cavalcanti
- Keizo Asami Institute (iLIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, PE, 50670-901, Brazil.
- Laboratory of Microbiology and Immunology, Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Rua do Alto do Reservatório s/n, Bela Vista, Vitória de Santo Antão, Pernambuco, 55608-680, Brazil.
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21
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Li S, Ondon BS, Ho SH, Li F. Emerging soil contamination of antibiotics resistance bacteria (ARB) carrying genes (ARGs): New challenges for soil remediation and conservation. ENVIRONMENTAL RESEARCH 2023; 219:115132. [PMID: 36563979 DOI: 10.1016/j.envres.2022.115132] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/04/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Soil plays a vital role as a nutrient source for microflora and plants in ecosystems. The accumulation and proliferation of antibiotics resistance bacteria (ARB) and antibiotics resistance genes (ARGs) causes emerging soil contamination and pollution, posing new challenges for soil remediation, recovery, and conservation. Fertilizer application in agriculture is one of the most important sources of ARB and ARGs contamination in soils. The recent existing techniques for the remediation of soil polluted with ARB and ARGs are very limited in terms of ARB and ARGs removal in soil. Bioelectrochemical remediation using bioelectrochemical systems such as microbial fuel cells and microbial electrolysis cells are promising technologies for the removal of ARB and ARGs in soil. Herein, diverse sources of ARB and ARGs in soil have been reviewed, their effects on soil microbial diversity have been analyzed, and the causes of ARB and ARGs rapid proliferation in soil are explained. Bioelectrochemical systems used for the remediation of soil contaminated with ARB and ARGs is still in its infancy stage and presents serious disadvantage and limits, therefore it needs to be well understood and implemented. In general, merging soil contamination of ARB and ARGs is an increasing concern threatening the soil ecosystem while the remediation technologies are still challenging. Efforts need to be made to develop new, effective, and efficient technologies for soil remediation and conservation to tackle the spread of ARB and ARGs and overcome the new challenges posed by ARB and ARGs contamination in soil.
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Affiliation(s)
- Shengnan Li
- Key Laboratory of Pollution Processes and Environmental Criteria at the Ministry of Education, Tianjin, China; Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Brim Stevy Ondon
- Key Laboratory of Pollution Processes and Environmental Criteria at the Ministry of Education, Tianjin, China; Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, 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
| | - Fengxiang Li
- Key Laboratory of Pollution Processes and Environmental Criteria at the Ministry of Education, Tianjin, China; Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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22
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Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes. Antibiotics (Basel) 2023; 12:antibiotics12020333. [PMID: 36830244 PMCID: PMC9952537 DOI: 10.3390/antibiotics12020333] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.
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23
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Bian J, Wang H, Ding H, Song Y, Zhang X, Tang X, Zhong Y, Zhao C. Unveiling the dynamics of antibiotic resistome, bacterial communities, and metals from the feces of patients in a typical hospital wastewater treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159907. [PMID: 36336059 DOI: 10.1016/j.scitotenv.2022.159907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/06/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Bacterial pathogens and antibiotic resistance genes (ARGs) are extensively disseminated into the environment via hospital wastewater (HWW), as it contains large quantities of feces from resident patients. However, studies on the antibiotic resistome and pathogenic bacteria from the gut of resident patients within the hospital wastewater treatment plant (hWWTP) are limited. Here, we examined and compared the occurrence and abundance of ARGs, mobile genetic elements (MGEs), metals, and bacterial communities from the feces of patients in a typical hWWTP system and determined the pathogenic hosts responsible for transferring ARGs. There were 176 ARGs and 43 MGEs detected in the feces of hospitalized patients, 129 genes were persistent, and 88 genes were enriched after HWW treatment, particularly for the blaVEB, blaNDM, and class 1 integron (intI1), with an average of 659-fold, 202-fold, and seven-fold enrichment, respectively. MGEs, especially Is613, in the feces of hospitalized patients were exceptionally abundant and even surpassed the abundance of total ARGs, which explained the persistence of ARGs in hWWTPs due to possible gene mobilization events. Bacteroidetes and Firmicutes were the most abundant phyla in these feces, accounting for 81 % of the total gut microbiota, while Epsilonbacteraeota and Proteobacteria dominated the hWWTPs. Additionally, 54 possible bacterial pathogens were found in the hospital environment, including four "ESKAPE" pathogens and 14 cancer-related pathogens. Many of them were strongly associated with different types of ARGs. Notably, Bacteroides was the major potential ARG-harboring pathogenic genus, as determined by the network analysis, and was highly abundant after the treatment. The altered microbial community was the major contributing factor shaping antibiotic resistome. This study might provide a comprehensive insight into the distribution profiles of ARGs and pathogens from the gut of inpatients throughout the HWW treatment system, which could be used as a reference for optimizing HWW treatment and monitoring public risk.
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Affiliation(s)
- Jing Bian
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, People's Republic of China; Department of Gastroenterology, Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing 400030, People's Republic of China
| | - Hang Wang
- Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming 650224, People's Republic of China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Haojie Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yunqian Song
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, People's Republic of China
| | - Xiaohui Zhang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, People's Republic of China
| | - Xianjun Tang
- Breast cancer Center, Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing 400030, People's Republic of China
| | - Yihua Zhong
- Department of Gastroenterology, Chongqing University Cancer Hospital, School of Medicine, Chongqing University, Chongqing 400030, People's Republic of China.
| | - Chun Zhao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, People's Republic of China.
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24
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Elarabi NI, Halema AA, Abdelhadi AA, Henawy AR, Samir O, Abdelhaleem HAR. Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater. AMB Express 2023; 13:14. [PMID: 36715862 PMCID: PMC9885416 DOI: 10.1186/s13568-023-01519-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes.
