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Tan Y, Scornet AL, Yap MNF, Zhang D. Machine learning-based classification reveals distinct clusters of non-coding genomic allelic variations associated with Erm-mediated antibiotic resistance. mSystems 2024; 9:e0043024. [PMID: 38953319 PMCID: PMC11264731 DOI: 10.1128/msystems.00430-24] [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: 03/25/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The erythromycin resistance RNA methyltransferase (erm) confers cross-resistance to all therapeutically important macrolides, lincosamides, and streptogramins (MLS phenotype). The expression of erm is often induced by the macrolide-mediated ribosome stalling in the upstream co-transcribed leader sequence, thereby triggering a conformational switch of the intergenic RNA hairpins to allow the translational initiation of erm. We investigated the evolutionary emergence of the upstream erm regulatory elements and the impact of allelic variation on erm expression and the MLS phenotype. Through systematic profiling of the upstream regulatory sequences across all known erm operons, we observed that specific erm subfamilies, such as ermB and ermC, have independently evolved distinct configurations of small upstream ORFs and palindromic repeats. A population-wide genomic analysis of the upstream ermB regions revealed substantial non-random allelic variation at numerous positions. Utilizing machine learning-based classification coupled with RNA structure modeling, we found that many alleles cooperatively influence the stability of alternative RNA hairpin structures formed by the palindromic repeats, which, in turn, affects the inducibility of ermB expression and MLS phenotypes. Subsequent experimental validation of 11 randomly selected variants demonstrated an impressive 91% accuracy in predicting MLS phenotypes. Furthermore, we uncovered a mixed distribution of MLS-sensitive and MLS-resistant ermB loci within the evolutionary tree, indicating repeated and independent evolution of MLS resistance. Taken together, this study not only elucidates the evolutionary processes driving the emergence and development of MLS resistance but also highlights the potential of using non-coding genomic allele data to predict antibiotic resistance phenotypes. IMPORTANCE Antibiotic resistance (AR) poses a global health threat as the efficacy of available antibiotics has rapidly eroded due to the widespread transmission of AR genes. Using Erm-dependent MLS resistance as a model, this study highlights the significance of non-coding genomic allelic variations. Through a comprehensive analysis of upstream regulatory elements within the erm family, we elucidated the evolutionary emergence and development of AR mechanisms. Leveraging population-wide machine learning (ML)-based genomic analysis, we transformed substantial non-random allelic variations into discernible clusters of elements, enabling precise prediction of MLS phenotypes from non-coding regions. These findings offer deeper insight into AR evolution and demonstrate the potential of harnessing non-coding genomic allele data for accurately predicting AR phenotypes.
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Affiliation(s)
- Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
| | - Alexandre Le Scornet
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mee-Ngan Frances Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, USA
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, Missouri, USA
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2
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Gong W, Guo L, Huang C, Xie B, Jiang M, Zhao Y, Zhang H, Wu Y, Liang H. A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172601. [PMID: 38657817 DOI: 10.1016/j.scitotenv.2024.172601] [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: 11/02/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.
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Affiliation(s)
- Weijia Gong
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China; State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin 150090, PR China.
| | - Lin Guo
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Chenxin Huang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Binghan Xie
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
| | - Mengmeng Jiang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Yuzhou Zhao
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - Haotian Zhang
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin 150030, PR China
| | - YuXuan Wu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China
| | - Heng Liang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin 150090, PR China
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Huang Y, Boyen F, Antonissen G, Vereecke N, Van Immerseel F. The Genetic Landscape of Antimicrobial Resistance Genes in Enterococcus cecorum Broiler Isolates. Antibiotics (Basel) 2024; 13:409. [PMID: 38786138 PMCID: PMC11117384 DOI: 10.3390/antibiotics13050409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff (ECOFF) values (COWT) for ten antimicrobials were determined in a collection of E. cecorum strains. Whole-genome sequencing data were analyzed for a selection of these E. cecorum strains to identify resistance determinants involved in the observed phenotypes. Wild-type and non-wild-type isolates were observed for the investigated antimicrobial agents. Several antimicrobial resistance genes (ARGs) were detected in the isolates, linking phenotypes with genotypes for the resistance to vancomycin, tetracycline, lincomycin, spectinomycin, and tylosin. These detected resistance genes were located on mobile genetic elements (MGEs). Point mutations were found in isolates with a non-wild-type phenotype for enrofloxacin and ampicillin/ceftiofur. Isolates showing non-wild-type phenotypes for enrofloxacin had point mutations within the GyrA, GyrB, and ParC proteins, while five amino acid changes in penicillin-binding proteins (PBP2x superfamily) were observed in non-wild-type phenotypes for the tested β-lactam antimicrobials. This study is one of the first that describes the genetic landscape of ARGs within MGEs in E. cecorum, in association with phenotypical resistance determination.
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Affiliation(s)
- Yue Huang
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (Y.H.); (G.A.)
| | - Filip Boyen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (Y.H.); (G.A.)
| | - Gunther Antonissen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (Y.H.); (G.A.)
| | - Nick Vereecke
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium;
- PathoSense BV, 2500 Lier, Belgium
| | - Filip Van Immerseel
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (Y.H.); (G.A.)
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Lee YJ, Kim K, Lee YJ. Dissemination and characteristics of high-level erythromycin-resistant Enterococcus faecalis from bulk tank milk of dairy companies in Korea. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2023; 87:51-58. [PMID: 36606037 PMCID: PMC9808847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 01/07/2023]
Abstract
Enterococci are environmental pathogens that can cause bovine mastitis, which is treated with macrolides, one of which is erythromycin (ERY). The aim of this study was to compare the characteristics of high-level erythromycin-resistant (HLER) Enterococcus faecalis (E. faecalis) isolates from bulk tank milk of 4 dairy companies, identified as A to D, in order to assess the threat to public health. Although isolates from company D showed the highest prevalence of E. faecalis, the prevalence of HLER E. faecalis in isolates from company A showed a significant difference. A total of 149 of the 301 HLER E. faecalis isolates showed the highest rate of resistance to tetracycline. In the distribution of antimicrobial resistance genes, 147 isolates carried the ermB gene alone and 2 isolates carried both ermA and ermB genes. Also, 72 and 60 isolates carried both tetM and tetL genes and the tetM gene alone, respectively, and 38 isolates carried the optrA gene. The prevalence of both aac(6')Ie-aph(2″)-la and ant(6')-Ia genes was the highest and 104 isolates harbored the Int-Tn gene carrying the Tn916/1545-like transposon. Although the distribution of the e rmB gene showed no significant difference among dairy companies, the prevalence of other resistance genes and transposons showed significant differences among dairy companies. Virulence genes were highly conserved in the HLER E. faecalis isolates. Our results indicated that there were significant differences in phenotypic and genotypic characteristics of HLER E. faecalis isolates in milk from 4 different dairy companies. A structured management protocol by companies and constant monitoring are therefore necessary to minimize public health hazards.
