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Cheng ZH, Luo XY, Liu DF, Han J, Wang HD, Min D, Yu HQ. Optimized Antibiotic Resistance Genes Monitoring Scenarios Promote Sustainability of Urban Water Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9636-9645. [PMID: 38770702 DOI: 10.1021/acs.est.4c02048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dissemination of antibiotic resistance genes (ARGs) in urban water bodies has become a significant environmental and health concern. Many approaches based on real-time quantitative PCR (qPCR) have been developed to offer rapid and highly specific detection of ARGs in water environments, but the complicated and time-consuming procedures have hindered their widespread use. Herein, we developed a facile one-step approach for rapid detection of ARGs by leveraging the trans-cleavage activity of Cas12a and recombinase polymerase amplification (RPA). This efficient method matches the sensitivity and specificity of qPCR and requires no complex equipment. The results show a strong correlation between the prevalence of four ARG markers (ARGs: sul1, qnrA-1, mcr-1, and class 1 integrons: intl1) in tap water, human urine, farm wastewater, hospital wastewater, municipal wastewater treatment plants (WWTPs), and proximate natural aquatic ecosystems, indicating the circulation of ARGs within the urban water cycle. Through monitoring the ARG markers in 18 WWTPs in 9 cities across China during both peak and declining stages of the COVID epidemic, we found an increased detection frequency of mcr-1 and qnrA-1 in wastewater during peak periods. The ARG detection method developed in this work may offer a useful tool for promoting a sustainable urban water cycle.
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Affiliation(s)
- Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xi-Yan Luo
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Jing Han
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Hao-Da Wang
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Di Min
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
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Wilson GJL, Perez-Zabaleta M, Owusu-Agyeman I, Kumar A, Ghosh A, Polya DA, Gooddy DC, Cetecioglu Z, Richards LA. Discovery of sulfonamide resistance genes in deep groundwater below Patna, India. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124205. [PMID: 38797351 DOI: 10.1016/j.envpol.2024.124205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Global usage of pharmaceuticals has led to the proliferation of bacteria that are resistant to antimicrobial treatments, creating a substantial public health challenge. Here, we investigate the emergence of sulfonamide resistance genes in groundwater and surface water in Patna, a rapidly developing city in Bihar, India. We report the first quantification of three sulfonamide resistance genes (sulI, sulII and sulIII) in groundwater (12-107 m in depth) in India. The mean relative abundance of gene copies was found to be sulI (2.4 × 10-2 copies/16S rRNA gene) > sulII (5.4 × 10-3 copies/16S rRNA gene) > sulIII (2.4 × 10-3 copies/16S rRNA gene) in groundwater (n = 15) and surface water (n = 3). A comparison between antimicrobial resistance (AMR) genes and wastewater indicators, particularly tryptophan:fulvic-like fluorescence, suggests that wastewater was associated with AMR gene prevalence. Urban drainage channels, containing hospital and domestic wastes, are likely a substantial source of antimicrobial resistance in groundwater and surface water, including the Ganges (Ganga) River. This study is a reference point for decision-makers in the fight against antimicrobial resistance because it quantifies and determines potential sources of AMR genes in Indian groundwater.
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Affiliation(s)
- George J L Wilson
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Williamson Building, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Mariel Perez-Zabaleta
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Isaac Owusu-Agyeman
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Arun Kumar
- Mahavir Cancer Sansthan and Research Center, Phulwarisharif, Patna, 801505, Bihar, India
| | - Ashok Ghosh
- Mahavir Cancer Sansthan and Research Center, Phulwarisharif, Patna, 801505, Bihar, India
| | - David A Polya
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Williamson Building, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Daren C Gooddy
- British Geological Survey, Maclean Building, Wallingford, Oxfordshire, OX10 8BB, United Kingdom
| | - Zeynep Cetecioglu
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Laura A Richards
- Department of Earth and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Williamson Building, Oxford Road, Manchester, M13 9PL, United Kingdom.
