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Cuetero-Martínez Y, Flores-Ramírez A, De Los Cobos-Vasconcelos D, Aguirre-Garrido JF, López-Vidal Y, Noyola A. Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment. CHEMOSPHERE 2023; 313:137383. [PMID: 36436581 DOI: 10.1016/j.chemosphere.2022.137383] [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: 09/01/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.
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Affiliation(s)
- Yovany Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico; Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Aarón Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Daniel De Los Cobos-Vasconcelos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana - Unidad Lerma, 52005 Lerma de Villada, Edo. Mex, Mexico
| | - Yolanda López-Vidal
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Adalberto Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico.
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Lu W, Li K, Huang J, Sun Z, Li A, Liu H, Zhou D, Lin H, Zhang X, Li Q, Lu J, Lin X, Li P, Zhang H, Xu T, Bao Q. Identification and characteristics of a novel aminoglycoside phosphotransferase, APH(3')-IId, from an MDR clinical isolate of Brucella intermedia. J Antimicrob Chemother 2021; 76:2787-2794. [PMID: 34329431 DOI: 10.1093/jac/dkab272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To describe a novel chromosomal aminoglycoside phosphotransferase named APH(3')-IId identified in an MDR Brucella intermedia ZJ499 isolate from a cancer patient. METHODS Species identity was determined by PCR and MALDI-TOF MS analysis. WGS was performed to determine the genetic elements conferring antimicrobial resistance. Gene cloning, transcriptional analysis and targeted gene deletion, as well as protein purification and kinetic analysis, were performed to investigate the mechanism of resistance. RESULTS APH(3')-IId consists of 266 amino acids and shares the highest identity (48.25%) with the previously known APH(3')-IIb. Expression of aph(3')-IId in Escherichia coli decreased susceptibility to kanamycin, neomycin, paromomycin and ribostamycin. The aph(3')-IId gene in ZJ499 was transcriptionally active under laboratory conditions and the relative abundance of this transcript was unaffected by treatment with the above four antibiotics. However, deletion of aph(3')-IId in ZJ499 results in decreased MICs of these drugs. The purified APH(3')-IId showed phosphotransferase activity against kanamycin, neomycin, paromomycin and ribostamycin, with catalytic efficiencies (kcat/Km) ranging from ∼105 to 107 M-1 s-1. Genetic environment and comparative genomic analyses suggested that aph(3')-IId is probably a ubiquitous gene in Brucella, with no mobile genetic elements detected in its surrounding region. CONCLUSIONS APH(3')-IId is a novel chromosomal aminoglycoside phosphotransferase and plays an important role in the resistance of B. intermedia ZJ499 to kanamycin, neomycin, paromomycin and ribostamycin. To the best of our knowledge, APH(3')-IId represents the fourth characterized example of an APH(3')-II enzyme.
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Affiliation(s)
- Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jiansheng Huang
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Aifang Li
- The Fifth Affiliated Hospital, Wenzhou Medical University, Lishui, Zhejiang 323000, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailong Lin
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xueya Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qiaoling Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Peizhen Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hailin Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Teng Xu
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou 014040, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China.,Department of Children's Respiratory Disease, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325027, China
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LaMartina EL, Mohaimani AA, Newton RJ. Urban wastewater bacterial communities assemble into seasonal steady states. MICROBIOME 2021; 9:116. [PMID: 34016155 PMCID: PMC8139061 DOI: 10.1186/s40168-021-01038-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Microorganisms in urban sanitary sewers exhibit community properties that suggest sewers are a novel ecosystem. Sewer microorganisms present both an opportunity as a control point for wastewater treatment and a risk to human health. If treatment processes are to be improved and health risks quantified, then it is necessary to understand microbial distributions and dynamics within this community. Here, we use 16S rRNA gene sequencing to characterize raw influent wastewater bacterial communities in a 5-year time series from two wastewater treatment plants in Milwaukee, WI; influent wastewater from 77 treatment plants across the USA; and wastewater in 12 Milwaukee residential sewers. RESULTS In Milwaukee, we find that in transit from residences to treatment plants, the human bacterial component of wastewater decreases in proportion and exhibits stochastic temporal variation. In contrast, the resident sewer community increases in abundance during transit and cycles seasonally according to changes in wastewater temperature. The result is a bacterial community that assembles into two distinct community states each year according to the extremes in wastewater temperature. Wastewater bacterial communities from other northern US cities follow temporal trends that mirror those in Milwaukee, but southern US cities have distinct community compositions and differ in their seasonal patterns. CONCLUSIONS Our findings provide evidence that environmental conditions associated with seasonal change and climatic differences related to geography predictably structure the bacterial communities residing in below-ground sewer pipes. Video abstract.
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Affiliation(s)
- Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Aurash A Mohaimani
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
- Present Address: Analytical Technologies, Biogen, 5000 Davis Dr, Morrisville, NC, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA.