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Ali SE, Mahana O, Mohan CV, Delamare-Deboutteville J, Elgendy MY. Genetic characterization and antimicrobial profiling of bacterial isolates collected from Nile tilapia (Oreochromis niloticus) affected by summer mortality syndrome. JOURNAL OF FISH DISEASES 2022; 45:1857-1871. [PMID: 36057979 DOI: 10.1111/jfd.13710] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
In recent years, Egyptian tilapia aquaculture has experienced mortality episodes during the summer months. The causative agents responsible for such mortalities have not been clearly identified. A total of 400 fish specimens were collected from affected tilapia farms within five Egyptian governorates. A total of 344 bacterial isolates were identified from the examined fish specimens. Bacterial isolates were grouped into seven genera based on API 20E results. The most prevalent pathogens were Aeromonas spp. (42%), Vibrio spp. (21%), and Streptococcus agalactiae (14.5%). Other emerging infections like, Plesiomonas shigelloides (10%), Staphyloccocus spp. (8%), Pseudomonas oryzihabitans, and Acinetobacter lwoffii (2.3%) were also detected. Sequence analysis of the 16S ribosomal RNA bacterial gene of some isolates, confirmed the phenotypic identification results. The analysis of antibiotic resistance genes revealed the presence of aac(6')-Ib-cr (35.7%), blaCTX gene (23.8%), qnrS (19%), ampC (16.7%), floR (14.3%), sul1, tetA, and van.C1 (2.4%) genes in some isolates. The antimicrobia resistance gene, qac was reported in 46% of screened isolates. Bacterial strains showed variable virulence genes profiles. Aeromonas spp. harboured (act, gcat, aerA, lip, fla, and ser) genes. All Vibrio spp. possessed the hlyA gene, while cylE, hylB, and lmb genes, were detected in S. agalactiae strains. Our findings point to the possible role of the identified bacterial pathogens in tilapia summer mortality syndrome and highlight the risk of the irresponsible use of antibiotics on antimicrobial resistance in aquaculture.
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Affiliation(s)
- Shimaa E Ali
- WorldFish, Abbassa, Sharqia, Egypt
- Department of Hydrobiology, Veterinary Research Institute, National Research Centre, Giza, Egypt
| | - Osama Mahana
- Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | | | | | - Mamdouh Y Elgendy
- Department of Hydrobiology, Veterinary Research Institute, National Research Centre, Giza, Egypt
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Wang K, Yin D, Sun Z, Wang Z, You S. Distribution, horizontal transfer and influencing factors of antibiotic resistance genes and antimicrobial mechanism of compost tea. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129395. [PMID: 35803190 DOI: 10.1016/j.jhazmat.2022.129395] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Compost tea was alternatives of chemical pesticide for green agriculture, but there were no reports about antibiotic resistance genes (ARGs) in compost tea. This study investigated the effect of livestock manures, sewage sludge, their composting products and liquid fermentation on ARGs, mobile genetic elements (MGEs), metal resistance genes (MRGs) and antimicrobial properties of various compost tea. The results showed aerobic liquid fermentation reduced ARGs by 65.93 % and 45.20 % in the compost tea of chicken manure and sludge, enriched ARGs by 8.57 % and 37.41 % in the compost tea of pig manure and bovine manure, and increased MGEs and MRGs by 1.25 × 10-5-5.53 × 10-3 and 2.03 × 10-5-2.03 × 10-3 in the four compost tea. The correlation coefficient of tetracycline and sulfonamide resistance genes between compost product and compost tea were 0.98 and 0.91. aadA2-02, sul2 and tetX abundant in the compost tea were positively correlated with MGEs and MRGs. Furthermore, liquid fermentation enriched the potential host of tetracycline and vancomycin resistance genes. Tetracycline resistance genes occupied 62.7 % of total ARGs in the compost tea. Alcaligenes and Bacillus enriched by 0.78-39.31 % in the four compost tea, which metabolites had high antimicrobial activity. The potential host of ARGs accounted for 42.1 % bacteria abundance in the four compost tea.
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Affiliation(s)
- Ke Wang
- National Engineering Research Center for Bioenergy, Harbin Institute of Technology, Harbin 150090, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; National Engineering Research Center for Safe Sludge Disposal and Resource Recovery, Harbin Institute of Technology, Harbin 150090, China.
| | - Dan Yin
- National Engineering Research Center for Bioenergy, Harbin Institute of Technology, Harbin 150090, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhen Sun
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhe Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Zaidi SEZ, Zaheer R, Barbieri R, Cook SR, Hannon SJ, Booker CW, Church D, Van Domselaar G, Zovoilis A, McAllister TA. Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum. Front Microbiol 2022; 13:859990. [PMID: 35832805 PMCID: PMC9271880 DOI: 10.3389/fmicb.2022.859990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.
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Affiliation(s)
- Sani-e-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- University of Lethbridge, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Ruth Barbieri
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shaun R. Cook
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | | | - Deirdre Church
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Calgary Laboratory Services, Calgary, AB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- *Correspondence: Tim A. McAllister,
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Deng Y, Mao C, Lin Z, Su W, Cheng C, Li Y, Gu Q, Gao R, Su Y, Feng J. Nutrients, temperature, and oxygen mediate microbial antibiotic resistance in sea bass (Lateolabrax maculatus) ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153120. [PMID: 35041966 DOI: 10.1016/j.scitotenv.2022.153120] [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: 11/14/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) have drawn increasing attention as novel environmental pollutants because of the threat they impose on human and animal health. The sea bass (Lateolabrax maculatus) is the third most cultured marine fish in China. Therefore, a study of ARG pollution in the sea bass culture environment is of great significance for the healthy and sustainable development of the sea bass industry. Here, we systematic investigated the contents of 23 antibiotic resistance-related genes (ARRGs), including 19 ARGs and four mobile genetic elements, and analyzed bacterial community composition and environmental parameters in sea bass ponds. The relative abundance (ARRG copies/16S ribosomal RNA gene copies) of ARRGs was up to 3.83 × 10-2. Sul1 was the most abundant ARRG, followed by ereA, intI-1, sul2, dfrA1, and aadA. Both the ARRG changes and aquatic microbiota succession were mainly driven by water temperature (WT), dissolved oxygen (DO), and NO3-. WT is positively correlated with the most ARGs and some of the top 38 Operational Taxonomic Units (OTUs) belonging to the orders of Frankiales, Micrococcales, Chitinophagales, and Sphingomonadales. Furthermore, WT is negatively related with some other OTUs of the orders Frankiales, Xanthomonadales, Micrococcales, and Rhizobiales. However, DO and NO3- have the opposite function with WT on specific taxa and ARGs. These results indicate that sea bass ponds are reservoirs of ARGs, and are driven mainly by the nutrient, temperature, and oxygen with inducing specific microbial taxa. The regulation of environmental factors (increasing DO and NO3-) can be conducted to reduce drug resistance risk in aquaculture ponds. Therefore, environmental factors and specific taxa could be the indicators of ARG contamination and can be used to establish an antibiotic elimination system and consequently realize a sustainable aquaculture industry.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Can Mao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China
| | - Ziyang Lin
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Wenxiao Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yong Li
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China
| | - Qunhong Gu
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China
| | - Ren Gao
- Zhaoqing Dahuanong Biology Medicine Co., Ltd., Guangdong, Zhaoqing 526238, China
| | - Youlu Su
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
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Wajima T, Hagimoto A, Tanaka E, Kawamura Y, Nakaminami H. Identification and characterization of a novel multidrug-resistant streptococcus, Streptococcus toyakuensis sp. nov., from a blood sample. J Glob Antimicrob Resist 2022; 29:316-322. [DOI: 10.1016/j.jgar.2022.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
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10
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Senghore M, Tientcheu PE, Worwui AK, Jarju S, Okoi C, Suso SMS, Foster-Nyarko E, Ebruke C, Sonko M, Kourna MH, Agossou J, Tsolenyanu E, Renner LA, Ansong D, Sanneh B, Cisse CB, Boula A, Miwanda B, Lo SW, Gladstone RA, Schwartz S, Hawkins P, McGee L, Klugman KP, Breiman RF, Bentley SD, Mwenda JM, Kwambana-Adams BA, Antonio M. Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction. Microb Genom 2021; 7. [PMID: 34328412 PMCID: PMC8477402 DOI: 10.1099/mgen.0.000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.