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Affiliation(s)
- Nagwa I. Elarabi
- grid.7776.10000 0004 0639 9286Genetics Department; Faculty of Agriculture, Cairo University, Giza, 12613 Egypt
| | - Asmaa A. Halema
- grid.7776.10000 0004 0639 9286Genetics Department; Faculty of Agriculture, Cairo University, Giza, 12613 Egypt ,grid.423564.20000 0001 2165 2866National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
| | - Abdelhadi A. Abdelhadi
- grid.7776.10000 0004 0639 9286Genetics Department; Faculty of Agriculture, Cairo University, Giza, 12613 Egypt ,grid.423564.20000 0001 2165 2866National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
| | - Ahmed R. Henawy
- grid.7776.10000 0004 0639 9286Department of Microbiology; Faculty of Agriculture, Cairo University, Giza, 12613 Egypt
| | - Omar Samir
- grid.428154.e0000 0004 0474 308XGenomic Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Heba A. R. Abdelhaleem
- grid.440875.a0000 0004 1765 2064Biotechnology College, Misr University for Science and Technology (MUST), 6(th) October City, Egypt
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25
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Gupta S, Graham DW, Sreekrishnan TR, Ahammad SZ. Heavy metal and antibiotic resistance in four Indian and UK rivers with different levels and types of water pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159059. [PMID: 36174689 DOI: 10.1016/j.scitotenv.2022.159059] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/04/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal pollution can enhance the level of antibiotic resistance, posing concerns to ecosystem and public health. Here, we investigated heavy metal concentrations, heavy metal resistant bacteria and antibiotic resistant bacteria and their corresponding resistant genes, and integrons in four different river environments, i.e., low heavy metals and low wastewater, high heavy metals and low wastewater, low heavy metals and high wastewater, and high heavy metals and high wastewater levels. Heavy metals were found to show positive and significant correlations with heavy metal resistance and antibiotic resistance and integrons (r > 0.60, p < 0.05), indicating that heavy metal selective pressure can cause heavy metal and antibiotic resistance to be transmitted simultaneously via integrons, which can result in the development of multi-resistant bacteria in the heavy metal-polluted environments. Moreover, there were significant associations between heavy metal resistance and antibiotic resistance (r > 0.60, p < 0.05), demonstrating heavy metal and antibiotic resistance are connected via a same or related mechanism. Class 1 integrons were found to have strong correlations with heavy metals and heavy metal resistance and antibiotic resistance (r > 0.60, p < 0.05), indicating a higher occurrence of antibiotic resistance co-selection in the heavy metal-polluted environments.
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Affiliation(s)
- Sonia Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - T R Sreekrishnan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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26
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Zhang S, Yang G, Jiang Y. Antibiotic and metal resistance of Stenotrophomonas maltophilia isolates from Eboling permafrost of the Tibetan Plateau. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:11798-11810. [PMID: 36097311 DOI: 10.1007/s11356-022-22888-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome sequencing of pathogenic bacteria Stenotrophomonas maltophilia from a less polluted environment of permafrost can help understand the intrinsic resistome of both antibiotics and metals. This study aimed to examine the maximum minimum inhibitory concentration (MIC) of both antibiotics and metals, as well as antibiotic resistance genes and metal resistance genes annotated from whole-genome sequences. The permafrost S. maltophilia was sensitive to ciprofloxacin, tetracycline, streptomycin, and bacitracin, and resistant to chloramphenicol, trimethoprim-sulfamethoxazole, erythromycin, Zn2+, Ni2+, Cu2+, and Cr6+, with a lower maximum MIC, compared with clinical S. maltophilia. The former strain belonged to the lower antibiotic resistance gene (ARG) and metal resistance gene (MRG) clusters compared with the latter ones. The permafrost strain contained no or only one kind of ARG or MRG on a single genomic island, which explained the aforementioned lower maximum MIC and less diversity of ARGs or MRGs. The result indicated that the co-occurrence of antibiotic and metal resistance was due to a certain innate ability of S. maltophilia. The continuous human use of antibiotics or metals induced selective pressure, resulting in higher MIC and more diverse ARGs and MRGs in human-impacted environments.
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Affiliation(s)
- Shuhong Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China.
| | - Guangli Yang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Yali Jiang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
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27
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Gaur VK, Sirohi R, Bhat MI, Gautam K, Sharma P, Srivastava JK, Pandey A. A review on the effect of micro- and nano-plastics pollution on the emergence of antimicrobial resistance. CHEMOSPHERE 2023; 311:136877. [PMID: 36257395 DOI: 10.1016/j.chemosphere.2022.136877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The recent upsurge in the studies on micro/nano plastics and antimicrobial resistance genes has proven their deleterious effects on the environmental and human health. Till-date, there is a scarcity of studies on the interactions of these two factors and their combined influence. The interaction of microplastics has led to the formation of new plastics namely plastiglomerates, pyroplastics. and anthropoquinas. It has long been ignored that the occurrence of microplastics has become a breeding ground for the emergence of antimicrobial resistance genes. Evidently microplastics are also associated with the occurrence of other pollutants such as polyaromatic hydrocarbons and pesticides. The increased use of antibiotics (after Covid breakout) has further elevated the detrimental effects on human health. Therefore, this study highlights the relation of microplastics with antibiotic resistance generation. The factors such as uncontrolled use of antibiotics and negligent plastic consumption has been evaluated. Furthermore, the future research prospective was provided that can be helpful in correctly identifying the seriousness of the environmental occurrence of these pollutants.
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Affiliation(s)
- Vivek Kumar Gaur
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India; School of Energy and Chemical Engineering, Ulsan National Institute for Science and Technology, Ulsan, 44919, Republic of Korea
| | - Ranjna Sirohi
- Department of Food Technology, School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, 248 007, Uttarakhand, India
| | - Mohd Ishfaq Bhat
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Krishna Gautam
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India
| | - Poonam Sharma
- Department of Bioengineering, Integral University, Lucknow, India
| | | | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, India.
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28
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Cultivable bacteria in the supraglacial lake formed after a glacial lake outburst flood in northern Pakistan. Int Microbiol 2022; 26:309-325. [PMID: 36484912 DOI: 10.1007/s10123-022-00306-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Recently, a supraglacial lake formed as a result of a glacial lake outburst flood (GLOF) in the Dook Pal Glacier. Lake debris and meltwater samples were collected from the supraglacial lake to determine bacterial diversity. Geochemical analyses of samples showed free amino acids (FAAs), anions, cations, and heavy metals. Comparable viable bacterial counts were observed in meltwater and debris samples. Using R2A media, a total of 52 bacterial isolates were identified: 40 from debris and 12 from meltwater. The relative abundance of Gram-positive (80.8%) bacteria was greater than Gram-negative (19.2%). Molecular identification of these isolates revealed that meltwater was dominated by Firmicutes (41.6%) and Proteobacteria (41.6%), while lake debris was dominated by Firmicutes (65.0%). The isolates belonged to 14 genera with the greatest relative abundance in Bacillus. Tolerance level of isolates to salts was high. Most of the Gram-positive bacteria were eurypsychrophiles, while most of the Gram-negative bacteria were stenopsychrophiles. Gram-negative bacteria displayed a higher minimum inhibitory concentration of selected heavy metals and antibiotics than Gram-positive. This first-ever study of culturable bacteria from a freshly formed supraglacial lake improves our understanding of the bacterial diversity and antibiotic resistance released from the glaciers as a result of GLOF.