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Fadare FT, Fadare TO, Okoh AI. Prevalence, molecular characterization of integrons and its associated gene cassettes in Klebsiella pneumoniae and K. oxytoca recovered from diverse environmental matrices. Sci Rep 2023; 13:14373. [PMID: 37658232 PMCID: PMC10474106 DOI: 10.1038/s41598-023-41591-7] [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: 07/18/2022] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
The high prevalence of infections arising from Klebsiella species is related to their ability to acquire and disseminate exogenous genes associated with mobile genetic elements such as integrons. We assessed the prevalence, diversity, and associated gene cassettes (GCs) of integrons in Klebsiella species. The isolates recovered from wastewater and hospital effluents, rivers, and animal droppings were identified using the conventional Polymerase Chain Reaction (PCR) with primers targeting the gryA, pehX, and 16S-23S genes. The antimicrobial resistance profile and the Extended-Spectrum and Metallo β-lactamases production were carried out using standard microbiological techniques. PCR, DNA sequencing analyses, and Restriction Fragment Length Polymorphism were used to characterize the integrons and their associated GCs. Furthermore, the genotypic relationships between the different isolated K. pneumoniae were determined using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR. About 98% (51/52) of the confirmed isolates harboured an integrase gene, with 80% intI1, while the remaining 20% concurrently harboured intI1 and intI2, with no intI3 observed. About 78% (40/51) of the bacterial strains were positive for a promoter, the P2R2, investigated, while 80% (41/51) harboured at least one of the qacEΔ1 and sul1. Three different GCs arrangements identified were aac(6')-Ib, aadA1-dfrA1, and dfrA1-sat2. At a similarity index of 60%, the ERIC-PCR fingerprints generated were categorized into nine clusters. Our study is the first to reveal the features of integrons in Klebsiella spp. recovered from environmental sources in the Eastern Cape Province, South Africa. We conclude that the organisms' sources are repositories of integrons harbouring various gene cassettes, which can be readily mobilized to other microorganisms in similar or varied niches.
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Affiliation(s)
- Folake Temitope Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa.
| | - Taiwo Olawole Fadare
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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Liguori K, Calarco J, Maldonado Rivera G, Kurowski A, Keenum I, Davis BC, Harwood VJ, Pruden A. Comparison of Cefotaxime-Resistant Escherichia coli and sul1 and intI1 by qPCR for Monitoring of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water. Antibiotics (Basel) 2023; 12:1252. [PMID: 37627672 PMCID: PMC10451376 DOI: 10.3390/antibiotics12081252] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Awareness of the need for surveillance of antimicrobial resistance (AMR) in water environments is growing, but there is uncertainty regarding appropriate monitoring targets. Adapting culture-based fecal indicator monitoring to include antibiotics in the media provides a potentially low-tech and accessible option, while quantitative polymerase chain reaction (qPCR) targeting key genes of interest provides a broad, quantitative measure across the microbial community. The purpose of this study was to compare findings obtained from the culture of cefotaxime-resistant (cefR) Escherichia coli with two qPCR methods for quantification of antibiotic resistance genes across wastewater, recycled water, and surface waters. The culture method was a modification of US EPA Method 1603 for E. coli, in which cefotaxime is included in the medium to capture cefR strains, while qPCR methods quantified sul1 and intI1. A common standard operating procedure for each target was applied to samples collected by six water utilities across the United States and processed by two laboratories. The methods performed consistently, and all three measures reflected the same overarching trends across water types. The qPCR detection of sul1 yielded the widest dynamic range of measurement as an AMR indicator (7-log versus 3.5-log for cefR E. coli), while intI1 was the most frequently detected target (99% versus 96.5% and 50.8% for sul1 and cefR E. coli, respectively). All methods produced comparable measurements between labs (p < 0.05, Kruskal-Wallis). Further study is needed to consider how relevant each measure is to capturing hot spots for the evolution and dissemination of AMR in the environment and as indicators of AMR-associated human health risk.
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Affiliation(s)
- Krista Liguori
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Jeanette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA (V.J.H.)
| | - Gabriel Maldonado Rivera
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Anna Kurowski
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Ishi Keenum
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Benjamin C. Davis
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA (V.J.H.)
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24060, USA (G.M.R.); (B.C.D.)