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4
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Lawpidet P, Tengjaroenkul B, Saksangawong C, Sukon P. Global Prevalence of Vancomycin-Resistant Enterococci in Food of Animal Origin: A Meta-Analysis. Foodborne Pathog Dis 2021; 18:405-412. [PMID: 33684315 DOI: 10.1089/fpd.2020.2892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE) are a leading cause of nosocomial infections in patients worldwide. VRE contamination in food of animal origin may create a risk for human health. This study was conducted to estimate the pooled prevalence of VRE in food of animal origin worldwide, to assess the result heterogeneity, and to determine cumulative evidence and the trend of the prevalence over time. Relevant studies were retrieved from PubMed, Scopus, and Web of Science. A random-effects model was used to calculate the pooled prevalence of VRE in food of animal origin. Subgroup meta-analysis was used to assess the heterogeneity of the results. A cumulative meta-analysis and meta-regression were conducted to determine cumulative evidence and the trend of the prevalence of VRE in food of animal origin over time, respectively. Of the 1352 retrieved studies, 50 articles were included. The pooled prevalence of VRE in food of animal origin was 11.7% (95% confidence interval [95% CI] = 8.4 to 16.0). Subgroup meta-analyses showed a significant difference in the prevalence of VRE for two characteristics. First, for the source of food, the prevalence of VRE was highest in aquatic food (43.4% [95% CI = 28.4 to 59.7]) and lowest in dairy food (4.1% [95% CI = 1.7 to 9.8]). Second, for continents, the prevalence of VRE was highest in Africa (18.5% [95% CI = 12.8 to 26.1]) and lowest in North America (0.3% [95% CI = 0.1 to 1.1]). Cumulative evidence showed two distinct features in two different periods. The pooled prevalence of VRE rapidly decreased from 79.3% in 1998 to 13.1% in 2003; it has slightly fluctuated between 10.5% and 20.5% since 2004. The results of the meta-regression indicated that the prevalence gradually decreased over time. In conclusion, the estimate of overall VRE prevalence worldwide in food of animal origin was ∼12%, indicating the burden of VRE contamination in food of animal origin.
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Affiliation(s)
| | - Bundit Tengjaroenkul
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Development on Toxic Substances, Microorganisms and Feed Additives in Livestock and Aquatic Animals for Food Safety, Khon Kaen University, Khon Kaen, Thailand
| | | | - Peerapol Sukon
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Development on Toxic Substances, Microorganisms and Feed Additives in Livestock and Aquatic Animals for Food Safety, Khon Kaen University, Khon Kaen, Thailand
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5
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Sanz C, Casado M, Navarro-Martin L, Tadić Đ, Parera J, Tugues J, Bayona JM, Piña B. Antibiotic and antibiotic-resistant gene loads in swine slurries and their digestates: Implications for their use as fertilizers in agriculture. ENVIRONMENTAL RESEARCH 2021; 194:110513. [PMID: 33242487 DOI: 10.1016/j.envres.2020.110513] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 05/23/2023]
Abstract
The spread of antibiotic resistance in bacteria is a matter of global concern, and the identification of possible sources of the associated genetic elements (antibiotic resistance genes -ARGs-, components of the horizontal gene transfer mechanism), is becoming an urgent need. While the transmission of ARGs in medical settings have been adequately characterized, ARG propagation in agroecosystems remains insufficiently studied. Particularly crucial is the determination of potential risks associated to the use of swine slurries and related products as component of organic fertilizers, an increasingly used farming practice. We determined ARGs and antibiotic loads analysed from swine slurries and digestates from eight farms from Catalonia (NE Spain), and compared the results with their microbiome composition. Both ARGs and antibiotic were conspicuous in farm organic wastes, and the levels of some antibiotics exceeded currently accepted minimum inhibitory concentrations. Particularly, the presence of high loads of fluoroquinolones was directly correlated to the prevalence of the related qnrS1 ARG in the slurry. We also found evidence that ARG loads were directly correlated to the prevalence of determined bacterial taxa (Actinobacteria, Proteobacteria, Spirochaeta), a parameter that could be potentially modulated by the processing of the raw slurry prior to their use as fertilizer.
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Affiliation(s)
- Claudia Sanz
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | - Marta Casado
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | | | - Đorđe Tadić
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | - Joan Parera
- DARP Catalunya Central, GENCAT, Carrer de La Llotja, S/n (Recinte Firal El Sucre), 08500, Vic, Spain
| | - Jordi Tugues
- DARP Catalunya Central, GENCAT, Carrer de La Llotja, S/n (Recinte Firal El Sucre), 08500, Vic, Spain
| | | | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain.
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Dash B, Sahu N, Singh AK, Gupta SB, Soni R. Arsenic efflux in Enterobacter cloacae RSN3 isolated from arsenic-rich soil. Folia Microbiol (Praha) 2020; 66:189-196. [PMID: 33131029 DOI: 10.1007/s12223-020-00832-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/30/2020] [Indexed: 11/28/2022]
Abstract
In the present study, bacterial isolates were screened for arsenic resistance efficiency. Environmental isolates were isolated from arsenic-rich soil samples (i.e., from Rajnandgaon district of Chhattisgarh state, India). Amplification and sequencing of 16S rRNA gene revealed that the isolates were of Bacillus firmus RSN1, Brevibacterium senegalense RSN2, Enterobacter cloacae RSN3, Stenotrophomonas pavanii RSN6, Achromobacter mucicolens RSN7, and Ochrobactrum intermedium RSN10. Arsenite efflux gene (arsB) was successfully amplified in E. cloacae RSN3. Atomic absorption spectroscopy (AAS) analysis showed an absorption of 32.22% arsenic by the RSN3 strain. Furthermore, results of scanning electron microscopy (SEM) for morphological variations revealed an initial increase in the cell size at 1 mM sodium arsenate; however, it was decreased at 10 mM concentration in comparison to control. This change of the cell size in different metal concentrations was due to the uptake and expulsion of the metal from the cell, which also confirmed the arsenite efflux system.