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29
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Mukherji S, Imchen M, Mondal S, Bhattacharyya A, Siddhardha B, Kumavath R, Ghosh A. Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban. CHEMOSPHERE 2022; 309:136806. [PMID: 36220439 DOI: 10.1016/j.chemosphere.2022.136806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Sangita Mondal
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anish Bhattacharyya
- School of Biological Sciences, Division of Genomics and Evolution, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periye P.O., Kasaragod, Kerala, 671316, India; Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014 India.
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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Khoo SC, Goh MS, Alias A, Luang-In V, Chin KW, Ling Michelle TH, Sonne C, Ma NL. Application of antimicrobial, potential hazard and mitigation plans. ENVIRONMENTAL RESEARCH 2022; 215:114218. [PMID: 36049514 PMCID: PMC9422339 DOI: 10.1016/j.envres.2022.114218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/06/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The tremendous rise in the consumption of antimicrobial products had aroused global concerns, especially in the midst of pandemic COVID-19. Antimicrobial resistance has been accelerated by widespread usage of antimicrobial products in response to the COVID-19 pandemic. Furthermore, the widespread use of antimicrobial products releases biohazardous substances into the environment, endangering the ecology and ecosystem. Therefore, several strategies or measurements are needed to tackle this problem. In this review, types of antimicrobial available, emerging nanotechnology in antimicrobial production and their advanced application have been discussed. The problem of antimicrobial resistance (AMR) due to antibiotic-resistant bacteria (ARB)and antimicrobial resistance genes (AMG) had become the biggest threat to public health. To deal with this problem, an in-depth discussion of the challenges faced in antimicrobial mitigations and potential alternatives was reviewed.
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Affiliation(s)
- Shing Ching Khoo
- Henan Province Engineering Research Centre for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; BIOSES Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Meng Shien Goh
- Henan Province Engineering Research Centre for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; BIOSES Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Amirah Alias
- Eco-Innovation Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Vijitra Luang-In
- Natural Antioxidant Innovation Research Unit, Department of Biotechnology, Faculty of Technology, Mahasarakham University, Khamriang, Kantarawichai, Maha Sarakham, 44150, Thailand
| | - Kah Wei Chin
- BIOSES Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Tiong Hui Ling Michelle
- BIOSES Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Christian Sonne
- Henan Province Engineering Research Centre for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark.
| | - Nyuk Ling Ma
- Henan Province Engineering Research Centre for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; BIOSES Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
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Robins K, McCann CM, Zhou XY, Su JQ, Cooke M, Knapp CW, Graham DW. Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157512. [PMID: 35872194 DOI: 10.1016/j.scitotenv.2022.157512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10-7 to 1.0 × 10-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10-6 to 2.85 × 10-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Clare M McCann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Xin-Yuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Martin Cooke
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Charles W Knapp
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow G1 1XJ, United Kingdom.
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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Muhammad J, Xu P, Khan S, Su JQ, Sarwar T, Nazneen S, Khan A. Arsenic contribution of poultry manure towards soils and food plants contamination and associated cancer risk in Khyber Pakhtunkhwa, Pakistan. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:3321-3342. [PMID: 34542787 DOI: 10.1007/s10653-021-01096-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Exposure to high level of arsenic (As) through the ingestion of contaminated soil, dust and food plants can pose health risk to humans. This study investigates the total arsenic (As), arsenobetaine (AsB), monomethylarsenate (MMA), dimethylarsenate (DMA), arsenite (As3+) and arsenate (As5+) concentrations in poultry feed, manure, agricultural soils and food plants collected from Khyber Pakhtunkhwa Province, Pakistan. The total mean As concentrations in the edible parts of food plants ranged from 0.096 mg kg-1 to 1.25 mg kg-1 with percentile (P) values (P25-0.039, P50-0.0765, P75-0.165 1 mg kg-1 to P25-0.95, P50-1.23, P75-1.6 1 mg kg-1) and exceeded the food safety limit (0.1 mg kg-1) of Food & Agriculture Organization (FAO) and World Health Organization (WHO) in all plant species except Pisum sativum (pea) and Mentha arvensis (mint). The risk to human health was assessed through the average daily intake (ADI), hazards quotient (HQ), health risk index (HRI) and lifetime cancer risk (LTCR). The highest average daily intake of As via the ingestion of Malva neglecta (mallow, a leafy plant) was observed for adults and children. The ADI for adults and children (2.36 × 10-4 mg kg-1 day-1 and 6.33 × 10-4 mg kg-1 day-1) was about 13% and 5%, respectively, of the Bench Mark Dose Limit (BMDL0.5) of 3.00 × 10-3 mg kg-1 day-1 set by WHO. The HRI was 3 times more in the children (2.1) than the adults (0.79), posing non-cancer health risks (health risk index > 1) for children. The LTCR values were slightly higher (1.53 × 10-4) relative to USEPA and WHO limits (1 × 10-6 to 1 × 10-4) for children whereas a minimal cancer risk was observed for adults via consumption of selected food plants. The results showed that poultry manure can contaminate food plants that may lead to cancer and non-cancer risks in agricultural areas, Pakistan. Thus, it is important to minimize As concentration in poultry feed to safeguard human health and environment from adverse effects.