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Affiliation(s)
- Madikay Senghore
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Peggy-Estelle Tientcheu
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Archibald Kwame Worwui
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sheikh Jarju
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Catherine Okoi
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sambou M S Suso
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Ebenezer Foster-Nyarko
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Chinelo Ebruke
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Mohamadou Sonko
- Hopital d'Enfants Albert Royer, BP 5297, Fann, Dakar, Senegal
| | | | - Joseph Agossou
- Department of Mother and Child, Faculty of Medicine, University of Parakou, Parakou, Benin.,Borgou Regional University Teaching Hospital, Parakou, Benin
| | - Enyonam Tsolenyanu
- Laboratoire Microbiologie, Centre Hospitalier Universitaire de Tokoin Lomé, BP 57, Lomé, Togo
| | - Lorna Awo Renner
- Central Laboratory Services, Korle-Bu Teaching Hospital, P.O. Box 77, Accra, Ghana
| | - Daniel Ansong
- Komfo Anokye Teaching Hospital, P.O. Box 1934, Kumasi, Ghana
| | - Bakary Sanneh
- Edward Francis Small Teaching Hospital, Banjul, The Gambia
| | - Catherine Boni Cisse
- Laboratoire Central du CHU de Yopougon, Institut Pasteur de Cote d'Ivoire, Abidjan, Ivory Coast
| | - Angeline Boula
- Centre Mere et Enfant de la Fondation, Chantal Biya, Yaounde, Cameroon
| | - Berthe Miwanda
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Paulina Hawkins
- Centers for Disease Control and Prevention, Atlanta, GA, USA.,Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, GA, USA
| | | | - Jason M Mwenda
- World Health Organization Regional Office for Africa, BP 6, Brazzaville, Republic of Congo
| | - Brenda Anna Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
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11
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Lin ZJ, Zhou ZC, Zhu L, Meng LX, Shuai XY, Sun YJ, Chen H. Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144814. [PMID: 33540158 DOI: 10.1016/j.scitotenv.2020.144814] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Wastewater treatment plants (WWTPs) in China have been upgraded or renovated with a variety of emerging processes, but a comprehensive understanding of the behavior of antibiotic resistance genes (ARGs) in these WWTPs is still lacking. Here, the distribution of ARGs and bacterial community were investigated in a wastewater treatment plant with upgrading processes (WWTP-UP). 238 unique ARGs were detected in all samples. During the study period, the average ARGs concentration decreased by 98.4% along the entire treatment process. The removal efficiency of A2/O-membrane bioreactor (MBR) process was significantly higher than that of A2/O-high efficiency flocculent settling/cloth media filter (HEFS/CMF) process (p < 0.05), which corresponded to 3.5 and 2.1 log values on average, respectively. Notably, 35 ARGs and 14 mobile genetic elements (MGEs) were persistent in all samples. Based on the co-occurrence pattern revealed by network analysis, persistent ARGs possibly spread through the transfer of persistent MGEs among persistent bacteria. Using multiple linear regression analysis, we obtained 3 to 5 possible indicators for major ARG types, which might be served to evaluate the general distribution of ARGs or even predict the abundance of different ARG types. Our findings provide new insights into the impacts of upgrading process on ARGs and highlight the need for better strategies to improve ARGs elimination in WWTPs.
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Affiliation(s)
- Ze-Jun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Chao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Zhu
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ling-Xuan Meng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-Yi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu-Jie Sun
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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12
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Zhang Y, Xu R, Xiang Y, Lu Y, Jia M, Huang J, Xu Z, Cao J, Xiong W, Yang Z. Addition of nanoparticles increases the abundance of mobile genetic elements and changes microbial community in the sludge anaerobic digestion system. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124206. [PMID: 33535360 DOI: 10.1016/j.jhazmat.2020.124206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
This study explored the fate of mobile genetic elements (MGEs) in anaerobic digestion (AD) system with four nanoparticles (NPs) added, including carbon NPs, Al2O3 NPs, ZnO NPs, and CuO NPs. 16S rRNA amplicon sequencing and quantitative PCR to investigate the microbial community, MGEs abundance and the potential host in the AD process. The results of high-throughput sequencing showed that ZnO NPs and CuO NPs significantly reduced the microbial diversity and significantly changed the microbial community structure. Simultaneously, the absolute abundance of MGEs increased by 145.01%, 159.67%, 354.70%, and 132.80% on the carbon NPs, Al2O3 NPs, ZnO NPs, and CuO NPs. The enrichment rate of tnpA-03 in ZnO NPs group was the highest, which could reach up to 2854.80%. Co-occurrence analysis revealed that Proteobacteria harbored the vast majority of MGEs followed by Firmicutes. Redundancy analysis and variation partitioning analysis showed that metabolites were the main factors that shifted the succession of bacterial communities. Moreover, there were significant positive correlations between metabolites and part MGEs (such as tnpA-01, tnpA-02, tnpA-03, tnpA-04, tnpA-05, tnpA-07 and ISCR1). This study provides a new perspective that NPs increase the risk of antibiotic resistance through MGEs during AD process.
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Affiliation(s)
- Yanru Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Rui Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science Technology, Guangzhou 510650, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, PR China
| | - Yinping Xiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Meiying Jia
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jing Huang
- Hunan Academy of Forestry and State Key Laboratory of Utilization of Woody Oil Resource, Changsha 410004, PR China
| | - Zhengyong Xu
- Hunan Provincial Science and Technology Affairs Center, Changsha 410013, PR China
| | - Jiao Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Weiping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
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13
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Milaković M, Križanović S, Petrić I, Šimatović A, González-Plaza JJ, Gužvinec M, Andrašević AT, Pole L, Fuka MM, Udiković-Kolić N. Characterization of macrolide resistance in bacteria isolated from macrolide-polluted and unpolluted river sediments and clinical sources in Croatia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:142357. [PMID: 33370905 DOI: 10.1016/j.scitotenv.2020.142357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 06/12/2023]
Abstract
Environments polluted with excessively high levels of antibiotics released from manufacturing sites can act as a source of transferable antibiotic resistance (AR) genes to human commensal and pathogenic bacteria. The aim of this study was to evaluate AR of bacteria isolated from the Sava river sediments (Croatia) at the discharge site of effluents from azithromycin production compared to those from the upstream site and isolates collected in Croatian hospitals. A total of 228 environmental strains of azithromycin-resistant bacteria were isolated and identified, with 124 from the discharge site and 104 from the upstream site. In addition, a total of 90 clinical, azithromycin-resistant streptococcal and staphylococcal isolates obtained from the Croatian Reference Center for Antibiotic Resistance Surveillance were analyzed. PCR screening of isolates on 11 relevant macrolide-resistance genes (MRGs) showed that discharge isolates had greater detection frequencies for 4 gene targets (ermB, msrE, mphE and ermF) compared to upstream isolates. Among clinical isolates, the most frequently detected gene was ermB, followed by msrD, mefE and mefC. The discharge site demonstrated a greater abundance of isolates with co-occurrence of two different MRGs (predominantly msrE-mphE) than the upstream site, but a lower abundance than the clinical sources (most commonly msrD-mefE). The simultaneous presence of three or even four MRGs was specific for the discharge and clinical isolates, but not for the upstream isolates. When MRG results were sorted by gene mechanism, the ribosomal methylation (erm) and protection genes (msr) were the most frequently detected among both the discharge and the clinical isolates. Following sequencing, high nucleotide sequence similarity was observed between ermB in the discharge isolates and the clinical streptococcal isolates, suggesting a possible transfer of the ermB gene between bacteria of clinical and environmental origin. Our study highlights the importance of environmental bacterial populations as reservoirs for clinically relevant macrolide-resistance genes.