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Affiliation(s)
- Biplab Dash
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Narayan Sahu
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Anup Kumar Singh
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - S B Gupta
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India
| | - Ravindra Soni
- Department of Agricultural Microbiology, College of Agriculture, Indira Gandhi Krishi Vishwavidyalaya, Krishak Nagar Jora, Raipur, 492012, CG, India.
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7
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Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum. Antibiotics (Basel) 2020; 9:antibiotics9040177. [PMID: 32294990 PMCID: PMC7235858 DOI: 10.3390/antibiotics9040177] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 01/27/2023] Open
Abstract
Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.
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8
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Becker J, Schüpbach-Regula G, Steiner A, Perreten V, Wüthrich D, Hausherr A, Meylan M. Effects of the novel concept 'outdoor veal calf' on antimicrobial use, mortality and weight gain in Switzerland. Prev Vet Med 2020; 176:104907. [PMID: 32066024 DOI: 10.1016/j.prevetmed.2020.104907] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 11/15/2022]
Abstract
The aim of the intervention study 'outdoor veal calf' was to evaluate a novel concept for calf fattening which aimed at reducing antimicrobial use without compromising animal health. Management practices such as commingling of calves from multiple birth farms, crowding, and suboptimal barn climate are responsible for high antimicrobial use and mortality in the veal calf population. The risk of selecting bacteria resistant to antimicrobials and of economic losses is accordingly elevated. The 'outdoor veal calf' concept, implemented in nineteen intervention farms (IF), is based on three main measures: 1. purchased calves are transported directly from neighboring birth farms to the fattening facility instead of commingling calves in livestock dealer trucks; 2. each calf is vaccinated against pneumonia after arrival and completes a three-week quarantine in an individual hutch; and 3. the calves spend the rest of the fattening period in outdoor hutches in groups not exceeding 10 calves. The covered and bedded paddock and the group hutches provide shelter from cold weather and direct sunshine, constant access to fresh air is warranted. Nineteen conventional calf fattening operations of similar size served as controls (CF). Every farm was visited once a month for a one-year period, and data regarding animal health, treatments, and production parameters were collected. Treatment intensity was assessed by use of the defined daily dose method (TIDDD in days per animal year), and calf mortality and daily weight gain were recorded in both farm groups. Mean TIDDD was 5.3-fold lower in IF compared to CF (5.9 ± 6.5 vs. 31.5 ± 27.4 days per animal year; p < 0.001). Mortality was 2.1-fold lower in IF than in CF (3.1% ± 2.3 vs. 6.3 % ± 4.9; p = 0.020). Average daily gain did not differ between groups (1.29 ± 0.17 kg/day in IF vs. 1.35 ± 0.16 kg/day in CF; p = 0.244). A drastic reduction in antimicrobial use and mortality was achieved in the novel 'outdoor veal calf' system without compromising animal health. The principles of risk reduction used in designing the system can be used to improve management and animal health, decrease the need for antimicrobial treatments and thus selection pressure on bacteria in veal operations.
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Affiliation(s)
- J Becker
- Clinic for Ruminants Vetsuisse-Faculty, University of Bern, Switzerland
| | - G Schüpbach-Regula
- Veterinary Public Health Institute, Vetsuisse-Faculty, University of Bern, Switzerland
| | - A Steiner
- Clinic for Ruminants Vetsuisse-Faculty, University of Bern, Switzerland
| | - V Perreten
- Institute of Veterinary Bacteriology, Vetsuisse-Faculty, University of Bern, Switzerland
| | - D Wüthrich
- Clinic for Ruminants Vetsuisse-Faculty, University of Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse-Faculty, University of Bern, Switzerland
| | - A Hausherr
- Clinic for Ruminants Vetsuisse-Faculty, University of Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse-Faculty, University of Bern, Switzerland
| | - M Meylan
- Clinic for Ruminants Vetsuisse-Faculty, University of Bern, Switzerland.
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9
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Abstract
High levels of antimicrobial drug resistance deleteriously affecting the outcome of treatment with antibacterial agents are causing increasing concern worldwide. This is particularly worrying in patients with cirrhosis with a depressed immune system and heightened susceptibility to infection. Antibiotics have to be started early before results of microbiological culture are available. Current guidelines for the empirical choice of antibiotics in this situation are not very helpful, and embracing antimicrobial stewardship including rapid de-escalation of therapy are not sufficiently emphasised. Multi-drug resistant organism rates to quinolone drugs of up to 40% are recorded in patients with spontaneous bacterial peritonitis on prophylactic antibiotics, leading to a break-through recurrence of intra-peritoneal infection. Also considered in this review is the value of rifaximin-α, non-selective beta-blockers, and concerns around proton pump inhibitor drug use. Fecal microbial transplantation and other gut-targeting therapies in lessening gut bacterial translocation are a promising approach, and new molecular techniques for determining bacterial sensitivity will allow more specific targeted therapy.