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Affiliation(s)
- Juma Muhammad
- Department of Environmental Sciences, University of Peshawar, Peshawar, 25120, Pakistan
- Department of Environmental Sciences, Shaheed Benazir Bhutto University, Sheringal, Dir Upper, Pakistan
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Ping Xu
- China National Rice Research Institute, Hangzhou, 310006, China
| | - Sardar Khan
- Department of Environmental Sciences, University of Peshawar, Peshawar, 25120, Pakistan.
| | - Jian Qiang Su
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Tasneem Sarwar
- Department of Environmental Sciences, University of Peshawar, Peshawar, 25120, Pakistan
| | - Shahla Nazneen
- Department of Environmental Sciences, University of Peshawar, Peshawar, 25120, Pakistan
| | - Alamgir Khan
- Department of Forestry, Shaheed Benazir Bhutto University, Sheringal, Dir Upper, Pakistan
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Jiao H, Huang Z, Chen Z, Wang H, Liu H, Wei Z. Lead removal in flue gas from sludge incineration by denitrification: Insights from metagenomics and metaproteomics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114059. [PMID: 36087469 DOI: 10.1016/j.ecoenv.2022.114059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Flue gas lead emission during sludge incineration damages to human health and ecological environment seriously. Therefore, a denitrifying bio-trickling filter (DNBTF) for lead removal in flue gas from sludge incineration was investigated. Lead removal efficiency was up to 90.7% in 60 days' operation. Lead speciation in biofilms of DNBTF consists of 84.27% residue lead, 15.18% organic bound lead, and less than 1% exchangeable and reducible lead. Lead resistant bacteria and lead resistant-denitrifying bacteria accounted for 85.04% and 58.25%, respectively. Lead resistant microorganisms(Pseudomonas, Azoarcus, Stappia, Pararhodobacter, Paracoccus, Azospirillum, Hyphomonas, Rhodobacter, Polymorphum, Brevunimonas, Stenotrophomonas) could resist the toxicity of Pb2+ in flue gas by transport protein and binding protein, and detoxify Pb2+ in flue gas by extracellular polymeric substances (EPS) adsorption, protein binding and precipitation under the action of resistance genes, such as pbrAB, golT, troABCD, znuABC, czcABCD, pcoB, copA, as shown by integrated metagenomic and metaproteomic analyses. The biofilm was characterized by FTIR, XRD, 3D-EEM, and SEM-EDS. XRD and SEM-EDS spectra indicated the formation of pyromorphite from bioconversion of lead in flue gas. Lead-containing flue gas was bio-stabilized in the form of pyromorphite and HA-Pb via complexation of humic acids in extracellular polymeric substances (EPS), biosorption and biodeposition. This provides a new way of sludge incineration flue gas lead removal using a denitrifying biotricking filter.
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Affiliation(s)
- Huaiyong Jiao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Zhenshan Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Zhuoyao Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Huiying Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Haixu Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Zaishan Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China.
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Hazra M, Joshi H, Williams JB, Watts JEM. Antibiotics and antibiotic resistant bacteria/genes in urban wastewater: A comparison of their fate in conventional treatment systems and constructed wetlands. CHEMOSPHERE 2022; 303:135148. [PMID: 35640694 DOI: 10.1016/j.chemosphere.2022.135148] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/09/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
There is a growing concern that the use and misuse of antibiotics can increase the detection of antibiotic resistant genes (ARGs) in wastewater. Conventional wastewater treatment plants provide a pathway for ARGs and antibiotic resistant bacteria (ARB) to be released into natural water bodies. Research has indicated that conventional primary and secondary treatment systems can reduce ARGs/ARB to varying degrees. However, in developing/low-income countries, only 8-28% of wastewater is treated via conventional treatment processes, resulting in the environment being exposed to high levels of ARGs, ARB and pharmaceuticals in raw sewage. The use of constructed wetlands (CWs) has the potential to provide a low-cost solution for wastewater treatment, with respect to removal of nutrients, pathogens, ARB/ARGs either as a standalone treatment process or when integrated with conventional treatment systems. Recently, CWs have also been employed for the reduction of antibiotic residues, pharmaceuticals, and emerging contaminants. Given the benefits of ARG removal, low cost of construction, maintenance, energy requirement, and performance efficiencies, CWs offer a promising solution for developing/low-income countries. This review promotes a better understanding of the performance efficiency of treatment technologies (both conventional systems and CWs) for the reduction of antibiotics and ARGs/ARB from wastewater and explores workable alternatives.
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Affiliation(s)
- Moushumi Hazra
- Department of Hydrology, Indian Institute of Technology, Roorkee, Uttarakhand, India.
| | - Himanshu Joshi
- Department of Hydrology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - John B Williams
- School of Civil Engineering and Surveying, University of Portsmouth, United Kingdom
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, United Kingdom
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Gupta S, Graham DW, Sreekrishnan TR, Ahammad SZ. Effects of heavy metals pollution on the co-selection of metal and antibiotic resistance in urban rivers in UK and India. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119326. [PMID: 35491000 DOI: 10.1016/j.envpol.2022.119326] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Heavy metal pollution and the potential for co-selection of resistance to antibiotics in the environment is growing concern. However, clear associations between heavy metals and antibiotic resistance in river systems have not been developed. Here we investigated relationships between total and bioavailable heavy metals concentrations; metal resistance gene (MRG) and antibiotic resistance gene (ARG) abundances; mobile genetic elements; and the composition of local bacterial communities in low and high metal polluted rivers in UK and India. The results indicated that MRGs conferring resistance to cobalt (Co) and nickel (Ni) (rcnA), and Co, zinc (Zn), and cadmium (Cd) (czcA), and ARGs conferring resistance to carbapenem and erythromycin were the dominating resistant genes across the samples. The relative MRGs, ARGs, and integrons abundances tended to increase at high metal polluted environments, suggesting high metals concentrations have a strong potential to promote metal and antibiotic resistance by horizontal gene transmission and affecting bacterial communities, leading to the development of multi-metal and multi-antibiotic resistance. Network analysis demonstrated the positive and significant relationships between MRGs and ARGs as well as the potential for integrons playing a role in the co-transmission of MRGs and ARGs (r > 0.80, p < 0.05). Additionally, the major host bacteria of various MRGs and ARGs that could be accountable for greater MRGs and ARGs levels at high metal polluted environments were also identified by network analysis. Spearman's rank-order correlations and RDA analysis further confirm relationships between total and bioavailable heavy metals concentrations and the relative MRG, ARG, and integron abundances, as well as the composition of related bacterial communities (r > 0.80 (or < -0.80), p < 0.05). These findings are critical for assessing the possible human health concerns associated with metal-driven antibiotic resistance and highlight the need of considering metal pollution for developing appropriate measures to control ARG transmission.