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Affiliation(s)
- Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ana Šimatović
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Juan J González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marija Gužvinec
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Arjana Tambić Andrašević
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Lucia Pole
- Department of Microbiology, University of Zagreb, Faculty of Agriculture, Svetošimunska 25, 10 000 Zagreb, Croatia
| | - Mirna Mrkonjić Fuka
- Department of Microbiology, University of Zagreb, Faculty of Agriculture, Svetošimunska 25, 10 000 Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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14
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Spatiotemporal Changes of Antibiotic Resistance and Bacterial Communities in Drinking Water Distribution System in Wrocław, Poland. WATER 2020. [DOI: 10.3390/w12092601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Antibiotic resistance of bacteria is an emerging problem in drinking water treatment. This paper presents the comparison of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) prevalence during the summer and winter season in a full-scale drinking water distribution system (DWDS) supplied by two water treatment plants (WTPs). The effect of distance from WTP and physical–chemical water parameters on its microbial properties was also tested. Bacterial consortia dwelling in bulk tap water were additionally compared by means of denaturating gradient gel electrophoresis (DGGE). The results showed that among ARB, bacteria resistant to ceftazidime (CAZ) were the most abundant, followed by bacteria resistant to amoxicillin (AML), ciprofloxacin (CIP), and tetracycline (TE). Numerous ARGs were detected in tested tap water samples. Only CAZ resistant bacteria were more prevalent in the season of increased antibiotic consumption, and only AML resistant bacteria relative abundances increase was statistically significant with the distance from a WTP. The investigated tap water meets all legal requirements. It is therefore safe to drink according to the law. Nevertheless, because antibiotic resistance could pose a threat to consumer health, it should be further monitored in DWDSs.
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15
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Yu K, Li P, Chen Y, Zhang B, Huang Y, Huang FY, He Y. Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system. WATER RESEARCH 2020; 173:115541. [PMID: 32036288 DOI: 10.1016/j.watres.2020.115541] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
Antibiotic resistome is a raising concern around the world, especially considering treated wastewater for reclamation. A wastewater reclamation system (WWRS), composed by a treatment system (TS) and a reclaimed system (RS) with supplementation from the treated effluent and considered as an integrated system of treatment and reclamation, was selected in this study. High-throughput qPCR (HT-qPCR) was applied to profile 283 antibiotic resistance genes (ARGs) and 12 mobile genetic elements (MGEs) in the WWRS. A total of 251 ARG and 12 MGE subtypes were detected in the WWRS. The TS exhibited good performance for the removal of ARGs with the number, relative and absolute abundances of ARGs largely decreased (99.07% removal efficiency) in the final effluent, which might be ascribed to biosolid sedimentation. Enhancement of biosolids removal contributed the lessening of ARGs. In the RS, high quality effluent significantly reduced the number and abundance of ARGs along the flow to downstream. MGEs were less reduced in the treated effluent than that of the influent (R2 = -0.16, p > 0.05), and exhibited close connections with ARGs. Arcobacter, Cloacibacterium, Cyanobacteria, Acinetobacter, Flavobacterium and Dechloromonas were the relatively abundant genera in the WWRS, and exhibited significantly correlations with ARGs. Microbial communities and MGEs contributed 65.64% to the changes of ARGs. These two factors may be the main drivers of ARG proliferation in the WWRS. Thus, attention should be paid to MGEs and those abundant genera when considering treated wastewater for reclamation.
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Affiliation(s)
- Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Peng Li
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yihan Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 246011, China
| | - Bo Zhang
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuansheng Huang
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai, 200240, China.
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16
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Liu Y, Dyall-Smith M, Marenda M, Hu HW, Browning G, Billman-Jacobe H. Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms. Antibiotics (Basel) 2020; 9:antibiotics9030120. [PMID: 32183177 PMCID: PMC7148458 DOI: 10.3390/antibiotics9030120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.
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Affiliation(s)
- Yuhong Liu
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Michael Dyall-Smith
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Marc Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Glenn Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
- Correspondence:
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17
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Akdoğan Kittana FN, Mustak IB, Hascelik G, Saricam S, Gurler N, Diker KS. Erythromycin-resistant Streptococcus pneumoniae: phenotypes, genotypes, transposons and pneumococcal vaccine coverage rates. J Med Microbiol 2019; 68:874-881. [PMID: 31116101 DOI: 10.1099/jmm.0.000995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
PURPOSE To assess the antibiotic resistance, transposon profiles, serotype distribution and vaccine coverage rates in 110 erythromycin-resistant S. pneumoniae clinical isolates. METHODOLOGY Erythromycin, clindamycin, tetracycline, chloramphenicol and kanamycin susceptibilities were assessed using the E-test/disc diffusion method. Inducible macrolide resistance was tested using the erythromycin-clindamycin double disc diffusion test. Serogrouping and serotyping were performed using latex particle agglutination and the Quellung reaction, respectively. Drug resistance genes and transposon-specific genes were investigated by PCR. RESULTS Of the isolates, 93 % were resistant to clindamycin; 81 % were resistant to tetracycline; 76 % were multi-drug-resistant, having resistance to both clindamycin and tetracycline; and 12 % had extended-drug resistance, being resistant to clindamycin, tetracycline, chloramphenicol and kanamycin. The majority of isolates (88.2 %) exhibited the cMLSB phenotype. The association between the cMLSB phenotype and tetracycline resistance was related to transposons Tn2010 (38.2 %), Tn6002 (21.8 %) and Tn3872 (18.2 %). M and iMLSB phenotypes were observed in 7 and 5 % of the isolates, respectively. The most frequent serotype was 19 F (40 %). Among the erythromycin-resistant pneumococci, vaccine coverage rates for the 13-valent pneumococcal conjugate vaccine (PCV-13) and the 23-valent pneumococcal polysaccharide vaccine (PPSV-23) were 76.4 and 79.1 %, respectively, compared to 82.2 and 85.1 % transposon-carrying isolates. CONCLUSIONS Multi-drug resistance among erythromycin-resistant S. pneumoniae isolates mainly occurs due to the horizontal spread of the Tn916 family of transposons. The majority of the transposon-carrying isolates are covered by 13- and 23-valent pneumococcal vaccines. Since serotype distribution and transposons in S. pneumoniae isolates may change over time, close monitoring is essential.