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10
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Xia J, Sun H, Zhang XX, Zhang T, Ren H, Ye L. Aromatic compounds lead to increased abundance of antibiotic resistance genes in wastewater treatment bioreactors. WATER RESEARCH 2019; 166:115073. [PMID: 31542545 DOI: 10.1016/j.watres.2019.115073] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/29/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Various aromatic compounds in wastewater, especially industrial wastewater, are treated by biological processes in bioreactors which are regarded as hotspots and reservoirs of antibiotic resistance genes (ARGs). Yet, little is known about the relationship between the aromatic compound degradation process and antibiotic resistance. Here, we report on the co-occurrence of ARGs and aromatic degradation genes (ADGs) in bacteria in bioreactors. We confirmed this by bioreactor experiments and bioinformatics analysis of over 10,000 publicly available bacterial genomes. We observed a significant enrichment of ARGs in bioreactors treating wastewater that contained p-aminophenol and p-nitrophenol. The potential hosts harboring ARGs and ADGs were mainly Pseudomonas, Leucobacter, Xanthobacter, Acinetobacter, and Burkholderiaceae. Genome analysis revealed that 67.6% of the publicly available bacterial genomes harboring ADGs also harbor ARGs. Over 80% of Burkholderiales, Xanthomonales, Enterobacteriaceae, Acinetobacter, Pseudomonas, and Nocardiaceae genomes harbor both ARGs and ADGs, which strongly suggests the co-occurrence of these genes. Furthermore, bacteria carrying ADGs harbored more than twice the number of ARGs than bacteria only carrying ARGs. Network analysis suggested that multidrug, beta-lactam, aminoglycoside, macrolide-lincosamide-streptogramin, and polymyxin resistance genes are the major ARGs associated with ADGs. Taken together, the presented findings improve the understanding of ARG prevalence in biological wastewater treatment plants, and highlight the potential risk of the effect of regular aromatic compounds on the selection and spread of ARGs.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China; School of Public Health, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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11
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Magesh S, Jonsson V, Bengtsson-Palme J. Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.36236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. Bioinformatic methods for metagenomic analysis have generally been poor at accounting for this fact, resulting in a somewhat limited picture of important aspects of microbial communities. Here, we address this problem by providing a software tool called Mumame, which can distinguish between wildtype and mutated sequences in shotgun metagenomic data and quantify their relative abundances. We demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets. We also identified that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. Mumame is freely available online (http://microbiology.se/software/mumame).
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12
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Kraemer SA, Ramachandran A, Perron GG. Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy. Microorganisms 2019; 7:E180. [PMID: 31234491 PMCID: PMC6616856 DOI: 10.3390/microorganisms7060180] [Citation(s) in RCA: 347] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/06/2023] Open
Abstract
The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.
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Affiliation(s)
- Susanne A Kraemer
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke Street W, Montreal, QC H4B1R6, Canada.
| | - Gabriel G Perron
- Department of Biology, Reem-Kayden Center for Sciences and Computation, Bard College, 31 Campus Road, Annandale-On-Hudson, NY 12504, USA.
- Center for the Study of Land, Water, and Air, Bard College, Annandale-On-Hudson, NY 12504, USA.
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13
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Alsan M, Kammili N, Lakshmi J, Xing A, Khan A, Rani M, Kolli P, Relman DA, Owens DK. Poverty and Community-Acquired Antimicrobial Resistance with Extended-Spectrum β-Lactamase-Producing Organisms, Hyderabad, India. Emerg Infect Dis 2019; 24:1490-1496. [PMID: 30014842 PMCID: PMC6056104 DOI: 10.3201/eid2408.171030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The decreasing effectiveness of antimicrobial agents is a global public health threat, yet risk factors for community-acquired antimicrobial resistance (CA-AMR) in low-income settings have not been clearly elucidated. Our aim was to identify risk factors for CA-AMR with extended-spectrum β-lactamase (ESBL)–producing organisms among urban-dwelling women in India. We collected microbiological and survey data in an observational study of primigravidae women in a public hospital in Hyderabad, India. We analyzed the data using multivariate logistic and linear regression and found that 7% of 1,836 women had bacteriuria; 48% of isolates were ESBL-producing organisms. Women in the bottom 50th percentile of income distribution were more likely to have bacteriuria (adjusted odds ratio 1.44, 95% CI 0.99–2.10) and significantly more likely to have bacteriuria with ESBL-producing organisms (adjusted odds ratio 2.04, 95% CI 1.17–3.54). Nonparametric analyses demonstrated a negative relationship between the prevalence of ESBL and income.
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14
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Patel M, Kumar R, Kishor K, Mlsna T, Pittman CU, Mohan D. Pharmaceuticals of Emerging Concern in Aquatic Systems: Chemistry, Occurrence, Effects, and Removal Methods. Chem Rev 2019; 119:3510-3673. [DOI: 10.1021/acs.chemrev.8b00299] [Citation(s) in RCA: 827] [Impact Index Per Article: 165.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Manvendra Patel
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rahul Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kamal Kishor
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Todd Mlsna
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Charles U. Pittman
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Dinesh Mohan
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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15
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Antibiotic Resistance in Pharmaceutical Industry Effluents and Effluent-Impacted Environments. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2019. [DOI: 10.1007/698_2019_389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Bengtsson-Palme J, Larsson DGJ, Kristiansson E. Using metagenomics to investigate human and environmental resistomes. J Antimicrob Chemother 2018; 72:2690-2703. [PMID: 28673041 DOI: 10.1093/jac/dkx199] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-41346, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-41346, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
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17
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Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. ENVIRONMENT INTERNATIONAL 2018; 112:279-286. [PMID: 29316517 DOI: 10.1016/j.envint.2017.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 05/28/2023]
Abstract
Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Anders Janzon
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Stathis D Kotsakis
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden.
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18
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Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev 2018; 42:4563583. [PMID: 29069382 PMCID: PMC5812547 DOI: 10.1093/femsre/fux053] [Citation(s) in RCA: 468] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/19/2017] [Indexed: 11/25/2022] Open
Abstract
Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.