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Affiliation(s)
- Sonia Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom
| | - T R Sreekrishnan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shaikh Ziauddin Ahammad
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Zhou S, Xiong C, Su Y, Wang Y, Gao Y, Tang Z, Liu B, Wu Y, Duan Y. Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: Distribution and influencing factors. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119158. [PMID: 35304179 DOI: 10.1016/j.envpol.2022.119158] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Both heavy metals and radiation could affect the proliferation and dissemination of emerging antibiotic resistance pollutants. As an environmental medium rich in radioactive metals, the profile of antibiotic resistance in uranium mine remains largely unknown. A uranium mine in Guangdong province, China was selected to investigate the distribution and influencing factors of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) including intracellular ARGs (iARGs), adsorbed-extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs). The result indicated that sulfonamide and tetracycline ARB could be generally detected in mining area with the absolute concentrations of 7.70 × 102-5.18 × 105 colony forming unit/g. The abundances of aeARGs in mine soil were significantly higher than those of iARGs (p < 0.05), highlighting the critical contribution of aeARGs to ARGs spread. The feARGs in mine drainage and its receiving river were abundant (3.38 × 104-1.86 × 107 copies/mL). ARB, aeARGs, and iARGs may correlate with nitrogen species and heavy metals (e.g., U and Mn), and feARGs presented a significant correlation with chemical oxygen demand (p < 0.05). These findings demonstrate the occurrence of ARB and ARGs in uranium mine for the first time, thereby contributing to the assessment and control of the ecological risk of antibiotic resistance in radioactive environments.
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Affiliation(s)
- Shuai Zhou
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; School of Civil Engineering, University of South China, Hengyang, 421001, China; Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Cong Xiong
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yinglong Su
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yuanyuan Gao
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Zhenping Tang
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang, 421001, China
| | - Boyang Liu
- School of Civil Engineering, University of South China, Hengyang, 421001, China
| | - Yueyue Wu
- Institute of Pathogenic Biology, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Yi Duan
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, University of South China, Hengyang, 421001, China; School of Civil Engineering, University of South China, Hengyang, 421001, China.
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Liu C, Li G, Qin X, Xu Y, Wang J, Wu G, Feng H, Ye J, Zhu C, Li X, Zheng X. Profiles of antibiotic- and heavy metal-related resistance genes in animal manure revealed using a metagenomic analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113655. [PMID: 35617901 DOI: 10.1016/j.ecoenv.2022.113655] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Farmed animals produce excrement containing excessive amounts of toxic heavy metals as a result of consuming compound feed as well as receiving medical treatments, and the presence of these heavy metals may aggravate the risk of spreading drug-resistance genes through co-selection during manure treatment and application processes. However, research on the association between heavy metals and antimicrobial resistance is still lacking. In this study, metagenomic sequencing was used to explore the effects of the co-selection of environmentally toxic heavy metals on the resistome in manure. A relevance network analysis showed that metal-resistance genes (MRGs), especially for copper (Cu) and zinc (Zn), were positively correlated with multiple types of antibiotic-resistance genes (ARGs) and formed a complex network. Most bacteria that co-occurred with both MRGs and ARGs simultaneously are members of Proteobacteria and accounted for 54.7% of the total microbial species in the relevance network. The remaining bacteria belonged to Firmicutes, Bacteroidetes and Actinobacteria. Among the four phyla, Cu- and Zn-resistance genes had more complex correlations with ARGs than other MRG types, reflecting the occurrence of ARG co-selection under the selective pressure of high Cu and Zn levels. In addition, approximately 64.8%, 59.1% and 68.4% of MRGs that correlated with the presence of plasmids, viruses and prophages, respectively, are Cu- or Zn-resistant, and they co-occurred with various ARGs, indicating that mobile genetic elements participate in mediating ARG co-selection in response to Cu and Zn pressure. The results indicated that the use of heavy-metal additives in feed induces the increases of drug resistance genes in manure through co-selection, aggravating the risk of antimicrobial resistance diffusion from animal farm to manure land applications.
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Affiliation(s)
- Chong Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guichun Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaobo Qin
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yansheng Xu
- Biogas Institute of Ministry of Agriculture and Rual Affairs, Chengdu, China
| | - Jiarui Wang
- Agro-environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Guosheng Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huabing Feng
- Division of Veterinary Medicine and Devices, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jing Ye
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohua Li
- Agro-environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China; Rural Energy & Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, China.
| | - Xiangqun Zheng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China; Agro-environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China.
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Najar IN, Das S, Kumar S, Sharma P, Mondal K, Sherpa MT, Thakur N. Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus. Front Microbiol 2022; 13:914037. [PMID: 36110304 PMCID: PMC9469766 DOI: 10.3389/fmicb.2022.914037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Hot springs are thought to be potential repositories for opportunistic infections, such as antibiotic-resistant strains. However, there is a scarcity of information on the mechanisms of antibiotic resistance gene (ARG) uptake, occurrence, and expression in thermophilic bacteria. Furthermore, because the genesis and proliferation of ARGs in environmental microorganisms are unknown, the research on antibiotic resistance profiles and probable mechanisms in thermophilic bacteria will become increasingly important. The goals of this study are to explore bacterial diversity, antibiotic and heavy metal resistance, and the prevalence and presence of ARG and metal resistance gene (MRG) in Geobacillus species. The 16S rRNA sequencing was used to determine the culturable bacterium diversity of 124 isolates. Standard Kirby Bauer Disc Diffusion and tube dilution procedures were used to determine antibiotic sensitivity and minimum inhibitory concentration (MIC). The tube dilution method was also used to check metal tolerance. To detect ARG and heavy MRG (HMRG), whole genome sequencing studies of the type species of the genus Geobacillus and five randomly selected Geobacillus species were performed. Graph Pad Prism and XLSTAT were used to perform statistical analyses such as ANOVA, EC50 analysis, and principal component analysis (PCA). The phylum Firmicutes and the genus Geobacillus dominated the culture-dependent bacterial diversity. Surprisingly, all thermophilic isolates, i.e., Geobacillus species, were sensitive to at least 10 different antibiotics, as evidenced by the lack of ARGs in whole genome sequencing analysis of numerous Geobacillus species. However, some of these isolates were resistant to at least five different heavy metals, and whole genome sequencing revealed the presence of MRGs in these thermophilic bacteria. The thermophilic genus Geobacillus is generally antibiotic sensitive, according to this study. In contrast, heavy metal is tolerated by them. As a result, it is possible that ARGs and MRGs do not coexist in these bacteria living in hot springs.