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Affiliation(s)
| | - Inci Basak Mustak
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
| | - Gulsen Hascelik
- 1 Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey
| | - Seyyide Saricam
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
| | - Nezahat Gurler
- 3 Istanbul University, Faculty of Medicine, Department of Medical Microbiology, Istanbul, Turkey
| | - Kadir Serdar Diker
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
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18
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Guo X, Yan Z, Zhang Y, Xu W, Kong D, Shan Z, Wang N. Behavior of antibiotic resistance genes under extremely high-level antibiotic selection pressures in pharmaceutical wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:119-128. [PMID: 28850832 DOI: 10.1016/j.scitotenv.2017.08.229] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/04/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Pharmaceutical wastewater treatment plants (PWWTPs), which receive wastewater containing extremely high levels of antibiotics, are regarded as potential hot spots for antibiotic-resistance development in the environment. Six sampling campaigns in six PWWTPs in Southeastern China were carried out to assess the prevalence and fate of antibiotic resistance genes (ARGs). Different genes were monitored in different PWWTPs (PWWTP A: lincosamides; PWWTP B: aminoglycosides and macrolides; PWWTP C: quinolones; PWWTP D: macrolides and quinolones; PWWTP E: cephalosporins; and PWWTP F: quinolones and macrolides) using real-time quantitative polymerase chain reactions (PCRs), according to the antibiotic type produced. The levels of typical ARG subtypes in the final effluents ranged from (1.03±0.91)×101 to (6.78±0.21)×107copies/mL. The absolute abundance of ARGs in effluents accounted for 0%-577% of influents to the six PWWTPs with a median value of 6%. Most of the ARGs are transported to the dewatered sludge, with concentrations from (1.38±0.21)×105 to (6.84±0.43)×1010copies/g dry weight (dw). In different treatment units (before/after biological units), a clear trend of proliferation or attenuation was not observed for the ARGs, aside from a strong attenuation in moving bed bio-film reactor (MBBR) in PWWTP C. Through correlation analyses, this study demonstrated that the bacterial abundance and antibiotic concentrations within the PWWTPs influenced the fate of the associated ARGs, and this was possibly related primarily to the intrinsic resistance mechanisms of corresponding ARGs. Macrolide ARGs, which tend to locate in plasmids and transposons, positively correlate weakly with total macrolide antibiotic concentrations but positively correlate strongly with 16S rRNA concentrations. Furthermore, ARG concentrations in the wastewater from fermentation were significantly higher than in the wastewater from chemical synthesis and preparation. This is the first comprehensive study on the behavior of antibiotic resistance genes under extremely high-level antibiotic selection pressures in pharmaceutical wastewater treatment plants (PWWTPs) in Southeastern China.
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Affiliation(s)
- Xinyan Guo
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China; Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Zheng Yan
- Chinese Society for Environmental Sciences, Beijing 100082, China
| | - Yi Zhang
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China
| | - Weili Xu
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China; Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Deyang Kong
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China; Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Zhengjun Shan
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China; Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Na Wang
- Nanjing Institute of Environmental Science, Ministry of Environmental Protection, Nanjing 210042, China; Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Environmental Protection of China, Nanjing 210042, China.
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19
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Alexander J, Knopp G, Dötsch A, Wieland A, Schwartz T. Ozone treatment of conditioned wastewater selects antibiotic resistance genes, opportunistic bacteria, and induce strong population shifts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 559:103-112. [PMID: 27058129 DOI: 10.1016/j.scitotenv.2016.03.154] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
An ozone treatment system was investigated to analyze its impact on clinically relevant antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). A concentration of 0.9±0.1g ozone per 1g DOC was used to treat conventional clarified wastewater. PCR, qPCR analyses, Illumina 16S Amplicon Sequencing, and PCR-DGGE revealed diverse patterns of resistances and susceptibilities of opportunistic bacteria and accumulations of some ARGs after ozone treatment. Molecular marker genes for enterococci indicated a high susceptibility to ozone. Although they were reduced by almost 99%, they were still present in the bacterial population after ozone treatment. In contrast to this, Pseudomonas aeruginosa displayed only minor changes in abundance after ozone treatment. This indicated different mechanisms of microorganisms to cope with the bactericidal effects of ozone. The investigated ARGs demonstrated an even more diverse pattern. After ozone treatment, the erythromycin resistance gene (ermB) was reduced by 2 orders of magnitude, but simultaneously, the abundance of two other clinically relevant ARGs increased within the surviving wastewater population (vanA, blaVIM). PCR-DGGE analysis and 16S-Amplicon-Sequencing confirmed a selection-like process in combination with a substantial diversity loss within the vital wastewater population after ozone treatment. Especially the PCR-DGGE results demonstrated the survival of GC-rich bacteria after ozone treatment.
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Affiliation(s)
- Johannes Alexander
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Gregor Knopp
- Technische Universität Darmstadt, Institute IWAR, Wastewater Technology, Franziska-Braun-Straße 7, 64287, Darmstadt, Germany
| | - Andreas Dötsch
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Arne Wieland
- Xylem Services GmbH, Boschstraße 4 - 14, 32051, Herford, Germany
| | - Thomas Schwartz
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021, Karlsruhe, Germany.
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Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillán-Barcia MP, de la Cruz F, Schlüter A, Pühler A, Pistorio M, Lagares A, Del Papa MF. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Sci Rep 2016; 6:28284. [PMID: 27321040 PMCID: PMC4913263 DOI: 10.1038/srep28284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/31/2016] [Indexed: 12/02/2022] Open
Abstract
The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.
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Affiliation(s)
- María C Martini
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mauricio Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Francisco J Albicoro
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | | | - Alejandro Petroni
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas (CSIC), 39011 Santander, Spain
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Institute for Genome Research and Systems Biology, D-33615 Bielefeld, Germany
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
| | - María F Del Papa
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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Xu L, Ouyang W, Qian Y, Su C, Su J, Chen H. High-throughput profiling of antibiotic resistance genes in drinking water treatment plants and distribution systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:119-126. [PMID: 26890482 DOI: 10.1016/j.envpol.2016.02.013] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/03/2016] [Accepted: 02/04/2016] [Indexed: 05/04/2023]
Abstract
Antibiotic resistance genes (ARGs) are present in surface water and often cannot be completely eliminated by drinking water treatment plants (DWTPs). Improper elimination of the ARG-harboring microorganisms contaminates the water supply and would lead to animal and human disease. Therefore, it is of utmost importance to determine the most effective ways by which DWTPs can eliminate ARGs. Here, we tested water samples from two DWTPs and distribution systems and detected the presence of 285 ARGs, 8 transposases, and intI-1 by utilizing high-throughput qPCR. The prevalence of ARGs differed in the two DWTPs, one of which employed conventional water treatments while the other had advanced treatment processes. The relative abundance of ARGs increased significantly after the treatment with biological activated carbon (BAC), raising the number of detected ARGs from 76 to 150. Furthermore, the final chlorination step enhanced the relative abundance of ARGs in the finished water generated from both DWTPs. The total enrichment of ARGs varied from 6.4-to 109.2-fold in tap water compared to finished water, among which beta-lactam resistance genes displayed the highest enrichment. Six transposase genes were detected in tap water samples, with the transposase gene TnpA-04 showing the greatest enrichment (up to 124.9-fold). We observed significant positive correlations between ARGs and mobile genetic elements (MGEs) during the distribution systems, indicating that transposases and intI-1 may contribute to antibiotic resistance in drinking water. To our knowledge, this is the first study to investigate the diversity and abundance of ARGs in drinking water treatment systems utilizing high-throughput qPCR techniques in China.