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Saha S, Xiong JQ, Patil SM, Ha GS, Hoh JK, Park HK, Chung W, Chang SW, Khan MA, Park HB, Jeon BH. Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131200. [PMID: 36958158 DOI: 10.1016/j.jhazmat.2023.131200] [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: 10/28/2022] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.
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Affiliation(s)
- Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Duluth, MN 55812, USA; Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong, China
| | - Swapnil M Patil
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Geon-Soo Ha
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Jeong-Kyu Hoh
- Department of Obstetrics and Gynecology, College of Medicine, Hanyang University, Seoul 04763, the Republic of Korea
| | - Hyun-Kyung Park
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, the Republic of Korea
| | - Woojin Chung
- Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, the Republic of Korea
| | - Soon Woong Chang
- Department of Environmental Energy Engineering, Kyonggi University, Suwon 16227, the Republic of Korea
| | - Moonis Ali Khan
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ho Bum Park
- Department of Energy Engineering, Hanyang University, Seoul 04763, the Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, the Republic of Korea.
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Haenelt S, Wang G, Kasmanas JC, Musat F, Richnow HH, da Rocha UN, Müller JA, Musat N. The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream. Front Microbiol 2023; 14:1058350. [PMID: 36760511 PMCID: PMC9907086 DOI: 10.3389/fmicb.2023.1058350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2. Methods Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene amplicon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ). Results Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1, sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and diversity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication. Discussion We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.
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Affiliation(s)
- Sarah Haenelt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Gangan Wang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jonas Coelho Kasmanas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,Isodetect Umweltmonitoring GmbH, Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jochen A. Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany,Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany,*Correspondence: Niculina Musat,
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Zhao CX, Su XX, Xu MR, An XL, Su JQ. Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 247:114282. [PMID: 36371907 DOI: 10.1016/j.ecoenv.2022.114282] [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: 07/11/2022] [Revised: 10/22/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.
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Affiliation(s)
- Cai-Xia Zhao
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Xuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, 400715 Chongqing, China
| | - Mei-Rong Xu
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li An
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Qiang Su
- Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Mustafa SS, Batool R, Kamran M, Javed H, Jamil N. Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods. Infect Drug Resist 2022; 15:5715-5728. [PMID: 36199818 PMCID: PMC9527703 DOI: 10.2147/idr.s368886] [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: 04/23/2022] [Accepted: 07/20/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Methodology Results Conclusion
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Affiliation(s)
- Syeda Samar Mustafa
- Institute of Microbiology and Molecular Genetics, Quaid e Azam Campus, University of the Punjab 54590, Lahore, Pakistan
- Correspondence: Syeda Samar Mustafa, Email
| | - Rida Batool
- Institute of Microbiology and Molecular Genetics, Quaid e Azam Campus, University of the Punjab 54590, Lahore, Pakistan
| | - Muhammad Kamran
- Queensland Alliance for Agriculture and Food Innovation Centre for Animal Science, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Hasnain Javed
- Provincial Public Health Reference Lab, Punjab AIDS Control Program, Lahore, Pakistan
| | - Nazia Jamil
- Institute of Microbiology and Molecular Genetics, Quaid e Azam Campus, University of the Punjab 54590, Lahore, Pakistan
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Raza S, Choi S, Lee M, Shin J, Son H, Wang J, Kim YM. Spatial and temporal effects of fish feed on antibiotic resistance in coastal aquaculture farms. ENVIRONMENTAL RESEARCH 2022; 212:113177. [PMID: 35346654 DOI: 10.1016/j.envres.2022.113177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
For the first time, both spatial and temporal effects of fish feed on changes in abundance of antibiotic resistance genes (ARGs) were investigated in South Korea via quantifying ARGs and analyzing physicochemical parameters in the influent (IN) and effluent before (BF) and 30 min after (AF) the fish feeding time of sixteen flow-through fish farms. The absolute abundance of ARGs in AF samples was 5 times higher than in BF and 12 times higher than in IN samples. Values of physicochemical parameters such as ammonia, total nitrogen, suspended solids and turbidity in the effluent significantly increased by 21.6, 4.2, 2.6 and 1.65 times, respectively, after fish feeding. Spatially, the fish farms on Jeju Island exhibited higher relative abundance (3.02 × 10-4 - 6.1 × 10-2) of ARGs compared to the farms in nearby Jeollanam-do (3.4 × 10-5 - 8.3 × 10-3). Seasonally, samples in summer and autumn showed a higher abundance of ARGs than in winter and spring. To assess risk to the food chain as well as public health, further studies are warranted to explore the pathogenic potential of these ARGs.