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Affiliation(s)
| | - Sayak Das
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Santosh Kumar
- Department of Microbiology, Sikkim University, Gangtok, India
| | - Prayatna Sharma
- Department of Microbiology, Sikkim University, Gangtok, India
| | | | | | - Nagendra Thakur
- Department of Microbiology, Sikkim University, Gangtok, India
- *Correspondence: Nagendra Thakur
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Álvarez-Marín MT, Zarzuela L, Camacho EM, Santero E, Flores A. Detection by metagenomic functional analysis and improvement by experimental evolution of β-lactams resistance genes present in oil contaminated soils. Sci Rep 2022; 12:10059. [PMID: 35768448 PMCID: PMC9243250 DOI: 10.1038/s41598-022-13883-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
The spread of antibiotic resistance genes has become a global health concern identified by the World Health Organization as one of the greatest threats to health. Many of antimicrobial resistance determinants found in bacterial pathogens originate from environmental bacteria, so identifying the genes that confer resistance to antibiotics in different habitats is mandatory to better understand resistance mechanisms. Soil is one of the most diverse environments considered reservoir of antimicrobial resistance genes. The aim of this work is to study the presence of genes that provide resistance to antibiotics used in clinical settings in two oil contaminated soils by metagenomic functional analysis. Using fosmid vectors that efficiently transcribe metagenomic DNA, we have selected 12 fosmids coding for two class A β-lactamases, two subclass B1 and two subclass B3 metallo-β-lactamases, one class D β-lactamase and three efflux pumps that confer resistance to cefexime, ceftriaxone, meropenem and/or imipenem. In some of them, detection of the resistance required heterologous expression from the fosmid promoter. Although initially, these environmental genes only provide resistance to low concentrations of antibiotics, we have obtained, by experimental evolution, fosmid derivatives containing β-lactamase ORFs with a single base substitution, which substantially increase their β-lactamase activity and resistance level. None of the mutations affect β-lactamase coding sequences and are all located upstream of them. These results demonstrate the presence of enzymes that confer resistance to relevant β-lactams in these soils and their capacity to rapidly adapt to provide higher resistance levels.
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Affiliation(s)
- M Teresa Álvarez-Marín
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Laura Zarzuela
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Eva M Camacho
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain
| | - Amando Flores
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Carretera de Utrera, Km. 1, 41013, Sevilla, Spain.
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Dey S, Rout AK, Behera BK, Ghosh K. Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies. ENVIRONMENTAL MICROBIOME 2022; 17:32. [PMID: 35739580 PMCID: PMC9230103 DOI: 10.1186/s40793-022-00430-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/14/2022] [Indexed: 05/03/2023]
Abstract
It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.
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Affiliation(s)
- Sujata Dey
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Golapbag, Burdwan, West Bengal, 713104, India.
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Ghosh A, Saha R, Bhadury P. Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem. PeerJ 2022; 10:e13169. [PMID: 35573175 PMCID: PMC9097664 DOI: 10.7717/peerj.13169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/04/2022] [Indexed: 01/12/2023] Open
Abstract
Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.
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Affiliation(s)
- Anwesha Ghosh
- Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Ratul Saha
- Wildlife and Habitats Division, WWF-India Sundarbans Landscape, Kolkata, West Bengal, India
| | - Punyasloke Bhadury
- Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, India,Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, India
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Hung WC, Rugh M, Feraud M, Avasarala S, Kurylo J, Gutierrez M, Jimenez K, Truong N, Holden PA, Grant SB, Liu H, Ambrose RF, Jay JA. Influence of soil characteristics and metal(loid)s on antibiotic resistance genes in green stormwater infrastructure in Southern California. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127469. [PMID: 34655877 DOI: 10.1016/j.jhazmat.2021.127469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/14/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
The synergetic effects of metal(loid)s and soil characteristics on bacterial antibiotic resistance genes (ARGs) in green stormwater infrastructure (GSI) has been relatively understudied. Surface soil samples from six GSIs in Southern California over three time periods were assessed for selected ARGs, class 1 integron-integrase genes (intI1), 16S rRNA genes, and bioavailable and total concentrations of nine metal(loid)s, to investigate the relationships among ARGs, soil characteristics, and co-occurring metal(loid)s. Significant correlations existed among relative gene abundances (sul1, sul2, tetW, and intI1), total metal(loid)s (arsenic, copper, lead, vanadium, and zinc), and bioavailable metal(loid) (arsenic) (r = 0.29-0.61, padj < 0.05). Additionally, soil texture, organic matter, and nutrients within GSI appeared to be significantly correlated with relative gene abundances of sul1, sul2, and tetW (r = -0.57 to 0.59, padj < 0.05). Multiple regression models significantly improved the estimation of ARGs in GSI when considering multiple effects of soil characteristics and metal(loid)s (r = 0.74, padj < 0.001) compared to correlation results. Total arsenic was a significant (positive) correlate in all the regression models of relative gene abundances. This work provides new insights into co-dependencies between GSI ARGs and co-occurring metal(loid)s, indicating the need for risk assessment of metal(loid)-influenced ARG proliferation.
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Affiliation(s)
- Wei-Cheng Hung
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA
| | - Megyn Rugh
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA
| | - Marina Feraud
- Bren School of Environmental Science and Management, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Sumant Avasarala
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37916, USA
| | - Jessica Kurylo
- Department of Environmental Health Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Mathew Gutierrez
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA
| | - Karina Jimenez
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA
| | - Nhi Truong
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA
| | - Patricia A Holden
- Bren School of Environmental Science and Management, UC Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stanley B Grant
- Occoquan Watershed Monitoring Laboratory, The Charles E. Via Jr. Department of Civil and Environmental Engineering, Virginia Tech, 9408 Prince William Street, Manassas, VA 20110, USA; Center for Coastal Studies, Virginia Tech, 1068A Derring Hall (0420), Blacksburg, VA 24061, USA
| | - Haizhou Liu
- Department of Chemical and Environmental Engineering, Bourns Hall A239, UC Riverside, Riverside, CA 92521, USA
| | - Richard F Ambrose
- Department of Environmental Health Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, UCLA, Los Angeles, CA, 90095, USA.