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Affiliation(s)
- Like Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weiying Ouyang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyun Qian
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chao Su
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Hao H, Zhou S, Cheng G, Dai M, Wang X, Liu Z, Wang Y, Yuan Z. Effect of Tulathromycin on Colonization Resistance, Antimicrobial Resistance, and Virulence of Human Gut Microbiota in Chemostats. Front Microbiol 2016; 7:477. [PMID: 27092131 PMCID: PMC4824762 DOI: 10.3389/fmicb.2016.00477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/22/2016] [Indexed: 11/13/2022] Open
Abstract
To evaluate microbiological safety of tulathromycin on human intestinal bacteria, tulathromycin (0, 0.1, 1, 10, and 100 μg/mL) was added into Chemostats. Before and after drug exposure, we monitored (1) population, SCFA products, antimicrobial resistance, and colonization resistance of gut microbiota, and (2) the antimicrobial resistance genes, transferability, virulent genes, pathogenicity of Enterococus faecalis. Results showed that low level of tulathromycin did not exhibit microbiological hazard on resistance selection and colonization resistance. However, high level of tulathromycin (10 and 100 μg/mL) may disturb colonization resistance of human gut microbiota and select antimicrobial resistant E. faecalis. Most of the selected resistant E. faecalis carried resistant gene of ermB, transferable element of Tn1545 and three virulence genes (esp, cylA, and ace). One of them (E. faecalis 143) was confirmed to have higher horizontal transfer risk and higher pathogenicity. The calculated no observable adverse effect concentration (NOAEC) and microbiological acceptable daily intake (mADI) in our study was 1 μg/mL and 14.66 μg/kg.bw/day, respectively.
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Affiliation(s)
- Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Shengxi Zhou
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Menghong Dai
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University Wuhan, China
| | - Zhenli Liu
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University Wuhan, China
| | - Yulian Wang
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural UniversityWuhan, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
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23
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Lobova TI, Yemelyanova E, Andreeva IS, Puchkova LI, Repin VY. Antimicrobial Resistance and Plasmid Profile of Bacterial Strains Isolated from the Urbanized Eltsovka-1 River (Russia). Microb Drug Resist 2015; 21:477-90. [DOI: 10.1089/mdr.2014.0203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tatiana I. Lobova
- Krasnoyarsk Scientific Centre of Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Elena Yemelyanova
- Novosibirsk State Medical University, Novosibirsk, Russia
- State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-Being, Novosibirsk, Russia
| | - Irina S. Andreeva
- State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-Being, Novosibirsk, Russia
| | - Larisa I. Puchkova
- State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-Being, Novosibirsk, Russia
| | - Vladimir Ye Repin
- State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-Being, Novosibirsk, Russia
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24
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Alexander J, Bollmann A, Seitz W, Schwartz T. Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 512-513:316-325. [PMID: 25634736 DOI: 10.1016/j.scitotenv.2015.01.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/12/2015] [Accepted: 01/18/2015] [Indexed: 05/29/2023]
Abstract
The dissemination of medically relevant antibiotic resistance genes (ARGs) (blaVIM-1, vanA, ampC, ermB, and mecA) and opportunistic bacteria (Enterococcus faecium/faecalis, Pseudomonas aeruginosa, Enterobacteriaceae, Staphylococcus aureus, and CNS) was determined in different anthropogenically influenced aquatic habitats in a selected region of Germany. Over a period of two years, four differently sized wastewater treatment plants (WWTPs) with and without clinical influence, three surface waters, four rain overflow basins, and three groundwater sites were analyzed by quantitative Polymerase Chain Reaction (qPCR). Results were calculated in cell equivalents per 100 ng of total DNA extracted from water samples and per 100 mL sample volume, which seems to underestimate the abundance of antibiotic resistance and opportunistic bacteria. High abundances of opportunistic bacteria and ARG were quantified in clinical wastewaters and influents of the adjacent WWTP. The removal capacities of WWTP were up to 99% for some, but not all investigated bacteria. The abundances of most ARG targets were found to be increased in the bacterial population after conventional wastewater treatment. As a consequence, downstream surface water and also some groundwater compartments displayed high abundances of all four ARGs. It became obvious that the dynamics of the ARG differed from the fate of the opportunistic bacteria. This underlines the necessity of an advanced microbial characterization of anthropogenically influenced environments.
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Affiliation(s)
- Johannes Alexander
- Karlsruhe Institute of Technology (KIT)-Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Anna Bollmann
- Zweckverband Landeswasserversorgung, Betriebs- und Forschungslaboratorium, Am Spitzigen Berg 1, 89129 Langenau, Germany
| | - Wolfram Seitz
- Zweckverband Landeswasserversorgung, Betriebs- und Forschungslaboratorium, Am Spitzigen Berg 1, 89129 Langenau, Germany
| | - Thomas Schwartz
- Karlsruhe Institute of Technology (KIT)-Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, P.O. Box 3640, 76021 Karlsruhe, Germany.
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25
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Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Comput Struct Biotechnol J 2015; 13:241-7. [PMID: 25904996 PMCID: PMC4404416 DOI: 10.1016/j.csbj.2015.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 02/04/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Dean B Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
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26
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Resistance determinants and their association with different transposons in the antibiotic-resistant Streptococcus pneumoniae. BIOMED RESEARCH INTERNATIONAL 2015; 2015:836496. [PMID: 25883976 PMCID: PMC4391698 DOI: 10.1155/2015/836496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/16/2015] [Accepted: 03/16/2015] [Indexed: 11/18/2022]
Abstract
Multiple resistance of Streptococcus pneumoniae is generally associated with their unique recombination-mediated genetic plasticity and possessing the mobile genetic elements. The aim of our study was to detect antibiotic resistance determinants and conjugative transposons in 138 antibiotic-resistant pneumococcal strains isolated from nasopharynx of healthy young children from Lublin, Poland. These strains resistant to tetracycline and/or to chloramphenicol/erythromycin/clindamycin were tested by PCR using the specific genes as markers. The presence of Tn916 family transposons, carrying tet(M) and int/xisTn916, was observed in all of the tested strains. Tn916 was detected in 16 strains resistant only to tetracycline. Tn6002 and Tn3872-related element were found among 99 erm(B)-carrying strains (83.8% and 3.0%, resp.). Eight strains harbouring mef(E) and erm(B) genes were detected, suggesting the presence of Tn2010 and Tn2017 transposons. Among 101 chloramphenicol-resistant strains, two variants of Tn5252-related transposon were distinguished depending on the presence of int/xis5252 genes specific for cat gene-containing Tn5252 (75.2% of strains) or int Sp23FST81 gene, specific for cat-containing ICESp23FST81 element (24.8% of strains). In 6 strains Tn916-like and Tn5252-like elements formed a Tn5253-like structure. Besides clonal dissemination of resistant strains of pneumococci in the population, horizontal transfer of conjugative transposons is an important factor of the high prevalence of antibiotic resistance.