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Affiliation(s)
- Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46, Gothenburg, Sweden
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19
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Philip JM, Aravind UK, Aravindakumar CT. Emerging contaminants in Indian environmental matrices - A review. CHEMOSPHERE 2018; 190:307-326. [PMID: 28992484 DOI: 10.1016/j.chemosphere.2017.09.120] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 05/03/2023]
Abstract
The emergence of issues related to environment from ECs is a topic under serious discussions worldwide in recent years. Indian scenario is not an exception as it is tremendously growing in its rate of production and consumption of compounds belongs to ECs categories. However, a comprehensive documentation on the occurrence of ECs and consequent ARGs as well as their toxic effects on vertebrates on Indian context is still lacking. In the present study, an extensive literature survey was carried out to get an idea on the geographical distribution of ECs in various environmental matrices (water, air, soil, sediment and sludge) and biological samples by dividing the entire subcontinent into six zones based on climatic, geographical and cultural features. A comprehensive assessment of the toxicological effects of ECs and the consequent antibiotic resistant genes has been included. It is found that studies on the screening of ECs are scarce and concentrated in certain geological locations. A total of 166 individual compounds belonging to 36 categories have been reported so far. Pharmaceuticals and drugs occupy the major share in these compounds followed by PFASs, EDCs, PCPs, ASWs and flame retardants. This review throws light on the alarming situation in India where the highest ever reported values of concentrations of some of these compounds are from India. This necessitates a national level monitoring system for ECs in order to assess the magnitude of environmental risks posed by these compounds.
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Affiliation(s)
- Jeeva M Philip
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, 686560, Kerala, India
| | - Usha K Aravind
- Advanced Centre of Environmental Studies and Sustainable Development, Mahatma Gandhi University, Kottayam, 686560, Kerala, India
| | - Charuvila T Aravindakumar
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, 686560, Kerala, India; Inter University Instrumentation Centre, Mahatma Gandhi University, Kottayam, 686560, Kerala, India.
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20
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Brinkac L, Voorhies A, Gomez A, Nelson KE. The Threat of Antimicrobial Resistance on the Human Microbiome. MICROBIAL ECOLOGY 2017; 74:1001-1008. [PMID: 28492988 PMCID: PMC5654679 DOI: 10.1007/s00248-017-0985-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/18/2017] [Indexed: 05/22/2023]
Abstract
Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance.
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Affiliation(s)
- Lauren Brinkac
- J. Craig Venter Institute|, Rockville, MD, 20850, USA.
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa.
| | | | - Andres Gomez
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
| | - Karen E Nelson
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
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21
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Jäckel C, Hertwig S, Scholz HC, Nöckler K, Reetz J, Hammerl JA. Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages. Front Microbiol 2017; 8:1207. [PMID: 28713341 PMCID: PMC5492332 DOI: 10.3389/fmicb.2017.01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.
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Affiliation(s)
- Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Holger C Scholz
- German Center for Infection Research, Bundeswehr Institute of MicrobiologyMunich, Germany
| | - Karsten Nöckler
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jochen Reetz
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
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22
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Masters NM, Wiegand A, Thompson JM, Vollmerhausen TL, Hatje E, Katouli M. Assessing the population dynamics of Escherichia coli in a metropolitan river after an extreme flood event. JOURNAL OF WATER AND HEALTH 2017; 15:196-208. [PMID: 28362301 DOI: 10.2166/wh.2016.285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigated Escherichia coli populations in a metropolitan river after an extreme flood event. Between nine and 15 of the 23 selected sites along the river were sampled fortnightly over three rounds. In all, 307 E. coli were typed using the PhP typing method and were grouped into common (C) or single (S) biochemical phenotypes (BPTs). A representative from each of the 31 identified C-BPTs was tested for 58 virulence genes (VGs) associated with intestinal and extra-intestinal E. coli, resistance to 22 antibiotics, production of biofilm and cytotoxicity to Vero cells. The number of E. coli in the first sampling round was significantly (P < 0.01) higher than subsequent rounds, whereas the number of VGs was significantly (P < 0.05) higher in isolates from the last sampling round when compared to previous rounds. Comparison of the C-BPTs with an existing database from wastewater treatment plants (WWTPs) in the same catchment showed that 40.6% of the river isolates were identical to the WWTP isolates. The relatively high number of VGs and antibiotic resistance among the C-BPTs suggests possessing and retaining these genes may provide niche advantages for those naturalised and/or persistent E. coli populations which may pose a health risk to the community.
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Affiliation(s)
- Nicole M Masters
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Aaron Wiegand
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Jasmin M Thompson
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Tara L Vollmerhausen
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Eva Hatje
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
| | - Mohammad Katouli
- Genecology Research Centre, School of Health and Sports Science, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia E-mail:
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23
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[Multidrug-resistant bacteria in Germany. The impact of sources outside healthcare facilities]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2017; 59:113-23. [PMID: 26446586 DOI: 10.1007/s00103-015-2261-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Currently, there is an ongoing discussion about the question whether the emergence of multidrug-resistant microorganisms (MDRO) among humans is due to transfer of these bacteria from animals. OBJECTIVES This review summarizes data on the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum beta-lactamase (ESBL) producing enterobacteria in animals and humans, and describes knowledge about transmission pathways. MATERIAL AND METHODS After a scientific literature analysis, relevant articles were identified by screening of titles and abstracts, amended by publications of infection control authorities and the respective reference lists. RESULTS MDRO are both transmitted in the nosocomial setting and are increasingly detected as sources of infection outside healthcare facilities. CONCLUSIONS Due to new transmission pathways of MDRO an inter-disciplinary approach towards prevention is necessary, involving medical, pharmaceutical and veterinary expertise.