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Affiliation(s)
- Shahbaz Raza
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sangki Choi
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Minjeong Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Heejong Son
- Busan Water Quality Institute, Busan, 50804, Republic of Korea
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, China.
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul, 04763, Republic of Korea.
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Chigor CB, Ibangha IAI, Nweze NO, Onuora VC, Ozochi CA, Titilawo Y, Enebe MC, Chernikova TN, Golyshin PN, Chigor VN. Prevalence of integrons in multidrug-resistant Escherichia coli isolates from waters and vegetables in Nsukka and Enugu, Southeast Nigeria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60945-60952. [PMID: 35437658 DOI: 10.1007/s11356-022-20254-6] [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: 10/13/2021] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Irrigation of fresh produce with poorly treated wastewater or contaminated freshwater sources can lead to produce contamination and foodborne illnesses, as well as the dissemination of antimicrobial resistance determinants. In this study, we assessed the presence of integrons in multidrug-resistant Escherichia coli isolated from the University of Nigeria, Nsukka Wastewater Treatment Plant effluent, tap water, vegetables from irrigated gardens and vegetables sold in selected markets from Nsukka and Enugu cities. E. coli was isolated following standard laboratory procedure and confirmed through beta-glucuronidase (uidA)-targeted polymerase chain reaction (PCR). The antibiotic resistance of the isolates was determined using Bauer-Kirby disk diffusion assay, and multiplex PCR was used to determine the presence of class 1 and 2 integrons. Our result revealed a total of 188 E. coli isolates from WWTP effluent (n = 41), tap water (n = 10) and vegetables from greenhouse (n = 46), farms (n = 55) and market (n = 36). Multidrug resistance was detected in all the isolates, ranging from three-drug resistance in a single isolate to 7-drug resistance patterns in two different isolates. Of the total isolates, class 1 integrons were abundantly detected in 175 (93.1%) and class 2 in 5 (2.7%). All the class 2 integrons were found in isolates that were positive for class 1. The abundance of multidrug-resistant E. coli harbouring class 1 integrons in the effluent and vegetable samples is a potential public health risk. Therefore, the appropriate measures for the safe use of poorly treated wastewater for vegetable farm irrigation are required to be put in place to reduce the microbial load of the discharged effluent. Also, education of farmers and the community on the dangers of wastewater effluent-grown plants and proper methods for cleaning harvested vegetable is recommended.
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Affiliation(s)
- Chinyere B Chigor
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Plant Science and Biotechnology, Faculty of Biological Sciences, University Nigeria, Nsukka, Enugu State, Nigeria
| | - Ini-Abasi I Ibangha
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Nkechinyere O Nweze
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Plant Science and Biotechnology, Faculty of Biological Sciences, University Nigeria, Nsukka, Enugu State, Nigeria
| | - Valentino C Onuora
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Chizoba A Ozochi
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Yinka Titilawo
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Department of Microbiology, Alex Ekwueme Federal University, Ndufu-Alike Ikwo, Ebonyi State, Nigeria
| | - Matthew C Enebe
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | | | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor Gwynedd, UK
| | - Vincent N Chigor
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State, Nigeria.
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria.