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Peng S, Zheng H, Herrero-Fresno A, Olsen JE, Dalsgaard A, Ding Z. Co-occurrence of antimicrobial and metal resistance genes in pig feces and agricultural fields fertilized with slurry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148259. [PMID: 34147788 DOI: 10.1016/j.scitotenv.2021.148259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance constitutes a global challenge to public health. The common addition of Zn, Cu and other metals to animal feed and the widespread presence of metal ions in livestock and their receiving environments may be a factor that facilitates the proliferation of antimicrobial resistance via co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). However, the extent of co-selection is not yet fully understood. In this study, we used a metagenomic approach to profile ARGs, MRGs and mobile genetic elements (MGEs) known to constitute potential ARG and MRG vectors of transmission, and we determined the concentration of metal ions to assess the interrelationships between the occurrence of ARGs, MRGs and metal concentrations in samples from pig farms in China. Samples analyzed included fresh pig feces, soils fertilized with treated slurry, and sediments from aquatic environments, where effluent from treated slurry was discharged. Resistance genes to tetracycline and zinc were the most commonly observed ARGs and MRGs for all three types of samples. Significant correlations were observed between the abundance of ARGs and MRGs, and between ARGs/MRGs and MGEs, and between metal and ARGs/MGEs as documented by Pearson's correlation analysis (r > 0.9, P < 0.001). Further network analysis revealed significant co-occurrence between specific ARGs and MRGs, between ARGs/MRGs and MGEs, and between specific metals (Zn, Cr, and Mn) and ARGs and MGEs. Collectively, our findings demonstrate a high level of co-occurrence of antimicrobial and metal resistance genes in slurry from pig farms and their surrounding environments. The results suggest that metals added to pig feed might facilitate co-selection of ARGs and MGEs in the pig production environments, thereby resulting in a bigger pool of mobile ARGs.
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Affiliation(s)
- Shifu Peng
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Hao Zheng
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore.
| | - Zhen Ding
- Department of Environment and Health, Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China.
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Zhao Y, Hu HW, Su JQ, Hao X, Guo H, Liu YR, Zhu YG. Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13913-13922. [PMID: 34613706 DOI: 10.1021/acs.est.1c04030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.
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Affiliation(s)
- Yi Zhao
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Xiuli Hao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaming Guo
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
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Uluseker C, Kaster KM, Thorsen K, Basiry D, Shobana S, Jain M, Kumar G, Kommedal R, Pala-Ozkok I. A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives. Front Microbiol 2021; 12:717809. [PMID: 34707579 PMCID: PMC8542863 DOI: 10.3389/fmicb.2021.717809] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/15/2021] [Indexed: 11/15/2022] Open
Abstract
This paper reviews current knowledge on sources, spread and removal mechanisms of antibiotic resistance genes (ARGs) in microbial communities of wastewaters, treatment plants and downstream recipients. Antibiotic is the most important tool to cure bacterial infections in humans and animals. The over- and misuse of antibiotics have played a major role in the development, spread, and prevalence of antibiotic resistance (AR) in the microbiomes of humans and animals, and microbial ecosystems worldwide. AR can be transferred and spread amongst bacteria via intra- and interspecies horizontal gene transfer (HGT). Wastewater treatment plants (WWTPs) receive wastewater containing an enormous variety of pollutants, including antibiotics, and chemicals from different sources. They contain large and diverse communities of microorganisms and provide a favorable environment for the spread and reproduction of AR. Existing WWTPs are not designed to remove micropollutants, antibiotic resistant bacteria (ARB) and ARGs, which therefore remain present in the effluent. Studies have shown that raw and treated wastewaters carry a higher amount of ARB in comparison to surface water, and such reports have led to further studies on more advanced treatment processes. This review summarizes what is known about AR removal efficiencies of different wastewater treatment methods, and it shows the variations among different methods. Results vary, but the trend is that conventional activated sludge treatment, with aerobic and/or anaerobic reactors alone or in series, followed by advanced post treatment methods like UV, ozonation, and oxidation removes considerably more ARGs and ARB than activated sludge treatment alone. In addition to AR levels in treated wastewater, it examines AR levels in biosolids, settled by-product from wastewater treatment, and discusses AR removal efficiency of different biosolids treatment procedures. Finally, it puts forward key-points and suggestions for dealing with and preventing further increase of AR in WWTPs and other aquatic environments, together with a discussion on the use of mathematical models to quantify and simulate the spread of ARGs in WWTPs. Mathematical models already play a role in the analysis and development of WWTPs, but they do not consider AR and challenges remain before models can be used to reliably study the dynamics and reduction of AR in such systems.
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Affiliation(s)
- Cansu Uluseker
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Krista Michelle Kaster
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Kristian Thorsen
- Department of Electrical Engineering and Computer Science, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Daniel Basiry
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Sutha Shobana
- Department of Chemistry and Research Centre, Aditanar College of Arts and Science, Tiruchendur, India
| | - Monika Jain
- Department of Natural Resource Management, College of Forestry, Banda University of Agricultural and Technology, Banda, India
| | - Gopalakrishnan Kumar
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Roald Kommedal
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Ilke Pala-Ozkok
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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Zhuang M, Achmon Y, Cao Y, Liang X, Chen L, Wang H, Siame BA, Leung KY. Distribution of antibiotic resistance genes in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117402. [PMID: 34051569 DOI: 10.1016/j.envpol.2021.117402] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/03/2021] [Accepted: 05/16/2021] [Indexed: 05/12/2023]
Abstract
The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.
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Affiliation(s)
- Mei Zhuang
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, 515063, China; Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yigal Achmon
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, 515063, China; Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yuping Cao
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, 515063, China; Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Xiaomin Liang
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China; Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Bupe A Siame
- Department of Biology, Trinity Western University, Langley, British Columbia, V2Y 1Y1, Canada
| | - Ka Yin Leung
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou, 515063, China; Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States. Microbiol Spectr 2021; 9:e0009721. [PMID: 34431703 PMCID: PMC8552609 DOI: 10.1128/spectrum.00097-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know. To fill this knowledge gap, we present a comprehensive analysis of gut bacteria associated with wild cotton mice (Peromyscus gossypinus) trapped from several areas affected by legacies of HM and radionuclide contamination. We explore how these contaminants affect gut microbial community (GMC) composition and diversity and the enrichment of antibiotic, biocide, and metal resistance genes. Although we were able to identify that a myriad of co-occurring antimicrobial and HM resistance genes appear in mice from all areas, including those without a history of contamination, the proportions of co-occurring ARGs and metal resistance genes (MRGs) are higher in sites with radionuclide contamination. These results support those from several previous studies and enhance our understanding of the coselection process, while providing new insights into the ubiquity of antimicrobial resistance in the resistome of wild animals. IMPORTANCE Antimicrobial resistance is a serious global public health concern because of its prevalence and ubiquitous distribution. The rapid dissemination of antibiotic resistance genes is thought to be the result of the massive overuse of antibiotics in agriculture and therapeutics. However, previous studies have demonstrated that the spread of antibiotic resistance genes can also be influenced by heavy metal contamination. This coselection phenomenon, whereby different resistance determinants are genetically linked on the same genetic element (coresistance) or a single genetic element provides resistance to multiple antimicrobial agents (cross-resistance), has profound clinical and environmental implications. In contrast to antibiotics, heavy metals can persist in the environment as a selection pressure for long periods of time. Thus, it is important to understand how antibiotic resistance genes are distributed in the environment and to what extent heavy metal contaminants may be driving their selection, which we have done in one environmental setting.