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Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production. PLoS One 2016; 11:e0165914. [PMID: 27812209 PMCID: PMC5094703 DOI: 10.1371/journal.pone.0165914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/29/2016] [Indexed: 01/31/2023] Open
Abstract
Biological treatment of waste water from bulk drug production, contaminated with high levels of fluoroquinolone antibiotics, can lead to massive enrichment of antibiotic resistant bacteria, resistance genes and associated mobile elements, as previously shown. Such strong selection may be boosted by the use of activated sludge (AS) technology, where microbes that are able to thrive on the chemicals within the wastewater are reintroduced at an earlier stage of the process to further enhance degradation of incoming chemicals. The microbial community structure within such a treatment plant is, however, largely unclear. In this study, Illumina-based 16S rRNA amplicon sequencing was applied to investigate the bacterial communities of different stages from an Indian treatment plant operated by Patancheru Environment Technology Limited (PETL) in Hyderabad, India. The plant receives waste water with high levels of fluoroquinolones and applies AS technology. A total of 1,019,400 sequences from samples of different stages of the treatment process were analyzed. In total 202, 303, 732, 652, 947 and 864 operational taxonomic units (OTUs) were obtained at 3% distance cutoff in the equilibrator, aeration tanks 1 and 2, settling tank, secondary sludge and old sludge samples from PETL, respectively. Proteobacteria was the most dominant phyla in all samples with Gammaproteobacteria and Betaproteobacteria being the dominant classes. Alcaligenaceae and Pseudomonadaceae, bacterial families from PETL previously reported to be highly multidrug resistant, were the dominant families in aeration tank samples. Despite regular addition of human sewage (approximately 20%) to uphold microbial activity, the bacterial diversity within aeration tanks from PETL was considerably lower than corresponding samples from seven, regular municipal waste water treatment plants. The strong selection pressure from antibiotics present may be one important factor in structuring the microbial community in PETL, which may affect not only resistance promotion but also general efficiency of the waste treatment process.
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25
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Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Rattray NJW, Goodacre R. Metabolomics Analysis Reveals the Participation of Efflux Pumps and Ornithine in the Response of Pseudomonas putida DOT-T1E Cells to Challenge with Propranolol. PLoS One 2016; 11:e0156509. [PMID: 27331395 PMCID: PMC4917112 DOI: 10.1371/journal.pone.0156509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/16/2016] [Indexed: 02/07/2023] Open
Abstract
Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden addition of 0.2, 0.4 and 0.6 mg mL-1 of this β-blocker to several strains of P. putida, including the wild type DOT-T1E and the efflux pump knockout mutants DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the efflux pump TtgABC plays a more important role than the TtgGHI pump in strain tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a rapid, high-throughput screening tool to investigate any phenotypic changes resulting from exposure to varying levels of propranolol. Multivariate statistical analysis of these MIR data revealed gradient trends in resultant ordination scores plots, which were related to the concentration of propranolol. MIR illustrated phenotypic changes associated with the presence of this drug within the cell that could be assigned to significant changes that occurred within the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during the growth of bacteria following toxic perturbation with the same concentration levels of propranolol. Metabolic profiling revealed that ornithine, which was only produced by P. putida cells in the presence of propranolol, presents itself as a major metabolic feature that has important functions in propranolol stress tolerance mechanisms within this highly significant and environmentally relevant species of bacteria.
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Affiliation(s)
- Ali Sayqal
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Yun Xu
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Drupad K. Trivedi
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Najla AlMasoud
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - David I. Ellis
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicholas J. W. Rattray
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Royston Goodacre
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- * E-mail:
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26
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Abstract
Ramanan Laxminarayan and Ranjit Roy Chaudhury examine the factors encouraging the emergence of antibiotic resistance in India, the implications nationally and internationally, and what might be done to help.
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Affiliation(s)
- Ramanan Laxminarayan
- Center for Disease Dynamics, Economics & Policy, Washington, D.C., United States of America
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, United States of America
- Public Health Foundation of India, New Delhi, India
- * E-mail:
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27
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Larsson DGJ. Pollution from drug manufacturing: review and perspectives. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0571. [PMID: 25405961 PMCID: PMC4213584 DOI: 10.1098/rstb.2013.0571] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
As long ago as the sixteenth century, Paracelsus recognized that ‘the dose makes the poison’. Indeed, environmental concentrations of pharmaceuticals excreted by humans are limited, most importantly because a defined dose is given to just a fraction of the population. By contrast, recent studies have identified direct emission from drug manufacturing as a source of much higher environmental discharges that, in some cases, greatly exceed toxic threshold concentrations. Because production is concentrated in specific locations, the risks are not linked to usage patterns. Furthermore, as the drugs are not consumed, metabolism in the human body does not reduce concentrations. The environmental risks associated with manufacturing therefore comprise a different, wider set of pharmaceuticals compared with those associated with risks from excretion. Although pollution from manufacturing is less widespread, discharges that promote the development of drug-resistant microorganisms can still have global consequences. Risk management also differs between production and excretion in terms of accountability, incentive creation, legal opportunities, substitution possibilities and costs. Herein, I review studies about industrial emissions of pharmaceuticals and the effects associated with exposure to such effluents. I contrast environmental pollution due to manufacturing with that due to excretion in terms of their risks and management and highlight some recent initiatives.