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Marzouk M, Ferjani A, Amamou S, Alibi S, Haj Ali M, Boukadida J. Phenotype, genotype, and serotype distribution of macrolide resistant invasive and non-invasive Streptococcus pneumoniae strains, in Sousse, Tunisia. Med Mal Infect 2014; 44:478-82. [DOI: 10.1016/j.medmal.2014.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/23/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
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Wang FH, Qiao M, Su JQ, Chen Z, Zhou X, Zhu YG. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9079-85. [PMID: 25057898 DOI: 10.1021/es502615e] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.
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Affiliation(s)
- Feng-Hua Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, People's Republic of China
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29
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Stoll C, Sidhu JPS, Tiehm A, Toze S. Prevalence of clinically relevant antibiotic resistance genes in surface water samples collected from Germany and Australia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:9716-26. [PMID: 22846103 DOI: 10.1021/es302020s] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The prevalence and proliferation of antibiotic resistant bacteria is profoundly important to human health, but the extent to which aquatic environments contribute toward the dissemination of antibiotic resistant genes (ARGs) is poorly understood. The prevalence of 24 ARGs active against eight antibiotic classes (β-lactams, aminoglycosides, glycopeptides, chloramphenicols, tetracycline, macrolides, trimethoprim, and sulfonamides) was evaluated in surface water samples collected from Germany and Australia with culture independent methods. The ARGs most frequently detected both in Germany and Australia were sulI, sulII (77-100%), and dfrA1 (43-55%) which code for resistance to sulfonamide and trimethoprim. Macrolides resistance gene ermB was relatively more prevalent in the surface water from Germany (68%) than Australia (18%). In contrast, the chloramphenicol resistance gene catII was more frequently detected in Australia (64%) than Germany (9%). Similarly, β-lactams resistance gene ampC was more prevalent in the samples from Australia (36%) than Germany (19%). This study highlights wide distribution of ARGs for sulfonamide, trimethoprim, macroline, β-lactams and chloramphenicol in the aquatic ecosystems. Aquatic ecosystems can therefore be reservoirs of ARGs genes which could potentially be transferred from commensal microorganisms to human pathogens.
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Affiliation(s)
- C Stoll
- DVGW-Technologiezentrum Wasser (TZW), Karlsruhe, Germany
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30
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Zhang T, Zhang XX, Ye L. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One 2011; 6:e26041. [PMID: 22016806 PMCID: PMC3189950 DOI: 10.1371/journal.pone.0026041] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022] Open
Abstract
The overuse or misuse of antibiotics has accelerated antibiotic resistance, creating a major challenge for the public health in the world. Sewage treatment plants (STPs) are considered as important reservoirs for antibiotic resistance genes (ARGs) and activated sludge characterized with high microbial density and diversity facilitates ARG horizontal gene transfer (HGT) via mobile genetic elements (MGEs). However, little is known regarding the pool of ARGs and MGEs in sludge microbiome. In this study, the transposon aided capture (TRACA) system was employed to isolate novel plasmids from activated sludge of one STP in Hong Kong, China. We also used Illumina Hiseq 2000 high-throughput sequencing and metagenomics analysis to investigate the plasmid metagenome. Two novel plasmids were acquired from the sludge microbiome by using TRACA system and one novel plasmid was identified through metagenomics analysis. Our results revealed high levels of various ARGs as well as MGEs for HGT, including integrons, transposons and plasmids. The application of the TRACA system to isolate novel plasmids from the environmental metagenome, coupled with subsequent high-throughput sequencing and metagenomic analysis, highlighted the prevalence of ARGs and MGEs in microbial community of STPs.
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Affiliation(s)
- Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.
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31
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Roberts AP, Mullany P. Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol Rev 2011; 35:856-71. [PMID: 21658082 DOI: 10.1111/j.1574-6976.2011.00283.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic-resistant Gram-positive bacteria are responsible for morbidity and mortality in healthcare environments. Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus and Streptococcus pneumoniae can all exhibit clinically relevant multidrug resistance phenotypes due to acquired resistance genes on mobile genetic elements. It is possible that clinically relevant multidrug-resistant Clostridium difficile strains will appear in the future, as the organism is adept at acquiring mobile genetic elements (plasmids and transposons). Conjugative transposons of the Tn916/Tn1545 family, which carry major antibiotic resistance determinants, are transmissible between these different bacteria by a conjugative mechanism during which the elements are excised by a staggered cut from donor cells, converted to a circular form, transferred by cell-cell contact and inserted into recipient cells by a site-specific recombinase. The ability of these conjugative transposons to acquire additional, clinically relevant antibiotic resistance genes importantly contributes to the emergence of multidrug resistance.
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Affiliation(s)
- Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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Sadowy E, Matynia B, Hryniewicz W. Population structure, virulence factors and resistance determinants of invasive, non-invasive and colonizing Streptococcus agalactiae in Poland. J Antimicrob Chemother 2010; 65:1907-14. [PMID: 20584746 DOI: 10.1093/jac/dkq230] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES To analyse Streptococcus agalactiae (group B Streptococcus; GBS) isolates collected in Poland from various human infections and carriage in respect of their clonality, distribution of virulence factors and antimicrobial resistance determinants, including the detection of transposons involved in the dissemination of antimicrobial resistance. METHODS One hundred and fourteen GBS isolates were analysed by multilocus sequence typing (MLST), serotyping and detection of alp genes of the alpha-like-protein (Alp) family. Determinants of resistance to macrolides and tetracycline, and associated transposons, were detected by PCR and analysed by sequencing. RESULTS GBS isolates represented 30 different sequence types (STs), grouped in four clonal complexes (CCs), and belonged to seven serotypes. Serotype III was predominant (36.0%), followed by Ia, V, Ib, II, IV and VI. The most common alp genes were rib (26.3%) and alp1/alp5 (23.7%). The bac gene encoding the beta-compound of the surface C-protein was present in 17.5% of isolates. Erythromycin resistance (18.4% of isolates) was found in all CCs, but was associated with serotype V and ST1. The most prevalent determinant of resistance was erm(B), usually located on the Tn3872-like transposon. Several changes were observed in the regulatory region of erm(B), some of them resulting in elevated ketolide MICs. Resistance to tetracycline was ubiquitous (91.2%) and its most common determinant was tet(M), occurring in several variants that were typically carried on Tn916-family transposons. CONCLUSIONS Analysis of bacterial serotypes, alp genes and antimicrobial resistance determinants in the background of MLST-based population structure strengthened evidence of the importance of horizontal gene transfer in GBS evolution.
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Affiliation(s)
- Ewa Sadowy
- National Medicines Institute, ul Chełmska 30/34, 00-725 Warsaw, Poland.
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Characterization of a small erythromycin resistance plasmid pLFE1 from the food-isolate Lactobacillus plantarum M345. Plasmid 2009; 61:159-70. [DOI: 10.1016/j.plasmid.2009.01.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Zhang XX, Zhang T, Fang HHP. Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol 2009; 82:397-414. [PMID: 19130050 DOI: 10.1007/s00253-008-1829-z] [Citation(s) in RCA: 565] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2008] [Revised: 12/11/2008] [Accepted: 12/13/2008] [Indexed: 12/30/2022]
Abstract
The use of antibiotics may accelerate the development of antibiotic resistance genes (ARGs) and bacteria which shade health risks to humans and animals. The emerging of ARGs in the water environment is becoming an increasing worldwide concern. Hundreds of various ARGs encoding resistance to a broad range of antibiotics have been found in microorganisms distributed not only in hospital wastewaters and animal production wastewaters, but also in sewage, wastewater treatment plants, surface water, groundwater, and even in drinking water. This review summarizes recently published information on the types, distributions, and horizontal transfer of ARGs in various aquatic environments, as well as the molecular methods used to detect environmental ARGs, including specific and multiplex PCR (polymerase chain reaction), real-time PCR, DNA sequencing, and hybridization based techniques.