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Narayanan M, Thangabalu R, Natarajan D, Kumarasamy S, Kandasamy S, Elfasakhany A, Pugazhendhi A. Reclamation competence of Crotalaria juncea with the amalgamation and influence of indigenous bacteria on a waste dump of bauxite mine. CHEMOSPHERE 2021; 279:130632. [PMID: 34134423 DOI: 10.1016/j.chemosphere.2021.130632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/11/2021] [Accepted: 04/16/2021] [Indexed: 05/16/2023]
Abstract
The accumulated bauxite mine soil had an acidic pH of 5.52 ± 0.12 and more heavy metals such as Cr, Cd, Zn, and Pb, which can cause severe soil and water pollution to the nearby farmlands and water reservoirs. Hence, the work was designed to find the possibility of reclamation of bauxite mine soil through Crotalaria juncea with the amalgamation of native metal degrading bacterial isolates. Out of 15 bacterial cultures, only 2 isolates (B3 and B14) showed excellent metal tolerance (for up to 750 mg L-1), solubilizing (15.27-38.7 mg kg-1) (including phosphate: 47.4 ± 1.79%), and degrading potential (22.8 ± 0.89 to 31.5 ± 1.6%) than the others. These B3 and B14 isolates were recognized as B. borstelensis UTM105 (1432 bp) and B. borstelensis AK2 (1494 bp) through molecular characterization. These isolates have produced a metal stress response protein (205-43 KDa molecular weight protein) during metal stress conditions. The phytoremediation competence of C. juncea under the influence of these bacterial isolates was assessed with various treatment (I-IV) schemes. The treatment IV (C. juncea with two bacterial isolates) showed substantial physiological and biochemical results compared with the control and the other treatments. The phytoremediation competence of C. juncea was also effective in treatment IV than the others. It reduced and extracted a reasonable quantity of metals from the bauxite mine soil. The intact results accomplished that these native metals tolerant, solubilizing, and degrading bacterial isolates, could be used as optimistic bacterial candidates in combination with C. juncea for the effective reclamation of metal enriched bauxite mine soil.
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Affiliation(s)
- Mathiyazhagan Narayanan
- PG and Research Centre in Biotechnology, MGR College, Adhiyamaan Educational and Research Institutions (AERI), Hosur, Krishnagiri, Tamil Nadu, India
| | - Ramar Thangabalu
- Department of Biotechnology, Periyar University, Salem, Tamil Nadu, India
| | | | - Suresh Kumarasamy
- PG and Research Centre in Biotechnology, MGR College, Adhiyamaan Educational and Research Institutions (AERI), Hosur, Krishnagiri, Tamil Nadu, India
| | | | - Ashraf Elfasakhany
- Mechanical Engineering Department, College of Engineering, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Arivalagan Pugazhendhi
- School of Renewable Energy, Maejo University, Chiang Mai, 50290, Thailand; College of Medical and Health Science, Asia University, Taichung, Taiwan.
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Environmental antimicrobial resistance and its drivers: a potential threat to public health. J Glob Antimicrob Resist 2021; 27:101-111. [PMID: 34454098 DOI: 10.1016/j.jgar.2021.08.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/21/2023] Open
Abstract
Imprudent and overuse of clinically relevant antibiotics in agriculture, veterinary and medical sectors contribute to the global epidemic increase in antimicrobial resistance (AMR). There is a growing concern among researchers and stakeholders that the environment acts as an AMR reservoir and plays a key role in the dissemination of antimicrobial resistance genes (ARGs). Various drivers are contributing factors to the spread of antibiotic-resistant bacteria and their ARGs either directly through antimicrobial drug use in health care, agriculture/livestock and the environment or antibiotic residues released from various domestic settings. Resistant micro-organisms and their resistance genes enter the soil, air, water and sediments through various routes or hotspots such as hospital wastewater, agricultural waste or wastewater treatment plants. Global mitigation strategies primarily involve the identification of high-risk environments that are responsible for the evolution and spread of resistance. Subsequently, AMR transmission is affected by the standards of infection control, sanitation, access to clean water, access to assured quality antimicrobials and diagnostics, travel and migration. This review provides a brief description of AMR as a global concern and the possible contribution of different environmental drivers to the transmission of antibiotic-resistant bacteria or ARGs through various mechanisms. We also aim to highlight the key knowledge gaps that hinder environmental regulators and mitigation strategies in delivering environmental protection against AMR.
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Rothrock MJ, Min BR, Castleberry L, Waldrip H, Parker D, Brauer D, Pitta D, Indugu N. Antibiotic resistance, antimicrobial residues, and bacterial community diversity in pasture-raised poultry, swine, and beef cattle manures. J Anim Sci 2021; 99:6263936. [PMID: 33944927 DOI: 10.1093/jas/skab144] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Animal manure can be a source of antibiotic-resistant genes (ARGs) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABRs) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine, and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARGs (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR (real-time PCR). Results indicated that the ARG abundances (Sul1 [P < 0.05] and TetA [P < 0.001]) were higher in layer hen manures (16.5 × 10-4 and 1.4 × 10-4 µg kg-1, respectively) followed by broiler chickens (2.9 × 10-4 and 1.7 × 10-4 µg kg-1, respectively), swine (0.22 × 10-4 and 0.20 × 10-4 µg kg-1, respectively) and beef cattle (0.19 × 10-4 and 0.02 × 10-4 µg kg-1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg-1) than for other animal species (1.8 to 0.06 µg kg-1), while chlortetracycline, lincomycin, and oxytetracycline ABRs were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic-resistant microorganisms (ARMs) and ARG.
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Affiliation(s)
| | - Byeng Ryel Min
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Lana Castleberry
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Heidi Waldrip
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - David Parker
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - David Brauer
- USDA-ARS, Conservation and Production Research Laboratory, Bushland, TX 79012, USA
| | - Dipti Pitta
- School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 16802, USA
| | - Nagaraju Indugu
- School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 16802, USA
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