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11
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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12
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Zieliński W, Korzeniewska E, Harnisz M, Drzymała J, Felis E, Bajkacz S. Wastewater treatment plants as a reservoir of integrase and antibiotic resistance genes - An epidemiological threat to workers and environment. ENVIRONMENT INTERNATIONAL 2021; 156:106641. [PMID: 34015664 DOI: 10.1016/j.envint.2021.106641] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 05/23/2023]
Abstract
Conventional mechanical and biological wastewater treatment is unable to completely eliminate all pollutants, which can therefore enter surface water bodies together with treated wastewater. In addition, bioaerosols produced during wastewater treatment can pose a threat to the health of the wastewater treatment plant staff. In order to control the impact of a wastewater treatment plant (WWTP) on the surrounding environment, including its employees, samples of wastewater and water from a river which received treated wastewater were analysed in terms of their content of antibiotics and heavy metals, levels of selected physiochemical parameters, concentrations of antibiotic-resistance genes (ARGs) and genes of integrases. Furthermore, a quantitative analysis of ARGs in the metagenomic DNA from nasal and throat swabs collected from the WWPT employees was made. Both untreated and treated wastewater samples were dominated by genes of resistance to sulphonamides (sul1, sul2), MLS group of drugs (ermF, ermB) and beta-lactams (blaOXA). A significant increase in the quantities of ARGs and concentrations of antibiotics was observed in the river following the discharge of treated wastewater in comparison to their amounts in the river water upstream from the point of discharge. Moreover, a higher concentration of ARGs was detected in the DNA from swabs obtained from the wastewater treatment plant employees than from ones collected from the control group. Many statistically significant (p < 0.05) correlations between the concentration of the gene of resistance to heavy metals cnrA versus ARGs, and between the ARGs content and the concentrations of heavy metals in both wastewater and river water samples were observed. The study has demonstrated that the mechanical and biological methods of wastewater treatment are not efficient and may affect the transmission of hazardous pollutants to the aquatic environment and to the atmospheric air. It has been shown that an activated sludge bioreactor can be a potential source of the presence of multi-drug resistant microorganisms in the air, which is a health risk to persons working in WWTPs. It has also been found that an environment polluted with heavy metals is where co-selection of antibiotic resistance may occur, in the development of which integrase genes play an essential role.
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Affiliation(s)
- Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland.
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland
| | - Justyna Drzymała
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland
| | - Ewa Felis
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Environmental Biotechnology Department, Faculty of Energy and Environmental Engineering, Silesian University of Technology, Akademicka 2 Str., 44-100 Gliwice, Poland
| | - Sylwia Bajkacz
- The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland
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13
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Czatzkowska M, Harnisz M, Korzeniewska E, Rusanowska P, Bajkacz S, Felis E, Jastrzębski JP, Paukszto Ł, Koniuszewska I. The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125773. [PMID: 33831706 DOI: 10.1016/j.jhazmat.2021.125773] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 05/23/2023]
Abstract
The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.
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Affiliation(s)
- Małgorzata Czatzkowska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Paulina Rusanowska
- Department of Environmental Engineering, University of Warmia and Mazury in Olsztyn, Warszawska 117a, 10-720 Olsztyn, Poland
| | - Sylwia Bajkacz
- Department of Inorganic, Analytical Chemistry and Electrochemistry, Silesian University of Technology, Krzywoustego 6, 44-100 Gliwice, Poland; Centre for Biotechnology, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Ewa Felis
- Department of Environmental Biotechnology, Silesian University of Technology, Akademicka 2, 44-100 Gliwice, Poland; Centre for Biotechnology, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Izabela Koniuszewska
- Department of Water Protection Engineering and Environmental Microbiology, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
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14
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Effects of Sulfamethoxazole on Growth and Antibiotic Resistance of A Natural Microbial Community. WATER 2021. [DOI: 10.3390/w13091262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Diffuse environmental antibiotic and antibiotic resistance gene contamination is increasing human and animal exposure to these emerging compounds with a consequent risk of reduction in antibiotic effectiveness. The present work investigated the effect of the antibiotic sulfamethoxazole (SMX) on growth and antibiotic resistance genes of a microbial community collected from an anaerobic digestion plant fed with cattle manure. Digestate samples were used as inoculum for concentration-dependent experiments using SMX at various concentrations. The antibiotic concentrations affecting the mixed microbial community in terms of growth and spread of resistant genes (sul1, sul2) were investigated through OD (Optical Density) measures and qPCR assays. Moreover, SMX biodegradation was assessed by LC-MS/MS analysis. The overall results showed that SMX concentrations in the range of those found in the environment did not affect the microbial community growth and did not select for antibiotic-resistant gene (ARG) maintenance or spread. Furthermore, the microorganisms tested were able to degrade SMX in only 24 h. This study confirms the complexity of antibiotic resistance spread in real matrices where different microorganisms coexist and suggests that antibiotic biodegradation needs to be included for fully understanding the resistance phenomena among bacteria.