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Affiliation(s)
- D G Joakim Larsson
- Institute of Biomedicine, The Sahlgrenska Academy, The University of Gothenburg, Gothenburg, Sweden
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28
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Flach CF, Johnning A, Nilsson I, Smalla K, Kristiansson E, Larsson DGJ. Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake. J Antimicrob Chemother 2015; 70:2709-17. [PMID: 26124213 DOI: 10.1093/jac/dkv167] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved. METHODS Sediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest(®) and captured conjugative resistance elements were characterized by WGS. RESULTS The polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics. CONCLUSIONS Our study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli.
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Affiliation(s)
- Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Ida Nilsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kornelia Smalla
- Julius Kühn-Institut-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Abejón R, De Cazes M, Belleville MP, Sanchez-Marcano J. Large-scale enzymatic membrane reactors for tetracycline degradation in WWTP effluents. WATER RESEARCH 2015; 73:118-131. [PMID: 25655319 DOI: 10.1016/j.watres.2015.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
A mathematical model to simulate the performance of enzymatic membrane reactors was developed. It was applied to investigate the effectiveness of laccase immobilized over ceramic membranes for the degradation of tetracycline, a common antibiotic appearing as micropollutant in effluents of WWTPs. A process based on large-scale enzymatic membrane reactors in series was proposed for the treatment of the effluents from municipal, hospital and industrial wastewater treatment plants (WWTPs). The obtained results demonstrated the need for high improvements in the amount of enzyme grafted on the membranes or on enzymatic kinetics to afford the technical and economic competitiveness of the investigated designs and the possibility to be implemented within existing installations.
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Affiliation(s)
- R Abejón
- Institut Européen des Membranes (IEM), ENSCM, UM2, CNRS - Université de Montpellier II2, CC 047, Place Eugène Bataillon, 34095 Montpellier, France
| | - M De Cazes
- Institut Européen des Membranes (IEM), ENSCM, UM2, CNRS - Université de Montpellier II2, CC 047, Place Eugène Bataillon, 34095 Montpellier, France
| | - M P Belleville
- Institut Européen des Membranes (IEM), ENSCM, UM2, CNRS - Université de Montpellier II2, CC 047, Place Eugène Bataillon, 34095 Montpellier, France
| | - J Sanchez-Marcano
- Institut Européen des Membranes (IEM), ENSCM, UM2, CNRS - Université de Montpellier II2, CC 047, Place Eugène Bataillon, 34095 Montpellier, France.
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30
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Lenain P, De Saeger S, Mattiasson B, Hedström M. Affinity sensor based on immobilized molecular imprinted synthetic recognition elements. Biosens Bioelectron 2015; 69:34-9. [PMID: 25703726 DOI: 10.1016/j.bios.2015.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/30/2015] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
Abstract
An affinity sensor based on capacitive transduction was developed to detect a model compound, metergoline, in a continuous flow system. This system simulates the monitoring of low-molecular weight organic compounds in natural flowing waters, i.e. rivers and streams. During operation in such scenarios, control of the experimental parameters is not possible, which poses a true analytical challenge. A two-step approach was used to produce a sensor for metergoline. Submicron spherical molecularly imprinted polymers, used as recognition elements, were obtained through emulsion polymerization and subsequently coupled to the sensor surface by electropolymerization. This way, a robust and reusable sensor was obtained that regenerated spontaneously under the natural conditions in a river. Small organic compounds could be analyzed in water without manipulating the binding or regeneration conditions, thereby offering a viable tool for on-site application.
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Affiliation(s)
- Pieterjan Lenain
- Laboratory of Food Analysis, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium.
| | - Sarah De Saeger
- Laboratory of Food Analysis, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
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31
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In vitro activity of five quinolones and analysis of the quinolone resistance-determining regions of gyrA, gyrB, parC, and parE in Ureaplasma parvum and Ureaplasma urealyticum clinical isolates from perinatal patients in Japan. Antimicrob Agents Chemother 2015; 59:2358-64. [PMID: 25645833 DOI: 10.1128/aac.04262-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ureaplasma spp. cause several disorders, such as nongonococcal urethritis, miscarriage, and preterm delivery with lung infections in neonates, characterized by pathological chorioamnionitis in the placenta. Although reports on antibiotic resistance in Ureaplasma are on the rise, reports on quinolone-resistant Ureaplasma infections in Japan are limited. The purpose of this study was to determine susceptibilities to five quinolones of Ureaplasma urealyticum and Ureaplasma parvum isolated from perinatal samples in Japan and to characterize the quinolone resistance-determining regions in the gyrA, gyrB, parC, and parE genes. Out of 28 clinical Ureaplasma strains, we isolated 9 with high MICs of quinolones and found a single parC gene mutation, resulting in the change S83L. Among 158 samples, the ParC S83L mutation was found in 37 samples (23.4%), including 1 sample harboring a ParC S83L-GyrB P462S double mutant. Novel mutations of ureaplasmal ParC (S83W and S84P) were independently found in one of the samples. Homology modeling of the ParC S83W mutant suggested steric hindrance of the quinolone-binding pocket (QBP), and de novo prediction of peptide structures revealed that the ParC S84P may break/kink the formation of the α4 helix in the QBP. Further investigations are required to unravel the extent and mechanism of antibiotic resistance of Ureaplasma spp. in Japan.