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Affiliation(s)
- Xu-Xiang Zhang
- Environmental Biotechnology Lab,Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
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New composite genetic element of the Tn916 family with dual macrolide resistance genes in a Streptococcus pneumoniae isolate belonging to clonal complex 271. Antimicrob Agents Chemother 2008; 53:1293-4. [PMID: 19104015 DOI: 10.1128/aac.01066-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Genetic elements responsible for erythromycin resistance in streptococci. Antimicrob Agents Chemother 2008; 53:343-53. [PMID: 19001115 DOI: 10.1128/aac.00781-08] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Shen X, Yang H, Yu S, Yao K, Wang Y, Yuan L, Yang Y. Macrolide-Resistance Mechanisms inStreptococcus pneumoniaeIsolates from Chinese Children in Association with Genes oftetMand Integrase of Conjugative Transposons 1545. Microb Drug Resist 2008; 14:155-61. [PMID: 18479199 DOI: 10.1089/mdr.2008.0773] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xuzhuang Shen
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui Yang
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shangjie Yu
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Kaihu Yao
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yonghong Wang
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Yuan
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yonghong Yang
- Laboratory of Microbiology and Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
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Telithromycin resistance in Streptococcus pneumoniae is conferred by a deletion in the leader sequence of erm(B) that increases rRNA methylation. Antimicrob Agents Chemother 2007; 52:435-40. [PMID: 18056269 DOI: 10.1128/aac.01074-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A telithromycin-resistant clinical isolate of Streptococcus pneumoniae (strain P1501016) has been found to contain a version of erm(B) that is altered by a 136-bp deletion in the leader sequence. By allele replacement mutagenesis, a second strain of S. pneumoniae (PC13) with a wild-type erm(B) gene was transformed to the telithromycin-resistant phenotype by introduction of the mutant erm(B) gene. Whereas the wild-type PC13 strain showed slight telithromycin resistance only after induction by erythromycin (telithromycin MIC increased from 0.06 to 0.5 microg/ml), the transformed PC13 strain is constitutively resistant (MIC of 16 mug/ml). Expression of erm(B) was quantified by real-time reverse transcription-PCR in the presence of erythromycin or telithromycin; erm(B) expression was significantly higher in the transformed PC13 strain than the wild-type strain. Furthermore, the transformed strain had significantly higher levels of ribosomal methylation in the absence as well as in the presence of the antibiotics. Growth studies showed that the transformed PC13 strain had a shorter lag phase than the wild-type strain in the presence of erythromycin. Telithromycin resistance is conclusively shown to be conferred by the mutant erm(B) gene that is expressed at a constitutively higher level than the inducible wild-type gene. Elevated erm(B) expression results in a higher level of rRNA methylation that presumably hinders telithromycin binding to the ribosome.
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Toltzis P, Dul M, Blumer J. Change in pneumococcal susceptibility to azithromycin during treatment for acute otitis media. Pediatr Infect Dis J 2007; 26:647-9. [PMID: 17596812 DOI: 10.1097/inf.0b013e3180618c02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Authorities have suggested restriction of azithromycin use as a principal strategy to contain the spread of azithromycin-nonsusceptible Streptococcus pneumoniae (ANSP). In 83 children persistently colonized by pneumococcus during and after treatment of acute otitis media, 17 acquired a new strain, 9 of which were less susceptible to azithromycin than the original isolate. New appearance of ANSP was documented after both beta-lactam and azithromycin exposure. ANSP is likely to disseminate even with significant reduction of azithromycin use unless other antibiotic use is decreased as well.
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Affiliation(s)
- Philip Toltzis
- Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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Al-Lahham A, Appelbaum PC, van der Linden M, Reinert RR. Telithromycin-nonsusceptible clinical isolates of Streptococcus pneumoniae from Europe. Antimicrob Agents Chemother 2006; 50:3897-900. [PMID: 17065627 PMCID: PMC1635229 DOI: 10.1128/aac.00057-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Telithromycin-nonsusceptible pneumococcal clinical isolates (n = 17) were analyzed for their antimicrobial susceptibility, macrolide resistance mechanisms, and genetic relatedness. All strains showed the erm(B) genotype and showed a wide range of combinations of macrolide resistance mechanisms. The predominant clone (n = 7) was serotype 14, sequence type 143.
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Affiliation(s)
- Adnan Al-Lahham
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital (RWTH), Pauwelsstr. 30, Aachen, Germany
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Tobes R, Pareja E. Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. BMC Genomics 2006; 7:62. [PMID: 16563168 PMCID: PMC1525189 DOI: 10.1186/1471-2164-7-62] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 03/24/2006] [Indexed: 02/04/2023] Open
Abstract
Background Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP) elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements. Results This global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates. Conclusion Our findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for genome manipulation.
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Affiliation(s)
- Raquel Tobes
- Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud – Armilla Granada 18100, Spain
| | - Eduardo Pareja
- Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud – Armilla Granada 18100, Spain
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Marimón JM, Pérez-Trallero E, Ercibengoa M, Gonzalez A, Fenoll A. Molecular epidemiology and variants of the multidrug-resistant Streptococcus pneumoniae Spain14-5 international clone among Spanish clinical isolates. J Antimicrob Chemother 2006; 57:654-60. [PMID: 16484341 DOI: 10.1093/jac/dkl028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To analyse the molecular structure of several antimicrobial resistance determinants in isolates of the Spain(14)-5 clone to better understand its emergence and spread. METHODS The distinct genes and mechanism of resistance to penicillin, erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim were studied in an apparently homogeneous group of 117 isolates of the multidrug-resistant Spain(14)-5 major clone isolated in Spain between 1981 and 2004. RESULTS Several genotyping techniques such as PFGE, BOX-PCR and multilocus sequence typing (MLST) revealed a high degree of homogeneity among these isolates over time. Nevertheless, distinct variants of the clone could be established according to the restriction fragment length polymorphism (RFLP) patterns of the penicillin-binding protein (pbp) genes and the sequences of the dihydrofolate reductase (dhfr) gene. In addition, an association between the pbp2b RFLP patterns, the ddl alleles identified by MLST and the dhfr alleles was found. The emergence of variants of the Spain(14)-5 clone, which had lost macrolide and tetracycline resistance, while harbouring the ins and xis genes of the Tn916-Tn1545 family of conjugative transposons, was documented. Two different tet(M) alleles were detected in isolates of the clone, one of them with a mosaic structure. CONCLUSIONS The finding of different patterns or alleles of the genes responsible for antibiotic resistance among isolates of the Spain(14)-5 clone from different Spanish cities indicates different evolutionary events within isolates of a unique Streptococcus pneumoniae clone.
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Affiliation(s)
- José María Marimón
- Servicio de Microbiología, Hospital Donostia Paseo Dr Beguiristain s/n 20014 San Sebastián, Spain
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