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15
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Phiri AF, Abia ALK, Amoako DG, Mkakosya R, Sundsfjord A, Essack SY, Simonsen GS. Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi. Trop Med Infect Dis 2021; 6:tropicalmed6020063. [PMID: 33925030 PMCID: PMC8167763 DOI: 10.3390/tropicalmed6020063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
Although numerous studies have investigated diarrhoea aetiology in many sub-Saharan African countries, recent data on Shigella species’ involvement in community-acquired acute diarrhoea (CA-AD) in Malawi are scarce. This study investigated the incidence, antibiotic susceptibility profile, genotypic characteristics, and clonal relationships of Shigella flexneri among 243 patients presenting with acute diarrhoea at a District Hospital in Lilongwe, Malawi. Shigella spp. were isolated and identified using standard microbiological and serological methods and confirmed by identifying the ipaH gene using real-time polymerase chain reaction. The isolates’ antibiotic susceptibility to 20 antibiotics was determined using the VITEK 2 system according to EUCAST guidelines. Genes conferring resistance to sulfamethoxazole (sul1, sul2 and sul3), trimethoprim (dfrA1, dfrA12 and dfrA17) and ampicillin (oxa-1 and oxa-2), and virulence genes (ipaBCD, sat, ial, virA, sen, set1A and set1B) were detected by real-time PCR. Clonal relatedness was assessed using ERIC-PCR. Thirty-four Shigella flexneri isolates were isolated (an overall incidence of 14.0%). All the isolates were fully resistant to sulfamethoxazole/trimethoprim (100%) and ampicillin (100%) but susceptible to the other antibiotics tested. The sul1 (79%), sul2 (79%), sul3 (47%), dfrA12 (71%) and dfrA17 (56%) sulfonamide and trimethoprim resistance genes were identified; Oxa-1, oxa-2 and dfrA1 were not detected. The virulence genes ipaBCD (85%), sat (85%), ial (82%), virA (76%), sen (71%), stx (71%), set1A (26%) and set1B (18%) were detected. ERIC-PCR profiling revealed that the Shigella isolates were genetically distinct and clonally unrelated, indicating the potential involvement of genetically distinct S. flexneri in CA-AD in Malawi. The high percentage resistance to ampicillin and sulfamethoxazole/trimethoprim and the presence of several virulence determinants in these isolates emphasises a need for continuous molecular surveillance studies to inform preventive measures and management of Shigella-associated diarrhoeal infections in Malawi.
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Affiliation(s)
- Abel F.N.D. Phiri
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
- National Microbiology Reference Laboratory, Ministry of Health, Lilongwe 3, Malawi
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
- Correspondence:
| | - Daniel Gyamfi Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
| | - Rajab Mkakosya
- Department of Pathology, College of Medicine, University of Malawi, Blantyre 3, Malawi;
| | - Arnfinn Sundsfjord
- Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway; (A.S.); (G.S.S.)
- Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.F.N.D.P.); (D.G.A.); (S.Y.E.)
| | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway; (A.S.); (G.S.S.)
- Faculty of Health Sciences, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway
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16
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Flament-Simon SC, de Toro M, Chuprikova L, Blanco M, Moreno-González J, Salas M, Blanco J, Redrejo-Rodríguez M. High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains. Sci Rep 2020; 10:12452. [PMID: 32719405 PMCID: PMC7385651 DOI: 10.1038/s41598-020-69356-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus–host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria.
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Affiliation(s)
- Saskia-Camille Flament-Simon
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, CIBIR (Centro de Investigación Biomédica de La Rioja), La Rioja, 26006, Logroño, Spain
| | - Liubov Chuprikova
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Juan Moreno-González
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Margarita Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Modesto Redrejo-Rodríguez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Departamento de Bioquímica & Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.