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32
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Abstract
Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.
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Affiliation(s)
- Marjorie E Doyle
- Food Research Institute, University of Wisconsin , Madison, Wisconsin
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33
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Antibiotic Resistance Elements in Wastewater Treatment Plants: Scope and Potential Impacts. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2015. [DOI: 10.1007/698_2015_361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front Microbiol 2014; 5:648. [PMID: 25520706 PMCID: PMC4251439 DOI: 10.3389/fmicb.2014.00648] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/07/2014] [Indexed: 11/27/2022] Open
Abstract
There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Fredrik Boulund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
| | - Jerker Fick
- Department of Chemistry, Umeå University Umeå, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
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35
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Rutgersson C, Fick J, Marathe N, Kristiansson E, Janzon A, Angelin M, Johansson A, Shouche Y, Flach CF, Larsson DGJ. Fluoroquinolones and qnr genes in sediment, water, soil, and human fecal flora in an environment polluted by manufacturing discharges. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:7825-32. [PMID: 24988042 DOI: 10.1021/es501452a] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
There is increasing concern that environmental antibiotic pollution promotes transfer of resistance genes to the human microbiota. Here, fluoroquinolone-polluted river sediment, well water, irrigated farmland, and human fecal flora of local villagers within a pharmaceutical industrial region in India were analyzed for quinolone resistance (qnr) genes by quantitative PCR. Similar samples from Indian villages farther away from industrial areas, as well as fecal samples from Swedish study participants and river sediment from Sweden, were included for comparison. Fluoroquinolones were detected by MS/MS in well water and soil from all villages located within three km from industrially polluted waterways. Quinolone resistance genes were detected in 42% of well water, 7% of soil samples and in 100% and 18% of Indian and Swedish river sediments, respectively. High antibiotic concentrations in Indian sediment coincided with high abundances of qnr, whereas lower fluoroquinolone levels in well water and soil did not. We could not find support for an enrichment of qnr in fecal samples from people living in the fluoroquinolone-contaminated villages. However, as qnr was detected in 91% of all Indian fecal samples (24% of the Swedish) it suggests that the spread of qnr between people is currently a dominating transmission route.
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Affiliation(s)
- Carolin Rutgersson
- Institute of Biomedicine, Department of Infectious Diseases, The Sahlgrenska Academy, University of Gothenburg , Gothenburg, Sweden
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36
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Marathe NP, Regina VR, Walujkar SA, Charan SS, Moore ERB, Larsson DGJ, Shouche YS. A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria. PLoS One 2013; 8:e77310. [PMID: 24204801 PMCID: PMC3812170 DOI: 10.1371/journal.pone.0077310] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/04/2013] [Indexed: 01/31/2023] Open
Abstract
The arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. Selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. We hypothesize that waste-water treatment plants (WWTPs) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there together with exceptionally strong and persistent selection pressures from the antibiotic-contaminated waste. Previous analyses of effluent from an Indian industrial WWTP that processes waste from bulk drug production revealed the presence of a range of drugs, including broad spectrum antibiotics at extremely high concentrations (mg/L range). In this study, we have characterized the antibiotic resistance profiles of 93 bacterial strains sampled at different stages of the treatment process from the WWTP against 39 antibiotics belonging to 12 different classes. A large majority (86%) of the strains were resistant to 20 or more antibiotics. Although there were no classically-recognized human pathogens among the 93 isolated strains, opportunistic pathogens such as Ochrobactrum intermedium, Providencia rettgeri, vancomycin resistant Enterococci (VRE), Aerococcus sp. and Citrobacter freundii were found to be highly resistant. One of the O. intermedium strains (ER1) was resistant to 36 antibiotics, while P. rettgeri (OSR3) was resistant to 35 antibiotics. Class 1 and 2 integrons were detected in 74/93 (80%) strains each, and 88/93 (95%) strains harbored at least one type of integron. The qPCR analysis of community DNA also showed an unprecedented high prevalence of integrons, suggesting that the bacteria living under such high selective pressure have an appreciable potential for genetic exchange of resistance genes via mobile gene cassettes. The present study provides insight into the mechanisms behind and the extent of multi-drug resistance among bacteria living under an extreme antibiotic selection pressure.
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MESH Headings
- Anti-Bacterial Agents/classification
- Anti-Bacterial Agents/pharmacology
- Bacteria/classification
- Bacteria/drug effects
- Bacteria/genetics
- Conjugation, Genetic
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Transfer, Horizontal
- Genome, Bacterial
- Humans
- Integrons/genetics
- Microbial Sensitivity Tests
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- Wastewater/microbiology
- Water Microbiology
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Affiliation(s)
- Nachiket P. Marathe
- Microbial Culture Collection (MCC), National Center for Cell Science, Pune, Maharashtra, India
| | - Viduthalai R. Regina
- Microbial Culture Collection (MCC), National Center for Cell Science, Pune, Maharashtra, India
| | - Sandeep A. Walujkar
- Microbial Culture Collection (MCC), National Center for Cell Science, Pune, Maharashtra, India
| | - Shakti Singh Charan
- Microbial Culture Collection (MCC), National Center for Cell Science, Pune, Maharashtra, India
| | - Edward R. B. Moore
- Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Yogesh S. Shouche
- Microbial Culture Collection (MCC), National Center for Cell Science, Pune, Maharashtra, India
- * E-mail:
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