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17
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Sauvêtre A, Węgrzyn A, Yang L, Vestergaard G, Miksch K, Schröder P, Radl V. Enrichment of endophytic Actinobacteria in roots and rhizomes of Miscanthus × giganteus plants exposed to diclofenac and sulfamethoxazole. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11892-11904. [PMID: 31981026 DOI: 10.1007/s11356-020-07609-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/01/2020] [Indexed: 06/10/2023]
Abstract
This study investigates how wastewater containing 2 mg l-1 of sulfamethoxazole (SMX) and 2 mg l-1 of diclofenac (DCF) affects the composition of bacterial communities present in the roots and rhizomes of Miscanthus × giganteus plants grown in laboratory-scale constructed wetlands. Bacterial communities in plant roots and rhizomes were identified in treated and control samples by 16S rRNA amplicon sequencing. Moreover, bacterial endophytes were isolated in R2A and 1/10 869 media and screened for their ability to metabolize SMX and DCF in liquid medium by HPLC. Our results show significant changes in the abundance of main genera, namely Sphingobium and Streptomyces between control and treated plants. Around 70% of the strains isolated from exposed plants belonged to the phylum Actinobacteria and were classified as Streptomyces, Microbacterium, and Glycomyces. In non-exposed plants, Proteobacteria represented 43.5% to 63.6% of the total. We identified 17 strains able to remove SMX and DCF in vitro. From those, 76% were isolated from exposed plants. Classified mainly as Streptomyces, they showed the highest SMX (33%) and DCF (41%) removal efficiency. These isolates, alone or in combination, might be used as bio-inoculants in constructed wetlands to enhance the phytoremediation of SMX and DCF during wastewater treatment.
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Affiliation(s)
- Andrés Sauvêtre
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- HydroSciences Montpellier, UMR 5569, Faculté de Pharmacie, University of Montpellier, Avenue Charles Flahault 15, 34000, Montpellier, France.
| | - Anna Węgrzyn
- Environmental Biotechnology Department, Faculty of Energy and Environmental Engineering, Silesian University of Technology, Gliwice, Poland., Konarskiego 18, 44-100, Gliwice, Poland
| | - Luhua Yang
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute for Microbiology, University of Copenhagen; Microbiology, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Korneliusz Miksch
- Environmental Biotechnology Department, Faculty of Energy and Environmental Engineering, Silesian University of Technology, Gliwice, Poland., Konarskiego 18, 44-100, Gliwice, Poland
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Viviane Radl
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
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18
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Nwaiwu O, Aduba CC. An in silico analysis of acquired antimicrobial resistance genes in Aeromonas plasmids. AIMS Microbiol 2020; 6:75-91. [PMID: 32226916 PMCID: PMC7099201 DOI: 10.3934/microbiol.2020005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022] Open
Abstract
Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.
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Affiliation(s)
- Ogueri Nwaiwu
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, United Kingdom
| | - Chiugo Claret Aduba
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria
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19
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Adelowo OO, Ikhimiukor OO, Knecht C, Vollmers J, Bhatia M, Kaster AK, Müller JA. A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance. PLoS One 2020; 15:e0229451. [PMID: 32130234 PMCID: PMC7055906 DOI: 10.1371/journal.pone.0229451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/06/2020] [Indexed: 01/30/2023] Open
Abstract
In many countries, emission of insufficiently treated wastewater into water bodies appears to be an important factor in spreading clinically relevant antimicrobial resistant bacteria. In this study, we looked for the presence of Enterobacteriaceae strains with resistance to 3rd generation cephalosporin antibiotics in four urban wetlands in southwestern Nigeria by isolation, whole genome sequencing and qPCR enumeration of marker genes. Genome analysis of multi-drug resistant and potentially pathogenic Escherichia coli isolates (members of the widely distributed ST10 complex) revealed the presence of the extended spectrum beta-lactamase gene blaCTX-M-15 on self-transmissible IncF plasmids. The gene was also present together with a blaTEM-1B gene on self-transmissible IncH plasmids in multi-drug resistant Enterobacter cloacae isolates. A Citrobacter freundii isolate carried blaTEM-1B on an IncR-type plasmid without discernable conjugation apparatus. All strains were isolated from a wetland for which previous qPCR enumeration of marker genes, in particular the ratio of intI1 to 16S rRNA gene copy numbers, had indicated a strong anthropogenic impact. Consistent with the isolation origin, qPCR analysis in this study showed that the blaCTX-M gene was present at an abundance of 1x10-4 relative to bacterial 16S rRNA gene copy numbers. The results indicate that contamination of these urban aquatic ecosystems with clinically relevant antibiotic resistant bacteria is substantial in some areas. Measures should therefore be put in place to mitigate the propagation of clinically relevant antimicrobial resistance within the Nigerian aquatic ecosystems.
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Affiliation(s)
- Olawale Olufemi Adelowo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
- * E-mail: , (OOA); (JAM)
| | - Odion Osebhahiemen Ikhimiukor
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Camila Knecht
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Otto-von-Guericke-Universität Magdeburg—Institute of Apparatus and Environmental Technology, Magdeburg, Germany
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Mudit Bhatia
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Anne-Kirstin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jochen A. Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- * E-mail: , (OOA); (JAM)
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20
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Brooks JP, Smith RK, Aldridge CA, Chaney B, Omer A, Dentinger J, Street GM, Baker BH. A preliminary investigation of wild pig (Sus scrofa) impacts in water quality. JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:27-37. [PMID: 33016358 DOI: 10.1002/jeq2.20036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/29/2019] [Indexed: 06/11/2023]
Abstract
The United States, particularly the southern portion, has recently suffered drastic population expansion of wild pigs causing destruction of prime farmland. An associated concern, which has been understudied, is the potential transfer of nutrients and pathogens to surface water. This study aimed to identify the abiotic and biotic impacts of captive wild pigs on water quality, including nutrients, fecal indicator and pathogenic bacteria, and antimicrobial resistance. Overall, the study demonstrated that wild pigs harbored Salmonella spp., Campylobacter spp., Escherichia coli, and Clostridium perfringens, which were found in water runoff collected directly beneath the hog paddock, often 2 log10 greater than above-paddock levels. However, the impacts to downstream water quality were limited, perhaps because of a relatively large riparian buffer between the paddock and surface water. A higher rate of ammonium concentration changes over time was detected in the runoff water below the paddock; additionally, microbial releases detected in runoff were also time dependent, possibly associated with increasing pig numbers. Antibiotic resistance was generally not associated with the wild pigs. Antibiotic resistance genes were found in upstream as well as downstream surface water, suggesting that nonpoint sources of microbial contamination were present. Interestingly, intI1 levels were greater in below-paddock runoff by nearly 2 log10 . Overall, it appears that wild pigs potentially pose a threat to water quality but only if they have direct access to the water. Pathogen, fecal indicator bacteria, and some nutrient release were significantly associated with wild pigs, but riparian buffers limited water quality impairment.
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Affiliation(s)
- John P Brooks
- USDA-ARS, Genetics and Sustainable Agriculture Unit, 810 HWY 12 E., Mississippi State, MS, 39762-5367, USA
| | - Renotta K Smith
- USDA-ARS, Genetics and Sustainable Agriculture Unit, 810 HWY 12 E., Mississippi State, MS, 39762-5367, USA
| | - Caleb A Aldridge
- Dep. of Wildlife, Fisheries and Aquaculture, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
| | - Brent Chaney
- Dep. of Forestry, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
| | - Austin Omer
- Dep. of Wildlife, Fisheries and Aquaculture, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
| | - Jane Dentinger
- Dep. of Wildlife, Fisheries and Aquaculture, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
| | - Garrett M Street
- Dep. of Wildlife, Fisheries and Aquaculture, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
| | - Beth H Baker
- Dep. of Wildlife, Fisheries and Aquaculture, Mississippi State Univ., 775 Stone Blvd., Mississippi State, MS, 39762-9690, USA
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